DNA polymerase beta
Homo sapiens
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein–DNA Monomer Protein × 1 DNA 3 PDB declaration: tetrameric（4） Consistent with all polymer counts | Chain A； UniProt 1–334 | Not recorded | 5'-D(P*GP*TP*CP*GP*G)-3' × 1 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3' × 1 5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3' × 1 BPI (1S)-1,2,3,4-TETRAHYDRO-BENZO[C]PHENANTHRENE-2,3,4-TRIOL × 1 NA SODIUM ION × 2 CL CHLORIDE ION × 2 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.1M HEPES, pH 7.50, 20% PEG 3000, 0.2M Sodium Chloride, VAPOR DIFFUSION, SITTING DROP, temperature 291K | Resolution 2.10 Å R-free 0.252 |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 2I9G | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1BPX DNA POLYMERASE BETA/DNA COMPLEX Deposited 1997-04-11 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；PROTEIN-DNA COMPLEX WAS CRYSTALLIZED USING A RESERVOIR CONTAINING 13.8% PEG 3350, 360 MM SODIUM ACETATE, AND 50 MM IMIDAZOLE, PH 7.0., VAPOR DIFFUSION
|
Resolution 2.40 Å |
| 1BPY HUMAN DNA POLYMERASE BETA COMPLEXED WITH GAPPED DNA AND DDCTP Deposited 1997-04-15 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–334（334 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；PROTEIN-DNA COMPLEX WAS CRYSTALLIZED USING A RESERVOIR CONTAINING 16.0% PEG 3350, 180 MM SODIUM ACETATE, AND 50 MM HEPES, PH 7.5., VAPOR DIFFUSION
|
Resolution 2.20 Å R-free 0.330 |
| 1BPZ HUMAN DNA POLYMERASE BETA COMPLEXED WITH NICKED DNA Deposited 1997-04-14 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；PROTEIN-DNA COMPLEX WAS CRYSTALLIZED USING A RESERVOIR CONTAINING 17.5% PEG 3350, 90 MM SODIUM ACETATE, AND 50 MM IMIDAZOLE, PH 7.0., VAPOR DIFFUSION
|
Resolution 2.60 Å |
| 1MQ2 Human DNA Polymerase Beta Complexed With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine and dAMP Deposited 2002-09-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | D5M 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；20% PEG 3350, 350 mM sodium acetate, 50 mM imidazole at 18 degrees (C), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K
|
Resolution 3.10 Å R-free 0.317 |
| 1MQ3 Human DNA Polymerase Beta Complexed With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine Template Paired with dCTP Deposited 2002-09-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 1 NA SODIUM ION × 2 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；291 K；14% PEG 3350, 350 mM sodium acetate and 50 mM imidazole at 18 degrees (C), pH 7.5, temperature 291.0K
|
Resolution 2.80 Å R-free 0.295 |
| 1TV9 HUMAN DNA POLYMERASE BETA COMPLEXED WITH NICKED DNA CONTAINING A MISMATCHED TEMPLATE ADENINE AND INCOMING CYTIDINE Deposited 2004-06-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
0–334（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；290 K；14% PEG 3350, 350mM sodium Acetate, 50mM imidazole, 10mM MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K, pH 7.50
|
Resolution 2.00 Å R-free 0.239 |
| 1TVA HUMAN DNA POLYMERASE BETA COMPLEXED WITH NICKED DNA CONTAINING A MISMATCHED TEMPLATE THYMIDINE AND INCOMING CYTIDINE Deposited 2004-06-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
0–334（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；290 K；20% PEG 3350, 350 mM sodium Acetate, 50mM imidazole, 10mM MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
|
Resolution 2.60 Å R-free 0.282 |
| 1ZJM Human DNA Polymerase beta complexed with DNA containing an A-A mismatched primer terminus Deposited 2005-04-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
0–334（335 aa）
|
Not recorded | NA SODIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；PEG 3350, Sodium Acetate, Imidazole, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.10 Å R-free 0.234 |
| 1ZJN Human DNA Polymerase beta complexed with DNA containing an A-A mismatched primer terminus with dGTP Deposited 2005-04-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
0–334（335 aa）
|
Not recorded | MG MAGNESIUM ION × 1 NA SODIUM ION × 3 DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；PEG 3350, Sodium Acetate, Imidazole, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.61 Å R-free 0.234 |
| 1ZQA DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF KCL (150 MILLIMOLAR) AT PH 7.5 Deposited 1996-04-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | K POTASSIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 3 DAYS: PEG 3350, 16% IMIDAZOLE, 100 MILLIMOLAR, PH 7.5 KCL, 150 MILLIMOLAR SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.20 Å |
| 1ZQB DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF BACL2 (150 MILLIMOLAR) Deposited 1996-04-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | BA BARIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 2 DAYS: PEG 3350, 16% IMIDAZOLE, 100 MILLIMOLAR, PH 6.5 BACL2, 150 MILLIMOLAR SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.20 Å |
| 1ZQC DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CACL2 (15 MILLIMOLAR) Deposited 1996-04-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | CA CALCIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 6 HOURS: PEG 3350, 16% IMIDAZOLE, 100 MILLIMOLAR, PH 6.5 CACL2, 15 MILLIMOLAR SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.20 Å |
| 1ZQD DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CACL2 (150 MILLIMOLAR) Deposited 1996-04-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | CA CALCIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% IMIDAZOLE, 100 MILLIMOLAR, PH 6.5 CACL2, 150 MILLIMOLAR SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.50 Å |
| 1ZQE DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CRCL3 (SATURATED SOLUTION) Deposited 1996-04-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | CR CHROMIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 2 DAYS: PEG 3350, 16% IMIDAZOLE, 100 MILLIMOLAR, PH 6.5 CRCL3, SATURATED SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.70 Å |
| 1ZQF DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CSCL (150 MILLIMOLAR) Deposited 1996-04-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | CS CESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 3 DAYS: PEG 3350, 16% IMIDAZOLE, 100 MILLIMOLAR, PH 6.5 CSCL, 150 MILLIMOLAR SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 2.90 Å |
| 1ZQG DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF A SODIUM-FREE ARTIFICIAL MOTHER LIQUOR AT PH 6.5 Deposited 1996-04-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 7 DAYS: PEG 3350, 16% IMIDAZOLE, 100 MILLIMOLAR, PH 6.5 SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.10 Å |
| 1ZQH DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF A SODIUM-FREE ARTIFICIAL MOTHER LIQUOR AT PH 7.5 Deposited 1996-04-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 4 DAYS: PEG 3350, 16% IMIDAZOLE, 100 MILLIMOLAR, PH 7.5 SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.10 Å |
| 1ZQI DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF KCL (150 MILLIMOLAR) Deposited 1996-04-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | K POTASSIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% IMIDAZOLE, 100 MILLIMOLAR, PH 6.5 KCL, 150 MILLIMOLAR SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 2.70 Å |
| 1ZQJ DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CACL2 (15 MILLIMOLAR) AND MGCL2 (15 MILLIMOLAR) Deposited 1996-04-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | CA CALCIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 12 HOURS: PEG 3350, 16% IMIDAZOLE, 100 MILLIMOLAR, PH 6.5 CACL2, 15 MILLIMOLAR MGCL2, 15 MILLIMOLAR SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.30 Å |
| 1ZQK DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF KCL (75 MILLIMOLAR) AND MGCL2 (75 MILLIMOLAR) Deposited 1996-04-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | K POTASSIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% IMIDAZOLE, 100 MILLIMOLAR, PH 6.5 KCL, 75 MILLIMOLAR MGCL2, 75 MILLIMOLAR SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.20 Å |
| 1ZQL DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF MNCL2 (15 MILLIMOLAR) AND MGCL2 (15 MILLIMOLAR) Deposited 1996-04-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | MN MANGANESE (II) ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 12 HOURS: PEG 3350, 16% IMIDAZOLE, 100 MILLIMOLAR, PH 6.5 MNCL2, 15 MILLIMOLAR MGCL2, 15 MILLIMOLAR SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.30 Å |
| 1ZQM DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF MNCL2 (15 MILLIMOLAR) Deposited 1996-04-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | MN MANGANESE (II) ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 36 HOURS: PEG 3350, 16% IMIDAZOLE, 100 MILLIMOLAR, PH 6.5 MNCL2, 15 MILLIMOLAR SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.20 Å |
| 1ZQN DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF BACL2 (15 MILLIMOLAR) AND NACL (15 MILLIMOLAR) Deposited 1996-04-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | BA BARIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 3 DAYS: PEG 3350, 16% IMIDAZOLE, 100 MILLIMOLAR, PH 6.5 BACL2, 15 MILLIMOLAR NACL, 15 MILLIMOLAR SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.00 Å |
| 1ZQO DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CACL2 (15 MILLIMOLAR) AND NACL (15 MILLIMOLAR) Deposited 1996-04-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 12 HOURS: PEG 3350, 16% IMIDAZOLE, 100 MILLIMOLAR, PH 6.5 CACL2, 15 MILLIMOLAR NACL, 15 MILLIMOLAR SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.20 Å |
| 1ZQP DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF KCL (75 MILLIMOLAR) AND NACL (75 MILLIMOLAR) Deposited 1996-04-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | K POTASSIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% IMIDAZOLE, 100 MILLIMOLAR, PH 6.5 KCL, 75 MILLIMOLAR NACL, 75 MILLIMOLAR SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 2.80 Å |
| 1ZQQ DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF MNCL2 (15 MILLIMOLAR) AND NACL (15 MILLIMOLAR) Deposited 1996-04-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% IMIDAZOLE, 100 MILLIMOLAR, PH 6.5 MNCL2, 15 MILLIMOLAR NACL, 15 MILLIMOLAR SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.30 Å |
| 1ZQR DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF NICL2 Deposited 1996-04-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NI NICKEL (II) ION × 2 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 12 HOURS: PEG 3350, 16% IMIDAZOLE, 100 MILLIMOLAR, PH 6.5 NICL2, 15 MILLIMOLAR SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.70 Å |
| 1ZQS DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF TLCL (0.5 MILLIMOLAR) Deposited 1996-04-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 1 HOUR: PEG 3350, 16% IMIDAZOLE, 100 MILLIMOLAR, PH 6.5 TLCL, 0.5 MILLIMOLAR SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.30 Å |
| 1ZQT DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (0.01 MILLIMOLAR) AND ZNCL2 (0.02 MILLIMOLAR) Deposited 1996-04-12 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | ZN ZINC ION × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 3 DAYS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DATP, 0.01 MILLIMOLAR ZNCL2, 0.02 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.40 Å |
| 2FMP DNA Polymerase beta with a terminated gapped DNA substrate and ddCTP with sodium in the catalytic site Deposited 2006-01-09 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–334（334 aa）
|
Not recorded | MG MAGNESIUM ION × 1 NA SODIUM ION × 5 DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM HEPES, pH 7.5, 180 mM Sodium Acetate, 16 % PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 1.65 Å R-free 0.217 |
| 2FMQ Sodium in active site of DNA Polymerase Beta Deposited 2006-01-09 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–334（334 aa）
|
Not recorded | MG MAGNESIUM ION × 1 NA SODIUM ION × 3 DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole, pH 7.5, 350 mM Sodium Acetate, 16 % PEG 3350 , VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.20 Å R-free 0.242 |
| 2FMS DNA Polymerase beta with a gapped DNA substrate and dUMPNPP with magnesium in the catalytic site Deposited 2006-01-09 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–334（334 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 4 DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；50 mM Imidazole, pH 8.0, 350 mM Sodium Acetate, 16 % PEG 3350 , VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.00 Å R-free 0.244 |
| 2P66 Human DNA Polymerase beta complexed with tetrahydrofuran (abasic site) containing DNA Deposited 2007-03-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 3 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；100 mM Bis-Tris, pH 6.5, 300 mM Sodium Acetate, 16% PEG-3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.50 Å R-free 0.280 |
| 2PXI Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monofluoromethylene triphosphate Deposited 2007-05-14 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 5 GFH 2'-DEOXY-5'-O-[(R)-{[(R)-[(R)-FLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]GUANOSINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole, 350 mM Sodium Acetate, PEG 3350 16%, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.10 Å R-free 0.270 |
| 3C2K DNA POLYMERASE BETA with a gapped DNA substrate and DUMPNPP with Manganese in the active site Deposited 2008-01-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MN MANGANESE (II) ION × 5 NA SODIUM ION × 2 CL CHLORIDE ION × 4 DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole pH 7.5, 350 mM Sodium Acetate, 18% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.40 Å R-free 0.278 |
| 3C2L Ternary complex of DNA POLYMERASE BETA with a C:DAPCPP mismatch in the active site Deposited 2008-01-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MN MANGANESE (II) ION × 6 NA SODIUM ION × 2 F2A 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole pH 7.5, 350 mM Sodium Acetate, 18% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.60 Å R-free 0.306 |
| 3C2M Ternary complex of DNA POLYMERASE BETA with a G:dAPCPP mismatch in the active site Deposited 2008-01-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MN MANGANESE (II) ION × 7 NA SODIUM ION × 6 EDO 1,2-ETHANEDIOL × 2 F2A 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole pH 7.5, 350 mM Sodium Acetate, 18% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.15 Å R-free 0.270 |
| 3GDX Dna polymerase beta with a gapped DND substrate and dTMP(CF2)PP Deposited 2009-02-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
10–335（326 aa）
|
Not recorded | 4BD 5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]thymidine × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；100 mM IMIDAZOLE,pH 8.0, SODIUM ACETATE 350 mM, PEG2000 MONOMETHYL ETHER 20%, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.20 Å R-free 0.266 |
| 3ISB Binary complex of human DNA polymerase beta with a gapped DNA Deposited 2009-08-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 4 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole pH 7.5, 350 mM Sodium acetate, 18% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.00 Å R-free 0.271 |
| 3ISC Binary complex of human DNA polymerase beta with an abasic site (THF) in the gapped DNA Deposited 2009-08-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole pH 7.5, 350 mM Sodium acetate, 18% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.00 Å R-free 0.227 |
| 3ISD Ternary complex of human DNA polymerase beta with an abasic site (THF): DAPCPP mismatch Deposited 2009-08-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 3 MN MANGANESE (II) ION × 8 F2A 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole pH 7.5, 350 mM Sodium acetate, 18% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.60 Å R-free 0.262 |
| 3JPN Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-dichloro methylene triphosphate Deposited 2009-09-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | G2C 2'-deoxy-5'-O-[(S)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole, pH 7.5, 350 mM Sodium Acetate, PEG3350 18%, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.15 Å R-free 0.242 |
| 3JPO Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monochloromethylene triphosphate Deposited 2009-09-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | G1C 5'-O-[(R)-{[(S)-[(S)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxyguanosine × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole, pH 7.5, 350 mM Sodium Acetate, PEG3350 18%, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.00 Å R-free 0.247 |
| 3JPP Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-MonoMethyl Methylene triphosphate Deposited 2009-09-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | G1M 2'-deoxy-5'-O-[(R)-hydroxy({(S)-hydroxy[(1R)-1-phosphonoethyl]phosphoryl}oxy)phosphoryl]guanosine × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 4 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole, pH 7.5, 350 mM Sodium Acetate, PEG3350 18%, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.10 Å R-free 0.250 |
| 3JPQ Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monoBromo methylene triphosphate Deposited 2009-09-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | GBR 5'-O-[(R)-{[(S)-[(R)-bromo(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxyguanosine × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole, pH 7.5, 350 mM Sodium Acetate, PEG3350 18%, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 1.90 Å R-free 0.234 |
| 3JPR Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-dimethyl methylene triphosphate Deposited 2009-09-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | G2M 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(1-methyl-1-phosphonoethyl)phosphoryl]oxy}phosphoryl]guanosine × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole, pH 7.5, 350 mM Sodium Acetate, PEG3350 18%, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.10 Å R-free 0.253 |
| 3JPS Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-fluoro methyl methylene triphosphate Deposited 2009-09-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | GFM 2'-deoxy-5'-O-[(S)-{[(S)-[(1R)-1-fluoro-1-phosphonoethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole, pH 7.5, 350 mM Sodium Acetate, PEG3350 18%
, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.00 Å R-free 0.237 |
| 3JPT Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-fluoro chloro methylene triphosphate Deposited 2009-09-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | GFC 5'-O-[(S)-{[(S)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxyguanosine × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole, pH 7.5, 350 mM Sodium Acetate, PEG3350 18%
, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.15 Å R-free 0.254 |
| 3LK9 DNA polymerase beta with a gapped DNA substrate and dTMP(CF2)P(CF2)P Deposited 2010-01-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | TFF 5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl](difluoro)methyl}(hydroxy)phosphoryl]thymidine × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 MM IMIDAZOLE,PH 7.5, SODIUM ACETATE 350 MM, PEG3350 16-18%, , VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.50 Å R-free 0.281 |
| 3MBY Ternary complex of DNA Polymerase BETA with template base A and 8oxodGTP in the active site with a dideoxy terminated primer Deposited 2010-03-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | 8DG 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole pH 7.5, sodium acetate 350 mM, 16-18% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.00 Å R-free 0.246 |
| 3OGU DNA Polymerase beta mutant 5P20 complexed with 6bp of DNA Deposited 2010-08-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–335（335 aa）
|
Mutation：S2G,F99L,E232K,V269M | NA SODIUM ION × 3 GOL GLYCEROL × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；10% PEG 3350, 0.1 M sodium chloride, 0.1 M MES, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.84 Å R-free 0.233 |
| 3RH4 DNA Polymerase Beta with a dideoxy-terminated primer with an incoming ribonucleotide (rCTP) Deposited 2011-04-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MN MANGANESE (II) ION × 8 NA SODIUM ION × 2 CL CHLORIDE ION × 6 CTP CYTIDINE-5'-TRIPHOSPHATE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；16% PEG3350, 350 mM sodium acetate, 50 mM imidazole, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 1.92 Å R-free 0.240 |
| 3RH5 DNA Polymerase Beta Mutant (Y271) with a dideoxy-terminated primer with an incoming deoxynucleotide (dCTP) Deposited 2011-04-11 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：Y271A | DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 2 MN MANGANESE (II) ION × 7 NA SODIUM ION × 2 CL CHLORIDE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；16% PEG3350, 350 mM sodium acetate, 50 mM imidazole, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.10 Å R-free 0.281 |
| 3RH6 DNA Polymerase Beta Mutant (Y271) with a dideoxy-terminated primer with an incoming ribonucleotide (rCTP) Deposited 2011-04-11 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：Y271A | CTP CYTIDINE-5'-TRIPHOSPHATE × 2 MN MANGANESE (II) ION × 6 NA SODIUM ION × 2 CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；16% PEG3350, 350 mM sodium acetate, 50 mM imidazole, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.05 Å R-free 0.266 |
| 3RJE Ternary complex of DNA Polymerase Beta with a gapped DNA containing 8odG at template position Deposited 2011-04-15 | Different construct Different ligand/ion Different experimental conditions | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole, pH 7.5
350 mM Sodium Acetate
18 % PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.10 Å R-free 0.252 |
| 3RJF Ternary complex of DNA Polymerase Beta with a gapped DNA containing (syn)8odG at template position paired with non-hydrolyzable dATP analog (dApCPP) Deposited 2011-04-15 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | F2A 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole, pH 7.5
350 mM Sodium Acetate
18 % PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.30 Å R-free 0.256 |
| 3RJG Binary complex of DNA Polymerase Beta with a gapped DNA containing 8odG:dA base-pair at primer Terminus Deposited 2011-04-15 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole, pH 7.5, 350 mM Sodium Acetate, 18 % PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.00 Å R-free 0.257 |
| 3RJH Ternary complex of DNA Polymerase Beta with a gapped DNA containing (syn)8odG:dA at primer terminus and dG:dCMP(CF2)PPin the active site Deposited 2011-04-15 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | 6CF 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole, pH 7.5, 350 mM Sodium Acetate, 18 % PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.20 Å R-free 0.259 |
| 3RJI Ternary complex of DNA Polymerase Beta with a gapped DNA containing 8odG at template position paired with non-hydrolyzable dCTP analog (dCMP(CF2)PP) Deposited 2011-04-15 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | 6CF 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole, pH 7.5, 350 mM Sodium Acetate, 18 % PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.30 Å R-free 0.266 |
| 3RJJ Ternary complex crystal structure of DNA Polymerase Beta with template 8odG provides insight into mutagenic lesion bypass Deposited 2011-04-15 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole, pH 7.5, 350 mM Sodium Acetate, 18 % PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.00 Å R-free 0.261 |
| 3RJK Ternary complex of DNA Polymerase Beta with a gapped DNA containing 8odG:dC base pair at primer terminus and dG:dCMP(CF2)PP in the active site Deposited 2011-04-15 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | 6CF 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole, pH 7.5, 350 mM Sodium Acetate, 18 % PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.10 Å R-free 0.258 |
| 3TFR Ternary complex structure of DNA polymerase beta with a gapped DNA substrate and a, b dAMP(CF2)PP in the active site Deposited 2011-08-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | F3A 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]adenosine × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole, 350 mM Sodium Acetate, 18 % PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.00 Å R-free 0.251 |
| 3TFS Ternary complex structure of DNA polymerase beta with a gapped DNA substrate and a, b dAMP(CFH)PP in the active site: Stereoselective binding of (S) isomer Deposited 2011-08-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | FHA 2'-deoxy-5'-O-[(S)-{(S)-fluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]adenosine × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole, 350 mM Sodium Acetate, 18 % PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.00 Å R-free 0.242 |
| 4DO9 Ternary complex of dna polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monofluoromethylene triphosphate: stereoselective binding of r-isomer Deposited 2012-02-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
Fragment：DNA Polymerase Beta
|
Not recorded | MG MAGNESIUM ION × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 5 GFH 2'-DEOXY-5'-O-[(R)-{[(R)-[(R)-FLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]GUANOSINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole, pH 7.5
350 mM Sodium Acetate
18% PEG3350
, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.05 Å R-free 0.243 |
| 4DOA Ternary complex of dna polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monofluoromethylene triphosphate: non-interactive binding of s-isomer Deposited 2012-02-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
Fragment：DNA Polymerase Beta
|
Not recorded | MG MAGNESIUM ION × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 5 FHG 2'-deoxy-5'-O-[(R)-{[(R)-[(S)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole, pH 7.5
350 mM Sodium Acetate
18% PEG3350
, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.05 Å R-free 0.243 |
| 4DOB Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monochlororomethylene triphosphate: Stereoselective binding of R-isomer Deposited 2012-02-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
Fragment：DNA Polymerase Beta
|
Not recorded | MG MAGNESIUM ION × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 5 GRC 5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxyguanosine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole, pH 7.5
350 mM Sodium Acetate
18 % PEG3350
, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.05 Å R-free 0.263 |
| 4DOC Ternary complex of dna polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monochlororomethylene triphosphate:binding of S-isomer Deposited 2012-02-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
Fragment：DNA Polymerase Beta
|
Not recorded | MG MAGNESIUM ION × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 5 G1C 5'-O-[(R)-{[(S)-[(S)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxyguanosine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole, pH 7.5
350 mM Sodium Acetate
18 % PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 1.95 Å R-free 0.249 |
| 4F5N Open ternary complex of R283K DNA polymerase beta with a metal free dCTP analog Deposited 2012-05-13 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：R283K | NA SODIUM ION × 3 6CF 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；50mM Imidazole, 350mM Sodium Acetate, 18% PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 1.80 Å R-free 0.220 |
| 4F5O Open ternary complex of R283K DNA polymerase beta with a one metal bound dCTP analog Deposited 2012-05-13 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：R283K | 6CF 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；50mM Imidazole, 350mM Sodium Acetate, 19% PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.00 Å R-free 0.267 |
| 4F5P Open ternary mismatch complex of R283K DNA polymerase beta with a dATP analog Deposited 2012-05-13 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：R283K | MG MAGNESIUM ION × 1 NA SODIUM ION × 2 F2A 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；50mM Imidazole, 350mM Sodium Acetate, 19% PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 1.85 Å R-free 0.245 |
| 4F5Q Closed ternary complex of R283K DNA polymerase beta Deposited 2012-05-13 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：R283K | MN MANGANESE (II) ION × 2 6CF 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；50mM Imidazole, 350mM Sodium Acetate, 18% PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.25 Å R-free 0.282 |
| 4F5R Open and closed ternary complex of R283K DNA polymerase beta with a dCTP analog in the same asymmetric unit Deposited 2012-05-13 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：R283K | NA SODIUM ION × 2 6CF 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine × 1 MN MANGANESE (II) ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；50mM Imidazole, 350mM Sodium Acetate, 16.5% PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.20 Å R-free 0.278 |
| 4F5R Open and closed ternary complex of R283K DNA polymerase beta with a dCTP analog in the same asymmetric unit Deposited 2012-05-13 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain B
1–335（335 aa）
|
Mutation：R283K | NA SODIUM ION × 2 6CF 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine × 1 MN MANGANESE (II) ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；50mM Imidazole, 350mM Sodium Acetate, 16.5% PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.20 Å R-free 0.278 |
| 4GXI R283K DNA polymerase beta binary complex with a templating 8OG Deposited 2012-09-04 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：R283K | NA SODIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8；291 K；50mM imidazole, 350mM Sodium Acetate, 18% Peg3350, pH 8.0, VAPOR DIFFUSION, temperature 291K
|
Resolution 1.95 Å R-free 0.259 |
| 4GXJ R283K DNA polymerase beta ternary complex with a templating 8OG and incoming dCTP analog Deposited 2012-09-04 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：R283K | 6CF 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine × 1 MN MANGANESE (II) ION × 7 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8；291 K；50mM Imidazole, 350mM Sodium Acetate, 18% Peg3350, pH 8.0, VAPOR DIFFUSION, temperature 291K
|
Resolution 2.20 Å R-free 0.292 |
| 4GXK R283K DNA polymerase beta ternary complex with a templating 8OG and incoming dATP analog Deposited 2012-09-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MN MANGANESE (II) ION × 4 F2A 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine × 1 NA SODIUM ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；291 K；50mM Imidazole, 350mM sodium acetate, 17% Peg3350, pH 7.5, VAPOR DIFFUSION, temperature 291K
|
Resolution 2.00 Å R-free 0.278 |
| 4JWM Ternary complex of D256E mutant of DNA Polymerase Beta Deposited 2013-03-27 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：D256E | DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole, 350 mM Sodium Acetate, 18 % PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.00 Å R-free 0.233 |
| 4JWN Ternary complex of D256A mutant of DNA Polymerase Beta Deposited 2013-03-27 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：D256A | DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole, 350 mM Sodium Acetate, 18 % PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.39 Å R-free 0.251 |
| 4KLD DNA polymerase beta matched substrate complex with Ca2+, 0 s Deposited 2013-05-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, temperature 291K
|
Resolution 1.92 Å R-free 0.251 |
| 4KLE DNA polymerase beta matched reactant complex with Mg2+, 10 s Deposited 2013-05-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 PPV PYROPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, temperature 291K
|
Resolution 1.97 Å R-free 0.248 |
| 4KLF DNA polymerase beta matched reactant complex with Mg2+, 20 s Deposited 2013-05-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 PPV PYROPHOSPHATE × 1 CL CHLORIDE ION × 2 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, temperature 291K
|
Resolution 1.85 Å R-free 0.231 |
| 4KLG DNA polymerase beta matched product complex with Mg2+, 40 s Deposited 2013-05-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 4 MG MAGNESIUM ION × 2 PPV PYROPHOSPHATE × 1 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, temperature 291K
|
Resolution 1.70 Å R-free 0.229 |
| 4KLH DNA polymerase beta matched product complex with Mn2+, 40 s Deposited 2013-05-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MN MANGANESE (II) ION × 3 PPV PYROPHOSPHATE × 1 CL CHLORIDE ION × 3 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, temperature 291K
|
Resolution 1.88 Å R-free 0.269 |
| 4KLI DNA polymerase beta matched product complex with Mg2+, 90 s Deposited 2013-05-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 PPV PYROPHOSPHATE × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, temperature 291K
|
Resolution 1.60 Å R-free 0.222 |
| 4KLJ DNA polymerase beta matched product complex with Mg2+, 5 min Deposited 2013-05-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 PPV PYROPHOSPHATE × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, temperature 291K
|
Resolution 1.80 Å R-free 0.227 |
| 4KLL DNA polymerase beta matched product complex with Mg2+, 45 min Deposited 2013-05-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 4 PPV PYROPHOSPHATE × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, temperature 291K
|
Resolution 1.84 Å R-free 0.230 |
| 4KLM DNA polymerase beta matched product complex with Mg2+, 11 h Deposited 2013-05-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | PPV PYROPHOSPHATE × 1 NA SODIUM ION × 3 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, temperature 291K
|
Resolution 1.75 Å R-free 0.239 |
| 4KLO DNA polymerase beta matched nick complex with Mg2+ and PPi, 30 min Deposited 2013-05-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 3 PPV PYROPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, temperature 291K
|
Resolution 1.84 Å R-free 0.230 |
| 4KLQ Observing a DNA polymerase choose right from wrong. Deposited 2013-05-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 PPV PYROPHOSPHATE × 1 MN MANGANESE (II) ION × 3 NA SODIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, temperature 291K
|
Resolution 2.00 Å R-free 0.267 |
| 4KLS DNA polymerase beta mismatched reactant complex with Mn2+, 10 min Deposited 2013-05-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 PPV PYROPHOSPHATE × 1 NA SODIUM ION × 3 MN MANGANESE (II) ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, temperature 291K
|
Resolution 1.98 Å R-free 0.285 |
| 4KLT DNA polymerase beta mismatched product complex with Mn2+, 30 min Deposited 2013-05-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 MN MANGANESE (II) ION × 3 PPV PYROPHOSPHATE × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, temperature 291K
|
Resolution 1.98 Å R-free 0.292 |
| 4KLU DNA polymerase beta mismatched product complex with Mn2+, 15 h Deposited 2013-05-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 MN MANGANESE (II) ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, temperature 291K
|
Resolution 1.97 Å R-free 0.251 |
| 4LVS DNA polymerase beta mismatched substrate complex with Mn2+, 2.5 min Deposited 2013-07-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 MN MANGANESE (II) ION × 6 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；50mM Imidazole, 350mM NaCl, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.00 Å R-free 0.281 |
| 4M2Y Structure of human DNA polymerase beta complexed with 8-BrG as the template base in a 1-nucleotide gapped DNA Deposited 2013-08-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
11–335（325 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；14-23% PEG 3340, 350mM sodium acetate in 50 mM imidazole, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
|
Resolution 2.27 Å R-free 0.269 |
| 4M47 structure of human DNA polymerase complexed with 8-BrG in the template base paired with incoming non-hydrolyzable GTP Deposited 2013-08-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
12–335（324 aa）
|
Not recorded | XG4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；14% - 23% PEG3400 and 350 mM sodium acetate in 50 mM imidazole , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
|
Resolution 2.37 Å R-free 0.273 |
| 4M9G DNA Polymerase Beta E295K Binary Complex Deposited 2013-08-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：E295K | NA SODIUM ION × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；14% PEG 3350, 300 mM sodium acetate pH 9, 50 mM HEPES pH 7.5, vapor diffusion, hanging drop, temperature 291K
|
Resolution 2.01 Å R-free 0.224 |
| 4M9H DNA Polymerase Beta E295K Soaked with dTTP Deposited 2013-08-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：E295K | NA SODIUM ION × 2 CL CHLORIDE ION × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；14% PEG 3350, 300 mM sodium acetate pH 9, 50 mM HEPES pH 7.5, vapor diffusion, hanging drop, temperature 291K
|
Resolution 2.39 Å R-free 0.228 |
| 4M9J DNA Polymerase Beta E295K Soaked with dUMPNPP Deposited 2013-08-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：E295K | NA SODIUM ION × 2 CL CHLORIDE ION × 2 MG MAGNESIUM ION × 1 DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；14% PEG 3350, 300 mM sodium acetate pH 9, 50 mM HEPES pH 7.5, vapor diffusion, hanging drop, temperature 291K
|
Resolution 2.04 Å R-free 0.230 |
| 4M9L DNA Polymerase Beta E295K Soaked with dCTP Deposited 2013-08-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：E295K | NA SODIUM ION × 3 MG MAGNESIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；14% PEG 3350, 300 mM sodium acetate pH 9, 50 mM HEPES pH 7.5, vapor diffusion, hanging drop, temperature 291K
|
Resolution 2.09 Å R-free 0.231 |
| 4M9N DNA Polymerase Beta E295K Soaked with dATP Deposited 2013-08-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：E295K | NA SODIUM ION × 2 MG MAGNESIUM ION × 1 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；14% PEG 3350, 300 mM sodium acetate pH 9, 50 mM HEPES pH 7.5, vapor diffusion, hanging drop, temperature 291K
|
Resolution 2.27 Å R-free 0.227 |
| 4MF2 Structure of human DNA polymerase beta complexed with O6MG as the template base in a 1-nucleotide gapped DNA Deposited 2013-08-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
11–335（325 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；14% 23% PEG3400, and 350 mM sodium acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
|
Resolution 2.40 Å R-free 0.279 |
| 4MF8 Structure of human DNA polymerase beta complexed with nicked DNA containing a mismatched template O6MG and incoming CTP Deposited 2013-08-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
7–335（329 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；14% 23% PEG3400, and 350 mM sodium acetate , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
|
Resolution 2.32 Å R-free 0.272 |
| 4MFA Structure of human DNA polymerase beta complexed with nicked DNA containing a mismatched template O6MG and incoming TTP Deposited 2013-08-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
11–335（325 aa）
|
Not recorded | NA SODIUM ION × 2 MG MAGNESIUM ION × 2 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；4% - 23% PEG3400, and 350 mM sodium acetate , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
|
Resolution 2.27 Å R-free 0.283 |
| 4MFC Structure of human DNA polymerase beta complexed with O6MG in the template base paired with incoming non-hydrolyzable CTP Deposited 2013-08-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
11–335（325 aa）
|
Not recorded | MG MAGNESIUM ION × 1 NA SODIUM ION × 2 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；14% - 23% PEG3400, and 350 mM sodium acetate , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.13 Å R-free 0.275 |
| 4MFF Structure of human DNA polymerase beta complexed with O6MG in the template base paired with incoming non-hydrolyzable TTP Deposited 2013-08-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
11–335（325 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 1FZ 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；14% - 23% PEG3400, and 350 mM sodium acetate , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
|
Resolution 2.55 Å R-free 0.294 |
| 4NLK Structure of human DNA polymerase beta complexed with 8BrG in the template base-paired with incoming non-hydrolyzable CTP Deposited 2013-11-14 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
7–335（329 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；14-23% PEG3400, 350 mM sodium acetate, 50 mM imidazole, pH 7.5, VAPOR DIFFUSION, SITTING DROP
|
Resolution 2.49 Å R-free 0.270 |
| 4NLN Structure of human DNA polymerase beta complexed with nicked DNA containing a template 8BrG and incoming CTP Deposited 2013-11-14 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
7–335（329 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；14-23% PEG3400, 350 mM sodium acetate, 50 mM imidazole, pH 7.5, VAPOR DIFFUSION, SITTING DROP
|
Resolution 2.26 Å R-free 0.273 |
| 4NLZ Structure of human DNA polymerase beta complexed with nicked DNA containing a mismatched template 8BrG and incoming GTP Deposited 2013-11-14 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
7–335（329 aa）
|
Not recorded | MG MAGNESIUM ION × 1 NA SODIUM ION × 2 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；14-23% PEG3400, 350 mM sodium acetate, 50 mM imidazole, pH 7.5, VAPOR DIFFUSION, SITTING DROP
|
Resolution 2.68 Å R-free 0.291 |
| 4NM1 Structure of human DNA polymerase beta complexed with a nicked DNA containing a 8BrG-C at N-1 position and G-C at N position Deposited 2013-11-14 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
7–335（329 aa）
|
Not recorded | PO4 PHOSPHATE ION × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；14-23% PEG3400, 350 mM sodium acetate, 50 mM imidazole, pH 7.5, VAPOR DIFFUSION, SITTING DROP
|
Resolution 2.42 Å R-free 0.256 |
| 4NM2 Structure of human DNA polymerase beta complexed with a nicked DNA containing a 8BrG-G at N-1 position and G-C at N position Deposited 2013-11-14 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
7–335（329 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；14-23% PEG3400, 350 mM sodium acetate, 50 mM imidazole, pH 7.5, VAPOR DIFFUSION, SITTING DROP
|
Resolution 2.52 Å R-free 0.277 |
| 4NXZ DNA polymerase beta with O6mG in the template base opposite to incoming non-hydrolyzable TTP with manganese in the active site Deposited 2013-12-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
10–335（326 aa）
Fragment：UNP residues 10-335
|
Not recorded | MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 1FZ 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；14%-23% PEG3400, 350 mM sodium acetate, 50 mM imidazole, pH 7.5, VAPOR DIFFUSION, SITTING DROP
|
Resolution 2.56 Å R-free 0.255 |
| 4NY8 DNA polymerase beta with O6mG in the template base opposite to incoming non-hydrolyzable CTP with manganese in the active site Deposited 2013-12-10 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
10–335（326 aa）
Fragment：UNP residues 10-335
|
Not recorded | MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；14%-23% PEG3400, 350 mM sodium acetate, 50 mM imidazole, pH 7.5, VAPOR DIFFUSION, SITTING DROP
|
Resolution 2.25 Å R-free 0.265 |
| 4O5C Structure of human DNA polymerase complexed with N7-MG as the template base in a 1-nucleotide gapped DNA Deposited 2013-12-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
7–335（329 aa）
Fragment：DNA polymerase beta
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；14%-23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole, pH 7.5, VAPOR DIFFUSION, SITTING DROP
|
Resolution 2.36 Å R-free 0.245 |
| 4O5E Structure of human DNA polymerase complexed with N7MG in the template base paired with incoming non-hydrolyzable TTP Deposited 2013-12-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
7–335（329 aa）
Fragment：DNA polymerase beta
|
Not recorded | MG MAGNESIUM ION × 1 NA SODIUM ION × 2 1FZ 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；14%-23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole, pH 7.5, VAPOR DIFFUSION, SITTING DROP
|
Resolution 2.53 Å R-free 0.273 |
| 4O5K Structure of human DNA polymerase complexed with N7MG in the template base paired with incoming non-hydrolyzable CTP Deposited 2013-12-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
10–335（326 aa）
Fragment：down primer DNA
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；14%-23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole, pH 7.5, VAPOR DIFFUSION, SITTING DROP
|
Resolution 2.06 Å R-free 0.252 |
| 4O9M Human DNA polymerase beta complexed with adenylated tetrahydrofuran (abasic site) containing DNA Deposited 2014-01-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | 2RW [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S)-3-hydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；100 mM Bis-Tris, 350 mM Sodium Acetate, 16% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.29 Å R-free 0.261 |
| 4P2H Structure of human DNA polymerase complexed with N7MG in the template opposite to incoming non-hydrolyzable TTP with manganese in the active site Deposited 2014-03-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
10–335（326 aa）
Fragment：UNP residues 10-335
|
Not recorded | MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 1FZ 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；14%-23% PEG3400, 350 mM sodium acetate, 50 mM imidazole
|
Resolution 1.99 Å R-free 0.249 |
| 4PGQ Structure of human DNA polymerase beta complexed with G in the template base paired with incoming non-hydrolyzable TTP Deposited 2014-05-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
7–335（329 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 1FZ 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；14%?23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.30 Å R-free 0.260 |
| 4PGX Structure of human DNA polymerase beta complexed with G in the template base paired with incoming non-hydrolyzable TTP and MANGANESE Deposited 2014-05-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
10–335（326 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 1FZ 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；14%?23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.08 Å R-free 0.227 |
| 4PGY Structure of human DNA polymerase beta complexed with a nicked DNA containing a GT at N-1 position and GC at N position Deposited 2014-05-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
7–335（329 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；14%?23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.26 Å R-free 0.265 |
| 4PH5 Structure of human DNA polymerase beta complexed with a nicked DNA containing a AC at N-1 position and GC at N position Deposited 2014-05-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
10–335（326 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；14%?23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.55 Å R-free 0.261 |
| 4PHA Structure of human DNA polymerase beta complexed with A in the template base paired with incoming non-hydrolyzable CTP Deposited 2014-05-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
7–335（329 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；14%?23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.52 Å R-free 0.278 |
| 4PHD Structure of human DNA polymerase beta complexed with A in the template base paired with incoming non-hydrolyzable CTP and MANGANESE Deposited 2014-05-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
7–335（329 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；14%?23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.21 Å R-free 0.295 |
| 4PHE Structure of human DNA polymerase beta complexed with T in the template base paired with incoming non-hydrolyzable GTP Deposited 2014-05-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
7–335（329 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 XG4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；14%?23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.15 Å R-free 0.261 |
| 4PHP Structure of human DNA polymerase beta complexed with T in the template base paired with incoming non-hydrolyzable GTP and MANGANESE Deposited 2014-05-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
10–335（326 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 XG4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；14%?23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.60 Å R-free 0.262 |
| 4PPX DNA Polymerase Beta E295K with Spiroiminodihydantoin in Templating Position Deposited 2014-02-27 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：E295K | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；14% PEG3350, 300 mM sodium acetate, pH 9.0, 50 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.08 Å R-free 0.217 |
| 4R63 Binary complex crystal structure of R258A mutant of DNA polymerase Beta Deposited 2014-08-22 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：R258A | NA SODIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；291 K；50 mM Imidazole, 350 mM Sodium Acetate, 16-18 % PEG 3350, pH 7.5, VAPOR DIFFUSION, temperature 291K
|
Resolution 1.85 Å R-free 0.232 |
| 4R64 Binary complex crystal structure of E295K mutant of DNA polymerase Beta Deposited 2014-08-22 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：E295K | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；291 K；16-18% PEG3350, 50 mM Imidazole, 350 mM Sodium Acetate, pH 7.5, VAPOR DIFFUSION, temperature 291K
|
Resolution 2.20 Å R-free 0.243 |
| 4R65 Ternary complex crystal structure of R258A mutant of DNA polymerase Beta Deposited 2014-08-22 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：R258A | DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；291 K；16-18% PEG3350, 50 mM Imidazole, 350 mM Sodium Acetate, pH 7.5, VAPOR DIFFUSION, temperature 291K
|
Resolution 1.95 Å R-free 0.222 |
| 4R66 Ternary complex crystal structure of E295K mutant of DNA polymerase Beta Deposited 2014-08-22 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：E295K | DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MN MANGANESE (II) ION × 4 NA SODIUM ION × 2 CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；291 K；16-18% PEG3350, 50 mM Imidazole, 350 mM Sodium Acetate, pH 7.5, VAPOR DIFFUSION, temperature 291K
|
Resolution 2.25 Å R-free 0.247 |
| 4RPX Precatalytic ternary complex of Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG) and dCTP in the presence of CaCl2 Deposited 2014-10-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 2 CA CALCIUM ION × 2 NA SODIUM ION × 7 CL CHLORIDE ION × 3 ACT ACETATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；50 MM IMIDAZOLE, 350 MM SODIUM Acetate, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.90 Å R-free 0.227 |
| 4RPY Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine(8-oxoG) and dCTP soaked with MgCl2 for 30 s Deposited 2014-10-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 3 NA SODIUM ION × 7 CL CHLORIDE ION × 4 ACT ACETATE ION × 2 PPV PYROPHOSPHATE × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；50 MM IMIDAZOLE, 350 MM SODIUM Acetate, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.90 Å R-free 0.230 |
| 4RPZ Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dCTP soaked with MgCl2 for 60 s Deposited 2014-10-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 3 NA SODIUM ION × 4 CL CHLORIDE ION × 3 PPV PYROPHOSPHATE × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；50 MM IMIDAZOLE, 350 MM SODIUM Acetate, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.19 Å R-free 0.251 |
| 4RQ0 Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dCTP soaked with MgCl2 for 80 s Deposited 2014-10-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | PPV PYROPHOSPHATE × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 3 CL CHLORIDE ION × 2 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；50 MM IMIDAZOLE, 350 MM SODIUM Acetate, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.20 Å R-free 0.268 |
| 4RQ1 Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine(8-oxoG) and dCTP soaked with MgCl2 for 1hr Deposited 2014-10-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；50 MM IMIDAZOLE, 350 MM SODIUM Acetate, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.70 Å R-free 0.280 |
| 4RQ2 Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dCTP soaked with MnCl2 for 35 s Deposited 2014-10-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | PPV PYROPHOSPHATE × 1 MN MANGANESE (II) ION × 6 NA SODIUM ION × 7 ACT ACETATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；50 MM IMIDAZOLE, 350 MM SODIUM Acetate, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.20 Å R-free 0.269 |
| 4RQ3 Precatalytic ternary complex of Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG) and dATP in the presence of CaCl2 Deposited 2014-10-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2 NA SODIUM ION × 4 CL CHLORIDE ION × 4 ACT ACETATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；50 MM IMIDAZOLE, 350 MM SODIUM Acetate, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.00 Å R-free 0.246 |
| 4RQ4 Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine(8-oxoG) and dATP soaked with MgCl2 for 30 s Deposited 2014-10-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 3 NA SODIUM ION × 2 CL CHLORIDE ION × 5 ACT ACETATE ION × 1 PPV PYROPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；50 MM IMIDAZOLE, 350 MM SODIUM Acetate, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.10 Å R-free 0.244 |
| 4RQ5 Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dATP soaked with MgCl2 for 60 s Deposited 2014-10-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 3 NA SODIUM ION × 2 ACT ACETATE ION × 2 CL CHLORIDE ION × 2 PPV PYROPHOSPHATE × 1 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；50 MM IMIDAZOLE, 350 MM SODIUM Acetate, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.32 Å R-free 0.266 |
| 4RQ6 Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine(8-oxoG) and dATP soaked with MgCl2 for 80 s Deposited 2014-10-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | PPV PYROPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 3 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；50 MM IMIDAZOLE, 350 MM SODIUM Acetate, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.25 Å R-free 0.252 |
| 4RQ7 Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dATP soaked with MgCl2 for 1hr Deposited 2014-10-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 4 CL CHLORIDE ION × 2 ACT ACETATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；50 MM IMIDAZOLE, 350 MM SODIUM Acetate, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.00 Å R-free 0.261 |
| 4RQ8 Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine(8-oxoG) and dATP soaked with MnCl2 for 35 s Deposited 2014-10-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | PPV PYROPHOSPHATE × 1 MN MANGANESE (II) ION × 6 NA SODIUM ION × 9 CL CHLORIDE ION × 6 ACT ACETATE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；50 MM IMIDAZOLE, 350 MM SODIUM Acetate, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.00 Å R-free 0.270 |
| 4RT2 Ternary complex crystal structure of DNA polymerase Beta with (alpha,beta)-CH2-(beta,gamma)-NH-dTTP Deposited 2014-11-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 1 N6T 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]methyl}phosphoryl]-3,4-dihydrothymidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；291 K；16-18% PEG3350, pH 7.5, vapor diffusion, temperature 291K
|
Resolution 1.92 Å R-free 0.211 |
| 4RT3 Ternary complex crystal structure of DNA polymerase Beta with (alpha, beta)-NH-(beta,gamma)-CH2-dTTP Deposited 2014-11-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 3 C6T 2'-deoxy-5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]amino}phosphoryl]-3,4-dihydrothymidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole, pH 7.5, 350 mM Sodium Acetate, 18 % PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 1.92 Å R-free 0.226 |
| 4TUP Structure of human DNA polymerase beta complexed with GG as the template (GG0b) in a 1-nucleotide gapped DNA Deposited 2014-06-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
7–335（329 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；18% PEG3400, and 350 mM sodium acetate in 50 mM imidazole
|
Resolution 1.80 Å R-free 0.236 |
| 4TUQ Human DNA polymerase beta inserting dCMPNPP opposite GG template (GG0b). Deposited 2014-06-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
10–335（326 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；20% PEG3400, and 350 mM sodium acetate in 50 mM imidazole
|
Resolution 2.37 Å R-free 0.259 |
| 4TUR Human DNA polymerase beta inserting dCMPNPP opposite the 5'G of cisplatin crosslinked Gs (Pt-GG2) Deposited 2014-06-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
7–335（329 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 CPT Cisplatin × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole
|
Resolution 2.17 Å R-free 0.256 |
| 4TUS Human DNA polymerase beta inserting dCMPNPP opposite the 5'G of cisplatin crosslinked Gs (Pt-GG2) WITH MANGANESE IN THE ACTIVE SITE. Deposited 2014-06-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
10–335（326 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 CPT Cisplatin × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole
|
Resolution 2.42 Å R-free 0.243 |
| 4UAW DNA polymerase beta substrate complex with a templating adenine and incoming 8-oxodGTP, 0 s Deposited 2014-08-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | 8DG 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 7.5
|
Resolution 1.90 Å R-free 0.240 |
| 4UAY DNA polymerase beta product complex with a templating adenine and inserted 8-oxodGMP, 40 s Deposited 2014-08-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 PPV PYROPHOSPHATE × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0
|
Resolution 1.98 Å R-free 0.247 |
| 4UAZ DNA polymerase beta reactant complex with a templating adenine and incoming 8-oxodGTP, 20 s Deposited 2014-08-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 8DG 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 PPV PYROPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0
|
Resolution 1.88 Å R-free 0.220 |
| 4UB1 DNA polymerase beta product complex with a templating adenine and 8-oxodGMP, 90 s Deposited 2014-08-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0
|
Resolution 2.34 Å R-free 0.277 |
| 4UB2 DNA polymerase beta product complex with a templating cytosine and 8-oxodGMP, 120 s Deposited 2014-08-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0
|
Resolution 2.51 Å R-free 0.292 |
| 4UB3 DNA polymerase beta closed product complex with a templating cytosine and 8-oxodGMP, 60 s Deposited 2014-08-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 PPV PYROPHOSPHATE × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0
|
Resolution 2.06 Å R-free 0.274 |
| 4UB4 DNA polymerase beta substrate complex with a templating cytosine and incoming dGTP, 0 s Deposited 2014-08-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | CA CALCIUM ION × 2 DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0
|
Resolution 1.95 Å R-free 0.235 |
| 4UB5 DNA polymerase beta substrate complex with a templating cytosine, incoming 8-oxodGTP, and Mn2+, 5 s Deposited 2014-08-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MN MANGANESE (II) ION × 5 8DG 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0
|
Resolution 2.15 Å R-free 0.289 |
| 4UBB DNA polymerase beta reactant complex with a templating cytosine and incoming 8-oxodGTP, 40 s Deposited 2014-08-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 3 CA CALCIUM ION × 1 8DG 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 PPV PYROPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0
|
Resolution 1.90 Å R-free 0.228 |
| 4UBC DNA polymerase beta substrate complex with a templating cytosine and incoming 8-oxodGTP, 0 s Deposited 2014-08-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | CA CALCIUM ION × 3 8DG 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0
|
Resolution 2.00 Å R-free 0.260 |
| 4YMM Structure of human DNA polymerase beta complexed with 7BG as the template base in a 1-nucleotide gapped DNA Deposited 2015-03-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.20 Å R-free 0.257 |
| 4YMN Structure of human DNA polymerase beta complexed with N7BG in the template base paired with incoming non-hydrolyzable CTP Deposited 2015-03-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 1 NA SODIUM ION × 2 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；297 K；14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.59 Å R-free 0.269 |
| 4YMO Structure of human DNA polymerase beta complexed with N7BG in the template opposite to incoming non-hydrolyzable CTP WITH MANGANESE IN THE ACTIVE SITE Deposited 2015-03-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；297 K；14 to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.15 Å R-free 0.226 |
| 4YN4 Structure of human DNA polymerase beta complexed with N7BG in the template opposite to incoming non-hydrolyzable dTTP WITH MANGANESE IN THE ACTIVE SITE Deposited 2015-03-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 1FZ 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；14 to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.24 Å R-free 0.255 |
| 4Z6C Structure of human DNA polymerase beta 279NA mutant complexed with G in the template base paired with incoming non-hydrolyzable CTP Deposited 2015-04-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.68 Å R-free 0.272 |
| 4Z6D Structure of human DNA polymerase beta 279NA mutant complexed with G in the template base paired with incoming non-hydrolyzable TTP Deposited 2015-04-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
Fragment：UNP residues 7-335
|
Not recorded | MG MAGNESIUM ION × 1 NA SODIUM ION × 2 1FZ 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.51 Å R-free 0.270 |
| 4Z6E Structure of human DNA polymerase beta 279NA mutant complexed with G in the template base paired with incoming non-hydrolyzable TTP and MANGANESE Deposited 2015-04-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
Fragment：UNP residues 10-335
|
Not recorded | MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 1FZ 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.75 Å R-free 0.248 |
| 4Z6F Structure of human DNA polymerase beta 279NA mutant complexed with G in the template base paired with incoming non-hydrolyzable TTP and MANGANESE Deposited 2015-04-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
Fragment：UNP residues 10-335
|
Not recorded | MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 1FZ 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.44 Å R-free 0.248 |
| 5BOL DNA polymerase beta ternary complex with a templating 5ClC and incoming dGTP analog Deposited 2015-05-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 1 1GC 2'-deoxy-5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；291 K；50mM Imidazole, 350mM Sodium Acetate, 18% Peg3350, pH 8.0, VAPOR DIFFUSION, temperature 291K
|
Resolution 1.98 Å R-free 0.247 |
| 5BOM DNA polymerase beta binary complex with a templating 5ClC Deposited 2015-05-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；291 K；50mM Imidazole, 350mM Sodium Acetate, 18% Peg3350, pH 8.0, VAPOR DIFFUSION, temperature 291K
|
Resolution 2.00 Å R-free 0.214 |
| 5BPC DNA polymerase beta ternary complex with a templating 5ClC and incoming dATP analog Deposited 2015-05-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MN MANGANESE (II) ION × 4 F2A 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；291 K；50mM Imidazole, 350mM Sodium Acetate, 18% Peg3350, pH 8.0, VAPOR DIFFUSION, temperature 291K
|
Resolution 2.00 Å R-free 0.259 |
| 5DB6 Structure of human DNA polymerase beta Host-Guest complex with the N7MG base paired with a dC Deposited 2015-08-20 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole
|
Resolution 2.83 Å R-free 0.266 |
| 5DB7 Structure of human DNA polymerase beta Host-Guest complex with the N7MG base paired with a dT Deposited 2015-08-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.21 Å R-free 0.273 |
| 5DB8 Structure of human DNA polymerase beta Host-Guest complex with the N7MG base paired with a dA Deposited 2015-08-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole
|
Resolution 2.55 Å R-free 0.258 |
| 5DB9 Structure of human DNA polymerase beta Host-Guest complex with the N7MG base paired with a dG Deposited 2015-08-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；14 to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.45 Å R-free 0.260 |
| 5DBA Structure of human DNA polymerase beta Host-Guest complex with the dG base paired with a dT Deposited 2015-08-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；14 to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 1.97 Å R-free 0.244 |
| 5DBB Structure of human DNA polymerase beta Host-Guest complex with the dG base paired with a dA Deposited 2015-08-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.25 Å R-free 0.265 |
| 5DBC Structure of human DNA polymerase beta Host-Guest complex with the dG base paired with a dG Deposited 2015-08-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.40 Å R-free 0.279 |
| 5EOZ Mutagenicity of 7-Benzyl guanine lesion and Replication by Human DNA Polymerase beta Deposited 2015-11-10 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.09 Å R-free 0.238 |
| 5HHH Structure of human DNA polymerase beta Host-Guest complexed with the control G for N7-CBZ-platination Deposited 2016-01-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
9–335（327 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.36 Å R-free 0.265 |
| 5HHI Structure of human DNA polymerase beta Host-Guest complexed with CBZ-platinated N7-G Deposited 2016-01-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
7–335（329 aa）
|
Not recorded | NA SODIUM ION × 2 61C platinum(4+) chloride azanide [2-(9H-carbazol-9-yl)ethyl]azanide (1:1:2:1) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；14 to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.52 Å R-free 0.279 |
| 5J0O Binary complex crystal structure of DNA polymerase Beta with A:A mismatch at the primer terminus Deposited 2016-03-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
Fragment：UNP residues 7-335
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM Imidazole, pH 7.5, 350 mM Sodium Acetate, 16-18 % PEG3350
|
Resolution 2.00 Å R-free 0.264 |
| 5J0P Binary complex crystal structure of DNA polymerase Beta with A:C mismatch at the primer terminus Deposited 2016-03-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
Fragment：DNA Polymerase Beta
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350,50 mM Imidazole, 350 mM Sodium Acetate
|
Resolution 2.20 Å R-free 0.320 |
| 5J0Q Binary complex crystal structure of DNA polymerase Beta with A:G mismatch at the primer terminus Deposited 2016-03-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
Fragment：DNA Polymerase Beta
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
|
Resolution 2.00 Å R-free 0.261 |
| 5J0R Binary complex crystal structure of DNA polymerase Beta with C:A mismatch at the primer terminus Deposited 2016-03-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
Fragment：DNA Polymerase Beta
|
Not recorded | NA SODIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
|
Resolution 2.00 Å R-free 0.272 |
| 5J0S Binary complex crystal structure of DNA polymerase Beta with C:T mismatch at the primer terminus Deposited 2016-03-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
|
Resolution 2.00 Å R-free 0.245 |
| 5J0T Binary complex crystal structure of DNA polymerase Beta with G:A mismatch at the primer terminus Deposited 2016-03-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
|
Resolution 2.00 Å R-free 0.258 |
| 5J0U Binary complex crystal structure of DNA polymerase Beta with G:G mismatch at the primer terminus Deposited 2016-03-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
|
Resolution 2.10 Å R-free 0.281 |
| 5J0W Binary complex crystal structure of DNA polymerase Beta with T:C mismatch at the primer terminus Deposited 2016-03-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
|
Resolution 2.40 Å R-free 0.306 |
| 5J0X Binary complex crystal structure of DNA polymerase Beta with T:G mismatch at the primer terminus Deposited 2016-03-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
|
Resolution 2.00 Å R-free 0.242 |
| 5J0Y Binary complex crystal structure of DNA polymerase Beta with T:T mismatch at the primer terminus Deposited 2016-03-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
|
Resolution 2.00 Å R-free 0.245 |
| 5J29 Ternary complex crystal structure of DNA polymerase Beta with A:A mismatch at the primer terminus Deposited 2016-03-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
|
Resolution 2.20 Å R-free 0.283 |
| 5J2A Ternary complex crystal structure of DNA polymerase Beta with A:C mismatch at the primer terminus Deposited 2016-03-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
|
Resolution 2.50 Å R-free 0.296 |
| 5J2B Ternary complex crystal structure of DNA polymerase Beta with A:C mismatch at the primer terminus Deposited 2016-03-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
|
Resolution 2.50 Å R-free 0.287 |
| 5J2C Ternary complex crystal structure of DNA polymerase Beta with C:A mismatch at the primer terminus Deposited 2016-03-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
|
Resolution 2.10 Å R-free 0.266 |
| 5J2D Ternary complex crystal structure of DNA polymerase Beta with C:C mismatch at the primer terminus Deposited 2016-03-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
|
Resolution 2.10 Å R-free 0.256 |
| 5J2E Ternary complex crystal structure of DNA polymerase Beta with C:T mismatch at the primer terminus Deposited 2016-03-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
|
Resolution 2.10 Å R-free 0.292 |
| 5J2F Ternary complex crystal structure of DNA polymerase Beta with G:A mismatch at the primer terminus Deposited 2016-03-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
|
Resolution 2.10 Å R-free 0.261 |
| 5J2G Ternary complex crystal structure of DNA polymerase Beta with G:G mismatch at the primer terminus Deposited 2016-03-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
|
Resolution 2.10 Å R-free 0.265 |
| 5J2H Ternary complex crystal structure of DNA polymerase Beta with G:T mismatch at the primer terminus Deposited 2016-03-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
|
Resolution 2.30 Å R-free 0.266 |
| 5J2I Ternary complex crystal structure of DNA polymerase Beta with T:C mismatch at the primer terminus Deposited 2016-03-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
|
Resolution 2.40 Å R-free 0.269 |
| 5J2J Ternary complex crystal structure of DNA polymerase Beta with T:G mismatch at the primer terminus Deposited 2016-03-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
|
Resolution 2.20 Å R-free 0.266 |
| 5J2K Ternary complex crystal structure of DNA polymerase Beta with T:T mismatch at the primer terminus Deposited 2016-03-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
|
Resolution 2.10 Å R-free 0.284 |
| 5TB8 Precatalytic ternary complex of Human DNA Polymerase Beta in closed conformation With Gapped DNA substrate incoming (-)3TC-TP and Mn2+. Deposited 2016-09-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | 1RZ Lamivudine Triphosphate × 1 MN MANGANESE (II) ION × 6 NA SODIUM ION × 5 CL CHLORIDE ION × 2 ACT ACETATE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；50 MM IMIDAZOLE, 350 MM SODIUM
ACETATE, 17% PEG3350, PH 8.0
|
Resolution 2.00 Å R-free 0.230 |
| 5TB9 Precatalytic ternary complex of Human DNA Polymerase Beta in closed conformation With Gapped DNA substrate incoming (-)FTC-TP and Mn2+. Deposited 2016-09-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | 1RY [[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MN MANGANESE (II) ION × 6 NA SODIUM ION × 4 ACT ACETATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；50 MM IMIDAZOLE, 350 MM SODIUM
ACETATE, 17% PEG3350, PH 8.0
|
Resolution 2.49 Å R-free 0.267 |
| 5TBA Postcatalytic ternary complex of Human DNA Polymerase Beta with Gapped DNA substrate, incorporated (-)3TC and PPi. Deposited 2016-09-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | PPV PYROPHOSPHATE × 1 NA SODIUM ION × 5 42E [(2R,5S)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-1,3-oxathiolan-2-yl]methyl dihydrogen phosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；50 MM IMIDAZOLE, 350 MM SODIUM
ACETATE, 17% PEG3350 , PH 8.0
|
Resolution 2.49 Å R-free 0.273 |
| 5TBB Postcatalytic ternary complex of Human DNA Polymerase Beta with Gapped DNA substrate, incorporated (-)FTC and PPi. Deposited 2016-09-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MN MANGANESE (II) ION × 1 NA SODIUM ION × 4 ACT ACETATE ION × 2 PPV PYROPHOSPHATE × 1 43X [(2R,5S)-5-(4-amino-5-fluoro-2-oxopyrimidin-1(2H)-yl)-1,3-oxathiolan-2-yl]methyl dihydrogen phosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；50 MM IMIDAZOLE, 350 MM SODIUM
ACETATE, 17% PEG3350, PH 8.0,
|
Resolution 2.39 Å R-free 0.269 |
| 5TBC PRECATALYTIC TERNARY COMPLEX OF HUMAN DNA POLYMERASE BETA WITH GAPPED DNA SUBSTRATE, INCORPORATED (-)3TC-MP AND AN ANOTHER INCOMING (-)3TC-TP NUCLEOTIDE. Deposited 2016-09-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | 1RZ Lamivudine Triphosphate × 1 NA SODIUM ION × 6 CL CHLORIDE ION × 1 42E [(2R,5S)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-1,3-oxathiolan-2-yl]methyl dihydrogen phosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；50 MM IMIDAZOLE, 350 MM SODIUM
ACETATE, 17% PEG3350 , PH 8.0
|
Resolution 1.85 Å R-free 0.279 |
| 5TZV Binary complex crystal structure of DNA Polymerase Beta with G:T mismatch at the primer terminus Deposited 2016-11-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 MM IMIDAZOLE, 350 MM SODIUM CHLORIDE, 17% PEG3350, pH 7.5
|
Resolution 2.00 Å R-free 0.229 |
| 5U2R PRECATALYTIC TERNARY COMPLEX OF HUMAN DNA POLYMERASE BETA WITH GAPPED DNA SUBSTARTE, INCOMING L-DCTP AND CA2+ Deposited 2016-11-30 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | 1S0 4-amino-1-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-L-erythro-pentofuranosyl}pyrimidin-2(1H)-one × 1 CA CALCIUM ION × 2 NA SODIUM ION × 2 ACT ACETATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；50 MM IMIDAZOLE, 350 MM SODIUM
ACETATE, 17% PEG3350,
|
Resolution 1.80 Å R-free 0.229 |
| 5U2S Pre-catalytic ternary complex of Human DNA Polymerase Beta With Gapped DNA substrate incoming (-)3TC-TP and Ca2+. Deposited 2016-11-30 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | 1RZ Lamivudine Triphosphate × 1 CA CALCIUM ION × 1 NA SODIUM ION × 4 ACT ACETATE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；50 MM IMIDAZOLE, 350 MM SODIUM
ACETATE, 17% PEG3350
|
Resolution 2.30 Å R-free 0.284 |
| 5U2T Pre-catalytic ternary complex of Human DNA Polymerase Beta With Gapped DNA substrate incoming (-)FTC-TP and Ca2+. Deposited 2016-11-30 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | 1RY [[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 CA CALCIUM ION × 1 NA SODIUM ION × 5 ACT ACETATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；50 MM IMIDAZOLE, 350 MM SODIUM
ACETATE, 17% PEG3350
|
Resolution 1.79 Å R-free 0.247 |
| 5U8G DNA Polymerase Beta crystallized in PEG 400 Deposited 2016-12-14 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
Fragment：DNA polymerase
|
Not recorded | NA SODIUM ION × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；24% PEG 400, 30 mM potassium sodium tartrate, 1% 1,4-dioxane
|
Resolution 2.17 Å R-free 0.225 |
| 5U8H DNA Polymerase Beta G231D crystallized in PEG 400 Deposited 2016-12-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：G231D | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；22% PEG 400, 100 mM potassium sodium tartrate, 1% isopropanol
|
Resolution 2.15 Å R-free 0.234 |
| 5U8I DNA Polymerase Beta S229L crystallized in PEG 400 Deposited 2016-12-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
Fragment：DNA polymerase
|
Mutation：S229 | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；24% PEG 400, 30 mM potassium sodium tartrate, 1% 1,4-dioxane
|
Resolution 2.45 Å R-free 0.231 |
| 5U9H DNA polymerase beta product complex with inserted Sp-isomer of dCTP-alpha-S Deposited 2016-12-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MN MANGANESE (II) ION × 4 PPV PYROPHOSPHATE × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0
|
Resolution 1.85 Å R-free 0.233 |
| 5UGN DNA polymerase beta imidodiphosphate reactant complex Deposited 2017-01-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | 2PN IMIDODIPHOSPHORIC ACID × 1 MG MAGNESIUM ION × 2 8CP 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]cytidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350
|
Resolution 2.00 Å R-free 0.243 |
| 5UGO DNA polymerase beta nick complex with imidodiphosphate Deposited 2017-01-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | 2PN IMIDODIPHOSPHORIC ACID × 1 CA CALCIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 7.5
|
Resolution 1.90 Å R-free 0.236 |
| 5UGP DNA polymerase beta complex with a 1nt gap and dCMPPNP Deposited 2017-01-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | 8CP 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]cytidine × 1 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350
|
Resolution 1.96 Å R-free 0.233 |
| 5V1F DNA polymerase beta substrate complex with 8-oxoG at the primer terminus and incoming dCTP Deposited 2017-03-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | CA CALCIUM ION × 2 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350
|
Resolution 2.18 Å R-free 0.296 |
| 5V1G DNA polymerase beta binary complex with 8-oxoG at the primer terminus Deposited 2017-03-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；50 mM imidazole, 350 mM sodium acetate, 17% PEG3350
|
Resolution 1.80 Å R-free 0.227 |
| 5V1H DNA polymerase beta binary complex with 8-oxoG:A at the primer terminus Deposited 2017-03-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；50 mM imidazole, 350 mM sodium acetate, 17% PEG3350
|
Resolution 1.95 Å R-free 0.272 |
| 5V1I DNA polymerase beta ternary product complex with 8-oxoG:C and inserted dCTP Deposited 2017-03-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 3 CL CHLORIDE ION × 4 PPV PYROPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350
|
Resolution 2.04 Å R-free 0.237 |
| 5V1J DNA polymerase beta open product complex with 8-oxoG:C and inserted dCTP Deposited 2017-03-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；50 mM imidazole, 350 mM sodium acetate, 17% PEG3350
|
Resolution 2.62 Å R-free 0.285 |
| 5V1N DNA polymerase beta substrate complex with 8-oxoG:A at the primer terminus and incoming dCTP Deposited 2017-03-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | CA CALCIUM ION × 2 NA SODIUM ION × 1 CL CHLORIDE ION × 2 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；50 mM imidazole, 350 mM sodium acetate, 17% PEG3350
|
Resolution 2.00 Å R-free 0.237 |
| 5V1O DNA polymerase beta product complex with 8-oxoG:A and inserted dCTP Deposited 2017-03-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 3 CL CHLORIDE ION × 3 PPV PYROPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；50 mM imidazole, 350 mM sodium acetate, 17% PEG3350
|
Resolution 1.80 Å R-free 0.215 |
| 5V1P DNA polymerase beta substrate complex with 8-oxoG:C at the primer terminus and incoming dCTP analog Deposited 2017-03-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 MG MAGNESIUM ION × 2 XC5 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine × 1 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；50 mM imidazole, 350 mM sodium acetate, 17% PEG3350
|
Resolution 1.99 Å R-free 0.231 |
| 5V1R DNA polymerase beta reactant complex with 8-oxoG:C at the primer terminus and incoming dCTP Deposited 2017-03-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 3 NA SODIUM ION × 2 CL CHLORIDE ION × 4 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 PPV PYROPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；50 mM imidazole, 350 mM sodium acetate, 17% PEG3350
|
Resolution 2.08 Å R-free 0.237 |
| 5VEZ DNA polymerase beta substrate complex with 8-oxoG:A at the primer terminus and incoming dCTP analog Deposited 2017-04-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 3 MG MAGNESIUM ION × 1 XC5 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；50 mM imidazole, 350 mM sodium chloride, 17% PEG3350
|
Resolution 2.04 Å R-free 0.232 |
| 5VRW Human DNA polymerase beta pre-catalytic 8-oxoG:dC extension complex with dTTP bound in non-planar conformation Deposited 2017-05-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | CA CALCIUM ION × 7 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 PEG DI(HYDROXYETHYL)ETHER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；50 mM imidizole pH 7-7.5, 350 mM sodium acetate, 16-18 % PEG 3350
|
Resolution 2.58 Å R-free 0.306 |
| 5VRX Human DNA polymerase beta pre-catalytic 8-oxoG:dC extension complex with dTTP bound in Watson-Crick conformation Deposited 2017-05-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | CA CALCIUM ION × 5 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 IMD IMIDAZOLE × 1 ACT ACETATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；50 mM imidazole pH 7.0-7.5, 350 mM sodium acetate, 16-18% PEG 3350
|
Resolution 2.20 Å R-free 0.260 |
| 5VRY Human DNA polymerase beta 8-oxoG:dC extension with dTTP after 20 s Deposited 2017-05-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 6 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 PPV PYROPHOSPHATE × 1 CL CHLORIDE ION × 1 IMD IMIDAZOLE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；50 mM imidazole pH 7.0-7.5, 350 mM sodium acetate, 16-18% PEG 3350
|
Resolution 1.90 Å R-free 0.243 |
| 5VRZ Human DNA polymerase beta 8-oxoG:dC extension with dTTP after 60 s Deposited 2017-05-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | TTP THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 5 PPV PYROPHOSPHATE × 1 NA SODIUM ION × 1 CL CHLORIDE ION × 2 IMD IMIDAZOLE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；50 mM imidazole pH 7.0-7.5, 350 mM sodium acetate, 16-18% PEG 3350
|
Resolution 2.05 Å R-free 0.242 |
| 5VS0 Human DNA polymerase beta 8-oxoG:dC extension with dTTP after 80 s Deposited 2017-05-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 6 CL CHLORIDE ION × 2 IMD IMIDAZOLE × 1 PPV PYROPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；50 mM imidazole pH 7.0-7.5, 350 mM sodium acetate, 16-18% PEG 3350
|
Resolution 2.10 Å R-free 0.262 |
| 5VS1 Human DNA polymerase beta pre-catalytic 8-oxoG:dA extension complex with dTTP bound in non-planar conformation Deposited 2017-05-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | CA CALCIUM ION × 5 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；50 mM imidazole pH 7.0-7.5, 350 mM sodium acetate, 16-18% PEG 3350
|
Resolution 2.50 Å R-free 0.272 |
| 5VS2 Human DNA polymerase beta pre-catalytic 8-oxoG:dA extension complex with dTTP bound in Watson-Crick conformation Deposited 2017-05-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | CA CALCIUM ION × 3 NA SODIUM ION × 2 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；50 mM imidazole pH 7.0-7.5, 350 mM sodium acetate, 16-18% PEG 3350
|
Resolution 2.33 Å R-free 0.250 |
| 5VS3 Human DNA polymerase beta 8-oxoG:dA extension with dTTP after 90 s Deposited 2017-05-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 6 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 PPV PYROPHOSPHATE × 1 ACT ACETATE ION × 3 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；50 mM imidazole pH 7.0-7.5, 350 mM sodium acetate, 16-18% PEG 3350
|
Resolution 1.70 Å R-free 0.249 |
| 5VS4 Human DNA polymerase beta 8-oxoG:dA extension with dTTP after 120 s Deposited 2017-05-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 6 PPV PYROPHOSPHATE × 1 ACT ACETATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；50 mM imidazole pH 7.0-7.5, 350 mM sodium acetate, 16-18% PEG 3350
|
Resolution 1.87 Å R-free 0.257 |
| 5WNX DNA polymerase beta substrate complex with incoming 6-TdGTP Deposited 2017-08-01 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 CL CHLORIDE ION × 1 SGT 2-amino-9-{2-deoxy-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-1,9-dihydro-6H-purine-6-thione × 1 CA CALCIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；50 mM imidazole, pH 7.5, 16% PEG3350 and 350 mM sodium acetate
|
Resolution 2.55 Å R-free 0.289 |
| 5WNY DNA polymerase beta substrate complex with incoming 5-FdUTP Deposited 2017-08-01 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 CL CHLORIDE ION × 4 CA CALCIUM ION × 2 B7P 2'-deoxy-5-fluorouridine 5'-(tetrahydrogen triphosphate) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；50 mM imidazole, pH 7.5, 16% PEG3350 and 350 mM sodium acetate
|
Resolution 2.10 Å R-free 0.237 |
| 5WNZ DNA polymerase beta substrate complex with incoming 5-FodCTP Deposited 2017-08-01 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 CL CHLORIDE ION × 1 CA CALCIUM ION × 2 B7J 2'-deoxy-5-formylcytidine 5'-(tetrahydrogen triphosphate) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；50 mM imidazole, pH 7.5, 16% PEG3350, and 350 mM sodium acetate.
|
Resolution 2.20 Å R-free 0.254 |
| 5WO0 DNA polymerase beta substrate complex with incoming 5-FodUTP Deposited 2017-08-01 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 CA CALCIUM ION × 2 CL CHLORIDE ION × 3 B7A 2'-deoxy-5-formyluridine 5'-(tetrahydrogen triphosphate) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；50 mM imidazole, pH 7.5, 16% PEG3350 and 350 mM sodium acetate
|
Resolution 1.60 Å R-free 0.231 |
| 6BEL Ternary complex crystal structure of DNA polymerase Beta with R-isomer of beta-gamma-CHF-dCTP Deposited 2017-10-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 3 CL CHLORIDE ION × 1 F3C 2'-deoxy-5'-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine × 1 DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 1.90 Å R-free 0.202 |
| 6BEM Ternary complex crystal structure of DNA polymerase Beta with S-isomer of beta-gamma-CHCL-dCTP Deposited 2017-10-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 3 CL CHLORIDE ION × 3 DJJ 5'-O-[(R)-{[(R)-[(S)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxycytidine × 1 DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 1.88 Å R-free 0.226 |
| 6BTE DNA Polymerase Beta I260Q Binary Complex Deposited 2017-12-06 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：I260Q | NA SODIUM ION × 2 CL CHLORIDE ION × 1 IOD IODIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；18-20% PEG 3350, 175-250 mM sodium acetate, 50 mM HEPES pH 7.5, 2 mM TCEP, 1% tert-butanol
|
Resolution 2.20 Å R-free 0.229 |
| 6BTF DNA Polymerase Beta I260Q Ternary Complex Deposited 2017-12-06 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：I260Q | NA SODIUM ION × 3 MG MAGNESIUM ION × 1 DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；18-20% PEG 3350, 175-250 mM sodium acetate, 50 mM HEPES pH 7.5, 2 mM TCEP, 1% tert-butanol
|
Resolution 1.75 Å R-free 0.214 |
| 6CLY Structure of human DNA polymerase beta complexed with 8-ClG as the template base in a 1-nucleotide gapped DNA Deposited 2018-03-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.19 Å R-free 0.268 |
| 6CPQ Structure of human DNA polymerase beta complexed with 8-ClG in the template base paired with incoming non-hydrolyzable CTP Deposited 2018-03-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 1.93 Å R-free 0.239 |
| 6CR3 Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CBr2, beta, gamma dATP analogue Deposited 2018-03-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | H84 2'-deoxy-5'-O-[(R)-{[(R)-[dibromo(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 1.95 Å R-free 0.227 |
| 6CR4 Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with dATP Deposited 2018-03-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 1.80 Å R-free 0.213 |
| 6CR5 Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CH2-beta, gamma dATP analogue Deposited 2018-03-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | FCJ 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]oxy}phosphoryl]adenosine × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 1.98 Å R-free 0.232 |
| 6CR6 Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CH-CH3, beta, gamma dATP analogue Deposited 2018-03-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 3 HGV 2'-deoxy-5'-O-[(R)-hydroxy({(R)-hydroxy[(1S)-1-phosphonoethyl]phosphoryl}oxy)phosphoryl]adenosine × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 2.10 Å R-free 0.293 |
| 6CR7 Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHF, beta, gamma dATP analogue Deposited 2018-03-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | V3A 9-{2-deoxy-5-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D-erythro-pentofuranosyl}-9H-purin-6-amine × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 2.29 Å R-free 0.240 |
| 6CR8 Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCL (R & S isomers), beta, gamma dATP analogue Deposited 2018-03-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | VA4 5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxyadenosine × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 2.05 Å R-free 0.248 |
| 6CR9 Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CFCL, beta, gamma dATP analogue Deposited 2018-03-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | VA5 9-{5-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2-deoxy-alpha-D-threo-pentofuranosyl}-9H-purin-6-amine × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 1.96 Å R-free 0.224 |
| 6CRB Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CF2, beta, gamma dATP analogue Deposited 2018-03-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | VA6 9-{2-deoxy-5-O-[(S)-{[(S)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D-erythro-pentofuranosyl}-9H-purin-6-amine × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 2.15 Å R-free 0.275 |
| 6CRC Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CCL2, beta, gamma dATP analogue Deposited 2018-03-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | VA7 2'-deoxy-5'-O-[(R)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 2.30 Å R-free 0.285 |
| 6CRH Structure of human DNA polymerase beta complexed with 8-ClG in the template base paired with incoming non-hydrolyzable GTP Deposited 2018-03-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 XG4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.33 Å R-free 0.244 |
| 6CTI Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CCL2, beta, gamma dTTP analogue Deposited 2018-03-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 3 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 2 VT8 5'-O-[(R)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 2.00 Å R-free 0.227 |
| 6CTJ Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCH3, beta, gamma dTTP analogue Deposited 2018-03-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 FDV 5'-O-[(R)-hydroxy({(R)-hydroxy[(1S)-1-phosphonoethyl]phosphoryl}oxy)phosphoryl]thymidine × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 2.10 Å R-free 0.257 |
| 6CTK Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHF-R/S isomers, beta, gamma dTTP analogue Deposited 2018-03-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 3 FDY 5'-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 2.15 Å R-free 0.244 |
| 6CTL Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCL-R/S isomers, beta, gamma dTTP analogue Deposited 2018-03-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 1 FDJ 5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 2.00 Å R-free 0.225 |
| 6CTM Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCL(R-isomer), beta, gamma dTTP analogue Deposited 2018-03-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 MG MAGNESIUM ION × 1 FDJ 5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine × 1 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 2.10 Å R-free 0.258 |
| 6CTN Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CFCL,beta-gamma dTTP analogue Deposited 2018-03-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 3 VT6 5'-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 1.92 Å R-free 0.235 |
| 6CTO Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CF2, beta, gamma dTTP analogue Deposited 2018-03-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 3 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 2 VT7 5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 2.04 Å R-free 0.232 |
| 6CTP Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CH2, beta, gamma dTTP analogue Deposited 2018-03-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | CL CHLORIDE ION × 3 NA SODIUM ION × 3 TTE PHOSPHOMETHYL PHOSPHONIC ACID DEOXYTHYMIDYLATE ESTER × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 2.20 Å R-free 0.290 |
| 6CTQ Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with dCTP Deposited 2018-03-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 3 CL CHLORIDE ION × 2 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 1.87 Å R-free 0.228 |
| 6CTR Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHF (R & S isomers), beta, gamma dCTP analogue Deposited 2018-03-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 3 CL CHLORIDE ION × 1 F3C 2'-deoxy-5'-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine × 1 FF4 2'-deoxy-5'-O-[(R)-{[(R)-[(S)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine × 1 DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 1.85 Å R-free 0.222 |
| 6CTT Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCL (R & S isomers, beta, gamma dCTP analogue Deposited 2018-03-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 3 FF7 5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxycytidine × 1 DJJ 5'-O-[(R)-{[(R)-[(S)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxycytidine × 1 DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 2.00 Å R-free 0.222 |
| 6CTU Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CFCL, beta, gamma dCTP analogue Deposited 2018-03-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 3 CL CHLORIDE ION × 1 VC6 4-amino-1-{5-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2-deoxy-alpha-L-threo-pentofuranosyl}pyrimidin-2(1H)-one × 1 DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 1.90 Å R-free 0.206 |
| 6CTV Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CF2, beta, gamma dCTP analogue Deposited 2018-03-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 3 CL CHLORIDE ION × 1 FFJ 2'-deoxy-5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine × 1 DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 2.02 Å R-free 0.220 |
| 6CTW Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CCL2, beta, gamma dCTP analogue Deposited 2018-03-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 3 VC8 4-amino-1-{2-deoxy-5-O-[(R)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-L-threo-pentofuranosyl}pyrimidin-2(1H)-one × 1 CL CHLORIDE ION × 1 DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 1.98 Å R-free 0.219 |
| 6CTX Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CBr2, beta, gamma dCTP analogue Deposited 2018-03-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 3 CL CHLORIDE ION × 1 VC9 2'-deoxy-5'-O-[(R)-{[(R)-[dibromo(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine × 1 DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 2.02 Å R-free 0.229 |
| 6CU9 Structure of human DNA polymerase beta complexed with 8-ClG in the template base paired with incoming non-hydrolyzable CTP and MANGANESE Deposited 2018-03-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.04 Å R-free 0.241 |
| 6CUA Structure of human DNA polymerase beta complexed with 8-ClG in the template base paired with incoming non-hydrolyzable GTP and MANGANESE Deposited 2018-03-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 XG4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.17 Å R-free 0.259 |
| 6CUB Structure of human DNA polymerase beta complexed with 8-ClG in the template base paired with incoming non-hydrolyzable ATP and MANGANESE Deposited 2018-03-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | DZ4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 1 MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.05 Å R-free 0.254 |
| 6DIA DNA polymerase beta substrate complex with templating cytosine and incoming Fapy-dGTP analog Deposited 2018-05-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
10–335（326 aa）
|
Not recorded | GKS 1-[2-amino-5-(formylamino)-6-oxo-1,6-dihydropyrimidin-4-yl]-2,5-anhydro-1,3-dideoxy-6-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-D-ribo-hexitol × 1 NA SODIUM ION × 2 CA CALCIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；50 mM imidazole, 350 mM sodium chloride, 15% PEG3350, pH 8.0
|
Resolution 1.97 Å R-free 0.246 |
| 6DIC D276G DNA polymerase beta substrate complex with templating cytosine and incoming Fapy-dGTP analog Deposited 2018-05-23 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
10–335（326 aa）
|
Mutation：D276G | NA SODIUM ION × 4 CA CALCIUM ION × 3 GKS 1-[2-amino-5-(formylamino)-6-oxo-1,6-dihydropyrimidin-4-yl]-2,5-anhydro-1,3-dideoxy-6-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-D-ribo-hexitol × 1 CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；50mM Imidazole, 350mM Sodium Acetate, 16% Peg3350
|
Resolution 1.99 Å R-free 0.232 |
| 6E3R Structure of human DNA polymerase beta complexed with 8OA as the template base in a 1-nucleotide gapped DNA Deposited 2018-07-14 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；14% TO 23% PEG3400, AND 350 MM SODIUM
ACETATE IN 50 MM IMIDAZOLE (PH 7.5), VAPOR DIFFUSION, SITTING
DROP, TEMPERATURE 298K
|
Resolution 2.26 Å R-free 0.272 |
| 6E3V Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable TTP Deposited 2018-07-15 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 1FZ 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；14% TO 23% PEG3400, AND 350 MM SODIUM
ACETATE IN 50 MM IMIDAZOLE (PH 7.5), VAPOR DIFFUSION, SITTING
DROP, TEMPERATURE 298K
|
Resolution 1.96 Å R-free 0.240 |
| 6E3W Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable GTP Deposited 2018-07-15 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 XG4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；14% TO 23% PEG3400, AND 350 MM SODIUM
ACETATE IN 50 MM IMIDAZOLE (PH 7.5), VAPOR DIFFUSION, SITTING
DROP, TEMPERATURE 298K
|
Resolution 2.02 Å R-free 0.245 |
| 6E3X Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable ATP Deposited 2018-07-15 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 MG MAGNESIUM ION × 2 DZ4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；14% TO 23% PEG3400, AND 350 MM SODIUM
ACETATE IN 50 MM IMIDAZOLE (PH 7.5), VAPOR DIFFUSION, SITTING
DROP, TEMPERATURE 298K
|
Resolution 2.65 Å R-free 0.266 |
| 6G2Q Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCL (S-isomer), beta, gamma dTTP analogue Deposited 2018-03-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
Fragment：Synthetic oligonucleotide
|
Not recorded | NA SODIUM ION × 3 EJH [(~{S})-chloranyl-[[[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]methyl]phosphonic acid × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 2.15 Å R-free 0.260 |
| 6MR7 DNA polymerase beta substrate complex with templating adenine and incoming Fapy-dGTP analog Deposited 2018-10-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
10–335（326 aa）
|
Not recorded | GKS 1-[2-amino-5-(formylamino)-6-oxo-1,6-dihydropyrimidin-4-yl]-2,5-anhydro-1,3-dideoxy-6-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-D-ribo-hexitol × 1 CA CALCIUM ION × 2 NA SODIUM ION × 4 EDO 1,2-ETHANEDIOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292 K；50 mM imidazole pH 7.5, 16% PEG3350, and 350 mM sodium acetate
|
Resolution 2.14 Å R-free 0.252 |
| 6MR8 D276G DNA polymerase beta substrate complex with templating adenine and incoming Fapy-dGTP analog Deposited 2018-10-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
11–335（325 aa）
|
Not recorded | GKS 1-[2-amino-5-(formylamino)-6-oxo-1,6-dihydropyrimidin-4-yl]-2,5-anhydro-1,3-dideoxy-6-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-D-ribo-hexitol × 1 NA SODIUM ION × 5 CA CALCIUM ION × 3 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；50 mM imidazole, pH 8.0, 18% PEG3350 and 350 mM sodium acetate
|
Resolution 1.90 Å R-free 0.239 |
| 6N2R Binary complex crystal structure of DNA polymerase Beta with 5-carboxy-dC (5-caC) at the templating position Deposited 2018-11-14 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 2.10 Å R-free 0.266 |
| 6N2S Ternary complex crystal structure of DNA polymerase Beta with 5-carboxy-dC (5-caC) at the templating position Deposited 2018-11-14 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
Fragment：DNA Polymerase Beta
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 1GC 2'-deoxy-5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 2000 Monomethyl Ether
|
Resolution 2.46 Å R-free 0.290 |
| 6N2T Ternary complex crystal structure of DNA polymerase Beta with 5-hydroxymethyl-dC (5-hmC) at the templating position Deposited 2018-11-14 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
Fragment：DNA Polymerase Beta
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 1GC 2'-deoxy-5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 2.60 Å R-free 0.290 |
| 6NKR Ternary complex crystal structure of K289M variant of DNA polymerase Beta with dGTP Deposited 2019-01-07 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：K289M | MG MAGNESIUM ION × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 2 DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
|
Resolution 2.45 Å R-free 0.290 |
| 6NKS Ternary complex crystal structure of K289M variant of DNA polymerase Beta with beta-gamma CHF analog of dGTP Deposited 2019-01-07 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：K289M | GFH 2'-DEOXY-5'-O-[(R)-{[(R)-[(R)-FLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]GUANOSINE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
|
Resolution 2.35 Å R-free 0.255 |
| 6NKT Ternary complex crystal structure of K289M variant of DNA polymerase Beta with beta-gamma difluoro analogue of dGTP Deposited 2019-01-07 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：K289M | NA SODIUM ION × 2 GFF 2'-DEOXY-5'-O-[({[DIFLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL}OXY)(HYDROXY)PHOSPHORYL]GUANOSINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
|
Resolution 2.60 Å R-free 0.303 |
| 6NKU Ternary complex crystal structure of DNA polymerase Beta with "hot-spot sequence" with dGTP Deposited 2019-01-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 3 CL CHLORIDE ION × 4 DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；16-18% PEG 3350, 350 mM Sodium Acetate, 50 mM Imidazole
|
Resolution 1.90 Å R-free 0.211 |
| 6NKV Ternary complex crystal structure of DNA polymerase Beta with "hot-spot sequence" with beta-gamma CHF analogue of dGTP Deposited 2019-01-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 3 CL CHLORIDE ION × 3 GFH 2'-DEOXY-5'-O-[(R)-{[(R)-[(R)-FLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]GUANOSINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
|
Resolution 1.85 Å R-free 0.203 |
| 6NKW Ternary complex crystal structure of DNA polymerase Beta with "hot-spot sequence" with beta-gamma-methylene dGTP Deposited 2019-01-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 3 CL CHLORIDE ION × 4 GGH 2'-DEOXY-5'-O-(HYDROXY{[HYDROXY(PHOSPHONOMETHYL)PHOSPHORYL]OXY}PHOSPHORYL)GUANOSINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
|
Resolution 1.98 Å R-free 0.217 |
| 6NKX Ternary complex crystal structure of K289M variant of DNA polymerase Beta with "hot-spot sequence" with dGTP Deposited 2019-01-07 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：K289M | NA SODIUM ION × 3 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 1.98 Å R-free 0.232 |
| 6NKY Ternary complex crystal structure of K289M variant of DNA polymerase Beta with "hot-spot sequence" with beta-gamma CHF analogue of dGTP Deposited 2019-01-07 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：K289M | MG MAGNESIUM ION × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 3 GFH 2'-DEOXY-5'-O-[(R)-{[(R)-[(R)-FLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]GUANOSINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；16-18% PEG 3350, 7.5, 50 mM Imidazole, 350 mM Sodium Acetate
|
Resolution 2.09 Å R-free 0.256 |
| 6NKZ Ternary complex crystal structure of K289M variant of DNA polymerase Beta with "hot-spot sequence" with beta-gamma methylene dGTP Deposited 2019-01-07 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：K289M | NA SODIUM ION × 3 MG MAGNESIUM ION × 1 GGH 2'-DEOXY-5'-O-(HYDROXY{[HYDROXY(PHOSPHONOMETHYL)PHOSPHORYL]OXY}PHOSPHORYL)GUANOSINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
|
Resolution 2.01 Å R-free 0.235 |
| 6NL0 Ternary complex crystal structure of K289M variant of DNA polymerase Beta with "hot-spot sequence" with beta-gamma CF2 analogue of dGTP Deposited 2019-01-07 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：K289M | MG MAGNESIUM ION × 1 NA SODIUM ION × 3 GFF 2'-DEOXY-5'-O-[({[DIFLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL}OXY)(HYDROXY)PHOSPHORYL]GUANOSINE × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 1.97 Å R-free 0.237 |
| 6PH5 Binary product complex crystal structure of DNA polymerase Beta with an extra-helical template base Deposited 2019-06-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
Fragment：DNA Polymerase Beta
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 2.60 Å R-free 0.279 |
| 6PH6 Ternary complex crystal structure of DNA polymerase Beta with 2nt-gap with dCTP bound downstream Deposited 2019-06-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
Fragment：DNA Polymerase Beta
|
Not recorded | DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 2.60 Å R-free 0.276 |
| 6PKZ Structure of human DNA polymerase beta N279A complexed with 8OA in the template base paired with incoming non-hydrolyzable GTP Deposited 2019-06-30 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：N279A | NA SODIUM ION × 2 MG MAGNESIUM ION × 1 XG4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；14-23% PEG3400, 350 MM SODIUM ACETATE
IN 50 MM IMIDAZOLE, PH 7.5, VAPOR DIFFUSION, SITTING DROP,
TEMPERATURE 295K
|
Resolution 2.74 Å R-free 0.249 |
| 6U2O Structure of human DNA polymerase beta misinserting dAMPNPP opposite the 5'G of the cisplatin Pt-GG intrastrand crosslink Deposited 2019-08-20 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 1 NA SODIUM ION × 2 DZ4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 1 CPT Cisplatin × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；295.15 K；23% PEG 3350, 50 mM Tris (pH 6.5), and 350 mM sodium acetate
|
Resolution 2.30 Å R-free 0.248 |
| 6U6B Structure of human DNA polymerase beta misinserting dAMPNPP opposite the 5'G of the cisplatin Pt-GG intrastrand crosslink with Manganese in the active site Deposited 2019-08-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 DZ4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 1 CPT Cisplatin × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；295.15 K；23% PEG 3350, 50 mM Tris (pH 6.5), and 350 mM sodium acetate
|
Resolution 3.11 Å R-free 0.268 |
| 6UOK Y271G DNA polymerase beta substrate complex with templating cytosine and incoming r8-oxo-GTP Deposited 2019-10-15 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain F
1–335（335 aa）
|
Mutation：Y271G | CL CHLORIDE ION × 1 NA SODIUM ION × 3 MN MANGANESE (II) ION × 5 8GT 8-OXO-GUANOSINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；19% PEG3350, 0.05M Imidazole (pH 8.0), 0.35 Sodium Acetate
|
Resolution 2.55 Å R-free 0.279 |
| 6UOK Y271G DNA polymerase beta substrate complex with templating cytosine and incoming r8-oxo-GTP Deposited 2019-10-15 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：Y271G | NA SODIUM ION × 3 MN MANGANESE (II) ION × 1 8GT 8-OXO-GUANOSINE-5'-TRIPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；19% PEG3350, 0.05M Imidazole (pH 8.0), 0.35 Sodium Acetate
|
Resolution 2.55 Å R-free 0.279 |
| 6UOL Y271G DNA polymerase beta substrate complex with a templating cytosine and incoming rGTP Deposited 2019-10-15 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 1 MN MANGANESE (II) ION × 5 NA SODIUM ION × 3 CL CHLORIDE ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；19% PEG3350, 0.35 M sodium acetate, 0.05 M Imidazole, pH 8.0.
|
Resolution 1.94 Å R-free 0.250 |
| 6UOM Y271G DNA polymerase beta ternary complex with templating adenine and incoming r8-oxo-GTP Deposited 2019-10-15 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：Y271G | EDO 1,2-ETHANEDIOL × 2 DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE × 1 NA SODIUM ION × 4 MN MANGANESE (II) ION × 2 8GT 8-OXO-GUANOSINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；50 mM imidazole, 350 mM sodium chloride, 19% PEG3350, pH 8.0
|
Resolution 2.05 Å R-free 0.244 |
| 6W2M Abortive ternary complex crystal structure of DNA polymerase Beta with 8OG-dC base pair at the primer terminus and flipped out dA Deposited 2020-03-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 2 SFV [[[(2~{R},3~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]methylphosphonic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16-18% PEG 3350
|
Resolution 2.00 Å R-free 0.238 |
| 7ICE DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF CACL2 Deposited 1996-04-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 3 DAYS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR CACL2, 0.1 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 2.80 Å |
| 7ICF DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CDCL2 (0.1 MILLIMOLAR) (FOUR-DAY SOAK) Deposited 1996-04-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | CD CADMIUM ION × 2 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 4 DAYS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR CDCL2, 0.1 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.10 Å |
| 7ICG DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF CDCL2 Deposited 1996-04-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR CDCL2, 0.01 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.00 Å |
| 7ICH DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF COCL2 Deposited 1996-04-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR COCL2, 0.1 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 2.90 Å |
| 7ICI DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CRCL3 (0.1 MILLIMOLAR) Deposited 1996-04-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR CRCL3, 0.1 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 2.80 Å |
| 7ICJ DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CUCL2 (0.1 MILLIMOLAR) Deposited 1996-04-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 1 CU COPPER (II) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR CRCL3, 0.1 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.50 Å |
| 7ICK DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF MGCL2 Deposited 1996-04-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR MGCL2, 0.1 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 2.90 Å |
| 7ICL DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF MNCL2 (0.1 MILLIMOLAR) Deposited 1996-04-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR MNCL2, 0.1 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.10 Å |
| 7ICM DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF MNCL2 (1.0 MILLIMOLAR) Deposited 1996-04-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR MNCL2, 1.0 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.00 Å |
| 7ICN DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF NICL2 Deposited 1996-04-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 4 DAYS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR NICL2, 0.1 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 2.80 Å |
| 7ICO DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF ZNCL2 Deposited 1996-04-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | ZN ZINC ION × 2 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR ZNCL2, 0.1 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.30 Å |
| 7ICP DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF ZNCL2 (0.01 MILLIMOLAR) Deposited 1996-04-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | ZN ZINC ION × 2 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR ZNCL2, 0.01 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.00 Å |
| 7ICQ DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF ZNCL2 Deposited 1996-04-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 4 DAYS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR ZNCL2, 0.1 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 2.90 Å |
| 7ICR DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF ZNCL2 Deposited 1996-04-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | ZN ZINC ION × 2 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR ZNCL2, 1 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.00 Å |
| 7ICS DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF ZNCL2 Deposited 1996-04-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR ZNCL2, 0.001 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 2.80 Å |
| 7ICT DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF ZNCL2 AND MGCL2 Deposited 1996-04-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 3 DAYS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR ZNCL2, 0.01 MILLIMOLAR MGCL2, 1 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 2.80 Å |
| 7ICU DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CDCL2 (0.1 MILLIMOLAR) Deposited 1996-04-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 CD CADMIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR CDCL2, 0.1 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.30 Å |
| 7ICV DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF MNCL2 (0.1 MILLIMOLAR) AND IN THE ABSENCE OF NACL Deposited 1996-10-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 2 DAYS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 MNCL2, 0.1 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 2.80 Å |
| 7K96 Human DNA polymerase beta ternary complex with templating cytosine and incoming deoxyguanosine diphosphate Deposited 2020-09-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | CL CHLORIDE ION × 9 NA SODIUM ION × 4 EDO 1,2-ETHANEDIOL × 4 CA CALCIUM ION × 3 DGI 2'-DEOXYGUANOSINE-5'-DIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；50 mM imidazole, 350 mM sodium chloride, 16-17% PEG3350
|
Resolution 2.10 Å R-free 0.246 |
| 7K97 Human DNA polymerase beta dGDP product complex with Mn2+ Deposited 2020-09-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
10–335（326 aa）
|
Not recorded | MN MANGANESE (II) ION × 8 NA SODIUM ION × 2 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292 K；50 mM imidazole, 350 mM sodium acetate, 18% PEG3350
|
Resolution 2.40 Å R-free 0.240 |
| 7MZ0 Structure of human DNA polymerase beta complexed with dzA as the template base in a 1-nucleotide gapped DNA Deposited 2021-05-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
7–335（329 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.02 Å R-free 0.276 |
| 7MZ1 Structure of human DNA polymerase beta complexed with dzA in the template base paired with incoming non-hydrolyzable TTP Deposited 2021-05-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
10–335（326 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 1FZ 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.17 Å R-free 0.259 |
| 7MZ2 Structure of human DNA polymerase beta complexed with dzA at N-1 of the template base paired with incoming dTTP Deposited 2021-05-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
10–335（326 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.09 Å R-free 0.243 |
| 7MZ3 Structure of human DNA polymerase beta complexed with 3-deaza-3-methyladenine (3dMeA) as the template base in a 1-nucleotide gapped DNA Deposited 2021-05-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
7–335（329 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.42 Å R-free 0.266 |
| 7MZ4 Structure of human DNA polymerase beta complexed with 3-deaza-3-methyladenine (3dMeA) in the template base paired with incoming dTTP Deposited 2021-05-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
7–335（329 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 1FZ 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；14 to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.08 Å R-free 0.270 |
| 7MZ8 Structure of human DNA polymerase beta complexed with 3-deaza-3-methyladenine (3dMeA) at N-1 of the template base paired with incoming dTTP Deposited 2021-05-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
7–335（329 aa）
|
Not recorded | MG MAGNESIUM ION × 1 NA SODIUM ION × 2 0KX 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
|
Resolution 2.60 Å R-free 0.263 |
| 7RBE Human DNA polymerase beta crosslinked binary complex - A Deposited 2021-07-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | QPJ 2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol × 1 NA SODIUM ION × 4 CIT CITRIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；0.1 M Citrate pH 5.5, 18% PEG6000
|
Resolution 1.89 Å R-free 0.268 |
| 7RBF Human DNA polymerase beta crosslinked binary complex - B Deposited 2021-07-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | QPJ 2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol × 1 EDO 1,2-ETHANEDIOL × 3 PEG DI(HYDROXYETHYL)ETHER × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.1 M Citrate pH 5.5, 18% PEG6000
|
Resolution 1.84 Å R-free 0.208 |
| 7RBG Human DNA polymerase beta crosslinked ternary complex 1 Deposited 2021-07-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 QPJ 2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol × 1 CA CALCIUM ION × 3 NA SODIUM ION × 2 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.1 M Citrate pH 5.5, 18% PEG6000
|
Resolution 1.90 Å R-free 0.223 |
| 7RBH Human DNA polymerase beta crosslinked ternary complex 2 Deposited 2021-07-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | QPJ 2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 2 CA CALCIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.1 M Citrate pH 5.5, 18% PEG6000
|
Resolution 1.75 Å R-free 0.225 |
| 7RBI Human DNA polymerase beta crosslinked complex, 20 s Ca to Mg exchange Deposited 2021-07-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | QPJ 2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol × 1 PPV PYROPHOSPHATE × 1 MG MAGNESIUM ION × 7 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.1 M Citrate pH 5.5, 18% PEG6000
|
Resolution 1.93 Å R-free 0.220 |
| 7RBJ Human DNA polymerase beta crosslinked complex, 30 s Ca to Mg exchange Deposited 2021-07-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | QPJ 2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol × 1 PPV PYROPHOSPHATE × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.1 M Citrate pH 5.5, 18% PEG6000
|
Resolution 1.91 Å R-free 0.229 |
| 7RBK Human DNA polymerase beta crosslinked complex, 40 s Ca to Mg exchange Deposited 2021-07-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | QPJ 2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 5 PPV PYROPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.1 M Citrate pH 5.5, 18% PEG6000
|
Resolution 2.20 Å R-free 0.251 |
| 7RBL Human DNA polymerase beta crosslinked complex, 60 s Ca to Mg exchange Deposited 2021-07-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | QPJ 2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol × 1 PPV PYROPHOSPHATE × 1 MG MAGNESIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.1 M Citrate pH 5.5, 18% PEG6000
|
Resolution 1.98 Å R-free 0.236 |
| 7RBM Human DNA polymerase beta crosslinked complex, 60 s Ca to Mn exchange Deposited 2021-07-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | QPJ 2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol × 1 PPV PYROPHOSPHATE × 1 MN MANGANESE (II) ION × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M Citrate pH 5.5, 18% PEG6000
|
Resolution 2.21 Å R-free 0.247 |
| 7RBN Human DNA polymerase beta crosslinked complex, 20 min Ca to Mg exchange Deposited 2021-07-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | QPJ 2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.1 M Citrate pH 5.5, 18% PEG6000
|
Resolution 2.90 Å R-free 0.268 |
| 7RBO Human DNA polymerase beta crosslinked complex, 60 min Ca to Mg exchange Deposited 2021-07-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | QPJ 2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.1 M Citrate pH 5.5, 18% PEG6000
|
Resolution 2.96 Å R-free 0.284 |
| 7S9J Crystal Structure of DNA Polymerase Beta with Fapy-dG base-paired with a dC Deposited 2021-09-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；14-19% PEG 3350, 50 mM Imidazole pH 8.0, 350 mM Sodium Acetate
|
Resolution 1.91 Å R-free 0.238 |
| 7S9K Crystal Structure of DNA Polymerase Beta with Fapy-dG base-paired with a dA Deposited 2021-09-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；14-19% PEG 3350, 50 mM Imidiazole pH 8.0, 350 mM Sodium Acetate
|
Resolution 1.97 Å R-free 0.224 |
| 7S9L Crystal Structure of DNA Polymerase Beta with Ring open intermediate Fapy-dG base-paired with a dC Deposited 2021-09-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 4 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；14-19% PEG 3350, 50 mM Imidazole pH 8.0, 350 mM Sodium Acetate
|
Resolution 2.05 Å R-free 0.263 |
| 7S9M Crystal Structure of DNA Polymerase Beta with Ring open intermediate Fapy-dG base-paired with a dA Deposited 2021-09-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 3 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；14-19% PEG 3350, 50 mM Imidazole pH 8.0, 350 mM Sodium Acetate
|
Resolution 2.31 Å R-free 0.300 |
| 7S9N Binary complex of DNA Polymerase Beta with Fapy-dG in the template position Deposited 2021-09-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；14-19% PEG 3350, 50 mM Imidazole pH 8.0, 350 mM Sodium Acetate
|
Resolution 1.71 Å R-free 0.236 |
| 7S9O Binary complex of DNA Polymerase Beta with Ring open Intermediate Fapy-dG in the template position Deposited 2021-09-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8；291 K；14-19% PEG 3350, 50 mM Imidazole pH 8.0, 350 mM Sodium Acetate
|
Resolution 2.23 Å R-free 0.278 |
| 7S9P Ternary complex of DNA Polymerase Beta with Template Fapy-dG and an incoming dCTP analog Deposited 2021-09-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | XC5 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine × 1 MN MANGANESE (II) ION × 3 NA SODIUM ION × 2 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；14-19% PEG 3350, 50 mM Imidazole pH 8.0, 350 mM Sodium Acetate
|
Resolution 1.86 Å R-free 0.228 |
| 7S9Q Ternary complex of DNA Polymerase Beta with Template Fapy-dG and an incoming dATP analog Deposited 2021-09-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 3 MN MANGANESE (II) ION × 3 F2A 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine × 1 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；14-19% PEG 3350, 50 mM Imidazole pH 8.0, 350 mM Sodium Acetate
|
Resolution 1.90 Å R-free 0.247 |
| 8ICA DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR) AND CACL2 (5 MILLIMOLAR) Deposited 1995-12-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | CA CALCIUM ION × 1 NA SODIUM ION × 2 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DATP, 1 MILLIMOLAR CACL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.00 Å |
| 8ICB DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF ARTIFICIAL MOTHER LIQUOR Deposited 1996-04-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 7 DAYS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR
|
Resolution 3.10 Å |
| 8ICC DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA (NO 5'-PHOSPHATE) Deposited 1996-04-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；SEE REFERENCE 1 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE., pH 6.50
|
Resolution 2.80 Å |
| 8ICE DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR) AND CDCL2 (1 MILLIMOLAR) Deposited 1996-04-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | CD CADMIUM ION × 2 NA SODIUM ION × 2 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DATP, 1 MILLIMOLAR CDCL2, 1 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.20 Å |
| 8ICF DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (10 MILLIMOLAR) AND MGCL2 (50 MILLIMOLAR) Deposited 1996-04-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DATP, 10 MILLIMOLAR MGCL2, 50 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 2.90 Å |
| 8ICG DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR) AND MGCL2 (5 MILLIMOLAR) Deposited 1996-04-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DATP, 1 MILLIMOLAR MGCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.30 Å |
| 8ICH DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DCTP (1 MILLIMOLAR) AND MGCL2 (5 MILLIMOLAR) Deposited 1996-04-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DCTP, 1 MILLIMOLAR MGCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.30 Å |
| 8ICI DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DGTP (1 MILLIMOLAR) AND MGCL2 (5 MILLIMOLAR) Deposited 1996-04-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DGTP, 1 MILLIMOLAR MGCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 2.80 Å |
| 8ICJ DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX + THYMIDINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DTTP AND MGCL2 Deposited 1996-04-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DTTP, 1 MILLIMOLAR MGCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.20 Å |
| 8ICK DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR), MGCL2 (5 MILLIMOLAR), AND MNCL2 (5 MILLIMOLAR) Deposited 1996-04-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DATP, 1 MILLIMOLAR MGCL2, 5 MILLIMOLAR MNCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 2.70 Å |
| 8ICL DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR) AND NICL2 (5 MILLIMOLAR) Deposited 1995-12-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NI NICKEL (II) ION × 2 NA SODIUM ION × 2 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DATP, 1 MILLIMOLAR NICL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.10 Å |
| 8ICM DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR), MNCL2 (5 MILLIMOLAR), AND AMMONIUM SULFATE (75 MILLIMOLAR) Deposited 1996-01-04 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | SO4 SULFATE ION × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NH4SO4, 75 MILLIMOLAR DATP, 1 MILLIMOLAR MNCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 2.90 Å |
| 8ICN DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF ATP (1 MILLIMOLAR) AND MNCL2 (5 MILLIMOLAR) Deposited 1995-12-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | MN MANGANESE (II) ION × 1 NA SODIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR ATP, 1 MILLIMOLAR MNCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 2.80 Å |
| 8ICO DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF AZT-TP (1 MILLIMOLAR) AND MNCL2 (5 MILLIMOLAR) Deposited 1995-12-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 AZT 3'-AZIDO-3'-DEOXYTHYMIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR AZT-TP, 1 MILLIMOLAR MNCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 2.70 Å |
| 8ICP DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR) AND MNCL2 (5 MILLIMOLAR) Deposited 1995-12-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | MN MANGANESE (II) ION × 1 NA SODIUM ION × 2 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DATP, 1 MILLIMOLAR MNCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 2.90 Å |
| 8ICQ DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF OF DATP (0.1 MILLIMOLAR) AND MNCL2 (0.5 MILLIMOLAR) Deposited 1996-01-04 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DATP, 0.1 MILLIMOLAR MNCL2, 0.5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.00 Å |
| 8ICR DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR) AND MNCL2 (5 MILLIMOLAR) Deposited 1996-01-04 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DATP, 1 MILLIMOLAR MNCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 2.90 Å |
| 8ICS DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DCTP (1 MILLIMOLAR) AND MNCL2 (5 MILLIMOLAR) Deposited 1995-12-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DCTP, 1 MILLIMOLAR MNCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 2.90 Å |
| 8ICT DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DCTP (1 MILLIMOLAR) AND MNCL2 (5 MILLIMOLAR) Deposited 1995-12-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DCTP, 1 MILLIMOLAR MNCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.10 Å |
| 8ICU DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DDATP (1 MILLIMOLAR) AND MNCL2 (5 MILLIMOLAR) Deposited 1995-12-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 DAD 2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DDATP, 1 MILLIMOLAR MNCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.00 Å |
| 8ICV DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DGTP (1 MILLIMOLAR) AND MNCL2 (5 MILLIMOLAR) Deposited 1996-01-04 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | MN MANGANESE (II) ION × 1 NA SODIUM ION × 2 DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DGTP, 1 MILLIMOLAR MNCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.20 Å |
| 8ICW DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DTTP (1 MILLIMOLAR) AND MNCL2 (5 MILLIMOLAR) Deposited 1995-12-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | MN MANGANESE (II) ION × 1 NA SODIUM ION × 2 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 4 DAYS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DTTP, 1 MILLIMOLAR MNCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.30 Å |
| 8ICX DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DTTP (1 MILLIMOLAR) AND MNCL2 (5 MILLIMOLAR) Deposited 1995-12-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 5 MINUTES: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DTTP, 1 MILLIMOLAR MNCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.00 Å |
| 8ICY DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX + THYMIDINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DTTP AND MNCL2 Deposited 1995-12-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | MN MANGANESE (II) ION × 1 NA SODIUM ION × 2 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DTTP, 1 MILLIMOLAR MNCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.10 Å |
| 8ICZ DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF OF DATP (1 MILLIMOLAR), MNCL2 (5 MILLIMOLAR), AND LITHIUM SULFATE (75 MILLIMOLAR) Deposited 1996-01-04 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | SO4 SULFATE ION × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 LI2SO4, 75 MILLIMOLAR DATP, 1 MILLIMOLAR MNCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.10 Å |
| 8VF8 Binary DNA Polymerase Beta bound to DNA containing primer terminal dC base-paired with FapydG Deposited 2023-12-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；14-22% PEG 3350
0.05 M Imidazole pH 8.0
0.35 M Sodium Acetate
|
Resolution 1.98 Å R-free 0.222 |
| 8VF9 Binary DNA Polymerase Beta bound to DNA containing primer terminal dA base-paired with FapydG Deposited 2023-12-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；14-22% PEG 3350
0.05 M Imidazole pH 8.0
0.35 M Sodium Acetate
|
Resolution 1.90 Å R-free 0.232 |
| 8VFA Ternary DNA Polymerase Beta bound to DNA containing primer terminal dC base-paired with FapydG Deposited 2023-12-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 NA SODIUM ION × 2 MN MANGANESE (II) ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；14-22% PEG 3350
0.05 M Imidazole pH 8.0
0.35 M Sodium Acetate
|
Resolution 2.05 Å R-free 0.267 |
| 8VFB Ternary DNA Polymerase Beta bound to DNA containing primer terminal dA base-paired with FapydG Deposited 2023-12-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | G2P PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 NA SODIUM ION × 1 MN MANGANESE (II) ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；14-22% PEG 3350
0.05 M Imidazole pH 8.0
0.35 M Sodium Acetate
|
Resolution 2.64 Å R-free 0.228 |
| 8VFC Binary DNA Polymerase Beta bound to DNA containing primer terminal T base-paired with FapydG Deposited 2023-12-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；14-22% PEG 3350
0.05 M Imidazole pH 8.0
0.35 M Sodium Acetate
|
Resolution 2.48 Å R-free 0.255 |
| 8VFD Ternary DNA Polymerase Beta bound to DNA containing template FapydG incoming TTP analog Deposited 2023-12-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 1 A1ACD 1-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]-beta-D-threo-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione × 1 MN MANGANESE (II) ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；14-22% PEG 3350
0.05 M Imidazole pH 8.0
0.35 M Sodium Acetate
|
Resolution 2.10 Å R-free 0.242 |
| 8VFE Binary DNA Polymerase Beta bound to DNA containing primer terminal FapydG base-paired with a T Deposited 2023-12-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；14-22% PEG 3350
0.05 M Imidazole pH 8.0
0.35 M Sodium Acetate
|
Resolution 2.09 Å R-free 0.235 |
| 8VFF Binary DNA Polymerase Beta bound to DNA containing primer terminal FapydG base-paired with a dA Deposited 2023-12-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；14-22% PEG 3350
0.05 M Imidazole pH 8.0
0.35 M Sodium Acetate
|
Resolution 1.69 Å R-free 0.232 |
| 8VFG Binary DNA Polymerase Beta bound to DNA containing primer terminal FapydG base-paired with a dC Deposited 2023-12-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；14-22% PEG 3350
0.05 M Imidazole pH 8.0
0.35 M Sodium Acetate
|
Resolution 1.54 Å R-free 0.236 |
| 8VFH Ternary DNA Polymerase Beta bound to DNA containing primer terminal FapydG base-paired with a dC Deposited 2023-12-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；14-22% PEG 3350
0.05 M Imidazole pH 8.0
0.35 M Sodium Acetate
|
Resolution 2.01 Å R-free 0.246 |
| 8VFI Ternary DNA Polymerase Beta bound to DNA containing primer terminal FapydG base-paired with a dA Deposited 2023-12-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 3 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；14-22% PEG 3350
0.05 M Imidazole pH 8.0
0.35 M Sodium Acetate
|
Resolution 1.77 Å R-free 0.229 |
| 8VFJ Polymerase Beta Host Guest Complex Containing FapydG base paired with TMP Deposited 2023-12-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；14-22% PEG 3350
0.05 M Imidazole pH 8.0
0.35 M Sodium Acetate
|
Resolution 2.14 Å R-free 0.265 |
| 9DWG DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 1, composite) Deposited 2024-10-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric |
Chain L
1–335（335 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and
5mM EDTA
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9DWH DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 2, composite) Deposited 2024-10-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric |
Chain L
1–335（335 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and
5mM EDTA
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9DWI DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-4.5 (State 3, composite) Deposited 2024-10-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 12-meric |
Chain L
1–335（335 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and
5mM EDTA
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9DWK DNA Polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-3.5 Deposited 2024-10-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: dodecameric |
Chain L
1–335（335 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.1；25mM HEPES (pH-7.1), 50 mM NaCl, 1mM TCEP, and
5mM EDTA
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 9DWM DNA polymerase Beta bound to a nucleosome containing a 1-nt gap at SHL-5.5 Deposited 2024-10-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: dodecameric |
Chain L
1–335（335 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.1；25mM HEPES (pH-7.1), 50mM NaCl, 1mM TCEP, and 5mM EDTA
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 9ICA DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX + 2'-DEOXYADENOSINE-5'-O-(1-THIOTRIPHOSPHATE), SOAKED IN THE PRESENCE OF DATP(ALPHA)S AND MNCL2 Deposited 1995-12-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 STP 2'-DEOXYADENOSINE 5'-O-(1-THIOTRIPHOSPHATE) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DATP(ALPHA)S, 1 MILLIMOLAR MNCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.00 Å |
| 9ICB DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX + 2'-DEOXYADENOSINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DATP AND COCL2 Deposited 1995-12-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | CO COBALT (II) ION × 2 NA SODIUM ION × 2 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DATP, 1 MILLIMOLAR COCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.20 Å |
| 9ICC DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX + 2'-DEOXYADENOSINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DATP AND CRCL3 Deposited 1995-12-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 CR CHROMIUM ION × 1 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DATP, 1 MILLIMOLAR CRCL3, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.10 Å |
| 9ICE DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR) AND CUCL2 (0.1 MILLIMOLAR) Deposited 1995-12-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DATP, 1 MILLIMOLAR CUCL2, 0.1 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.30 Å |
| 9ICF DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX + 2'-DEOXYADENOSINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DATP AND ZNCL2 Deposited 1995-12-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | ZN ZINC ION × 2 NA SODIUM ION × 2 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DATP, 1 MILLIMOLAR ZNCL2, 1 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.00 Å |
| 9ICG DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DCTP (1 MILLIMOLAR) AND ZNCL2 (1 MILLIMOLAR) Deposited 1995-12-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | ZN ZINC ION × 3 NA SODIUM ION × 2 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DCTP, 1 MILLIMOLAR ZNCL2, 1 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.00 Å |
| 9ICH DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DGTP (1 MILLIMOLAR) AND ZNCL2 (1 MILLIMOLAR) Deposited 1995-12-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | ZN ZINC ION × 3 NA SODIUM ION × 2 DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DGTP, 1 MILLIMOLAR ZNCL2, 1 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 2.90 Å |
| 9ICI DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DTTP (1 MILLIMOLAR) AND ZNCL2 (1 MILLIMOLAR) Deposited 1995-12-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | ZN ZINC ION × 2 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DTTP, 1 MILLIMOLAR ZNCL2, 1 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.10 Å |
| 9ICJ DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA Deposited 1995-12-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | SO4 SULFATE ION × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；SEE REFERENCE 1 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSIONS FOR THIS ENTRY., pH 6.50
|
Resolution 3.10 Å |
| 9ICK DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF ARTIFICIAL MOTHER LIQUOR Deposited 1995-12-16 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 7 DAYS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 2.70 Å |
| 9ICL DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF PYROPHOSPHATE AND MNCL2 Deposited 1996-01-04 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR PYROPHOSPHATE (PPI), 1 MILLIMOLAR MNCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSIONS FOR THIS STRUCTURE.
|
Resolution 2.80 Å |
| 9ICM DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DOUBLE STRANDED DNA (NO 5'-PHOSPHATE) Deposited 1995-12-16 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE SAME CRYSTAL STRUCTURE REPORTED IN ENTRY 9ICW, WITH THE EXCEPTION THAT THE DNA STRAND DESIGNATED AS THE PRIMER IS NOT 5'-PHOSPHORYLATED. SEE REFERENCE 1 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSIONS FOR THIS STRUCTURE., pH 6.50
|
Resolution 2.90 Å |
| 9ICN DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX + 2',3'-DIDEOXYCYTIDINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DDCTP AND MGCL2 Deposited 1995-12-16 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | MG MAGNESIUM ION × 1 NA SODIUM ION × 2 DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DDCTP, 20 MILLIMOLAR MGCL2, 20 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.00 Å |
| 9ICO DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF DTTP AND MGCL2 Deposited 1995-12-16 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DTTP, 1 MILLIMOLAR MGCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 2.90 Å |
| 9ICP DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF PYROPHOSPHATE (1 MILLIMOLAR) AND MGCL2 (5 MILLIMOLAR) Deposited 1995-12-16 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR PYROPHOSPHATE (PPI), 1 MILLIMOLAR MGCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.10 Å |
| 9ICQ DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR) AND MNCL2 (5 MILLIMOLAR) Deposited 1996-01-04 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DATP, 1 MILLIMOLAR MNCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 2.90 Å |
| 9ICR DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX + 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DCTP AND MNCL2 Deposited 1996-01-04 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DCTP, 1 MILLIMOLAR MNCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.00 Å |
| 9ICS DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX + 2',3'-DIDEOXYCYTIDINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DDCTP AND MNCL2 Deposited 1995-12-16 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DDCTP, 10 MILLIMOLAR MNCL2, 10 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 2.90 Å |
| 9ICT DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX + 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DGTP AND MNCL2 Deposited 1995-12-16 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 NA SODIUM ION × 2 DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DGTP, 1 MILLIMOLAR MNCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 3.00 Å |
| 9ICU DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DTTP (1 MILLIMOLAR) AND MNCL2 (5 MILLIMOLAR) Deposited 1995-12-16 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | MN MANGANESE (II) ION × 1 NA SODIUM ION × 2 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DTTP, 1 MILLIMOLAR MNCL2, 5 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 2.90 Å |
| 9ICV DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX + 2'-DEOXYADENOSINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DATP AND ZNCL2 Deposited 1995-12-16 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | ZN ZINC ION × 3 NA SODIUM ION × 2 DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR DATP, 0.1 MILLIMOLAR ZNCL2, 0.2 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
|
Resolution 2.70 Å |
| 9ICW DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; NATIVE STRUCTURE Deposited 1995-12-16 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | SO4 SULFATE ION × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；SEE REFERENCE 1 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSIONS FOR THIS STRUCTURE., pH 6.50
|
Resolution 2.60 Å |
| 9ICX DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA (NON GAPPED DNA ONLY) Deposited 1996-10-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；SEE REFERENCE 1 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE., pH 6.50
|
Resolution 2.60 Å |
| 9ICY DNA POLYMERASE BETA (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA (NON GAPPED DNA ONLY) Deposited 1996-10-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | SO4 SULFATE ION × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；SEE REFERENCE 1 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE., pH 6.50
|
Resolution 3.00 Å |
| 9Y15 WT human DNA polymerase beta, Binary complex templating dA Deposited 2025-08-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 3 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；13-16% PEG 3350, 150-300 mM sodium acetate, 50 mM HEPES, 1 mM TECP
250uM protein with 300 uM DNA assembly mixed 1:1 with reagent
|
Resolution 1.85 Å R-free 0.212 |
| 9Y16 WT human DNA polymerase beta, Binary complex templating dG Deposited 2025-08-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 3 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；13-16% PEG 3350, 150-300 mM sodium acetate, 50 mM HEPES, 1 mM TECP
250uM protein with 300 uM DNA assembly mixed 1:1 with reagent
|
Resolution 1.80 Å R-free 0.209 |
| 9Y17 WT human DNA polymerase beta, Binary complex templating dT Deposited 2025-08-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；13-16% PEG 3350, 150-300 mM sodium acetate, 50 mM HEPES, 1 mM TECP
250uM protein with 300 uM DNA assembly mixed 1:1 with reagent
|
Resolution 1.85 Å R-free 0.208 |
| 9Y18 WT human DNA polymerase beta, Binary complex templating dC Deposited 2025-08-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；13-16% PEG 3350, 150-300 mM sodium acetate, 50 mM HEPES, 1 mM TECP
250uM protein with 300 uM DNA assembly mixed 1:1 with reagent
|
Resolution 1.80 Å R-free 0.205 |
| 9Y19 WT human DNA polymerase beta, Ternary complex dA:dUmpNpp Deposited 2025-08-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 MG MAGNESIUM ION × 2 DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；13-16% PEG 3350, 150-300 mM sodium acetate, 50 mM HEPES, 1 mM TECP
250uM protein with 300 uM DNA assembly mixed 1:1 with reagent
|
Resolution 1.90 Å R-free 0.197 |
| 9Y1A WT human DNA polymerase beta, Ternary complex dT:dAmpCpp Deposited 2025-08-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 MG MAGNESIUM ION × 2 F2A 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；13-16% PEG 3350, 150-300 mM sodium acetate, 50 mM HEPES, 1 mM TECP
250uM protein with 300 uM DNA assembly mixed 1:1 with reagent
|
Resolution 1.93 Å R-free 0.201 |
| 9Y1B WT human DNA polymerase beta, Ternary complex dC:dGmpCpp Deposited 2025-08-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 MG MAGNESIUM ION × 2 1GC 2'-deoxy-5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine × 1 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；13-16% PEG 3350, 150-300 mM sodium acetate, 50 mM HEPES, 1 mM TECP
250uM protein with 300 uM DNA assembly mixed 1:1 with reagent
|
Resolution 1.90 Å R-free 0.225 |
| 9Y1C WT human DNA polymerase beta, Ternary complex dG:dCmpCpp Deposited 2025-08-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Not recorded | NA SODIUM ION × 2 MG MAGNESIUM ION × 2 XC5 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；13-16% PEG 3350, 150-300 mM sodium acetate, 50 mM HEPES, 1 mM TECP
250uM protein with 300 uM DNA assembly mixed 1:1 with reagent
|
Resolution 1.90 Å R-free 0.198 |
| 9Y1D S180R human DNA polymerase beta, Binary complex templating dA Deposited 2025-08-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：S180R | NA SODIUM ION × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；13-16% PEG 3350, 150-300 mM sodium acetate, 50 mM HEPES, 1 mM TECP
250uM protein with 300 uM DNA assembly mixed 1:1 with reagent
|
Resolution 1.70 Å R-free 0.195 |
| 9Y1E S180R human DNA polymerase beta, Binary complex templating dG Deposited 2025-08-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：S180R | NA SODIUM ION × 3 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；13-16% PEG 3350, 150-300 mM sodium acetate, 50 mM HEPES, 1 mM TECP
250uM protein with 300 uM DNA assembly mixed 1:1 with reagent
|
Resolution 1.60 Å R-free 0.206 |
| 9Y1F S180R human DNA polymerase beta, Binary complex templating dT Deposited 2025-08-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：S180R | NA SODIUM ION × 2 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；13-16% PEG 3350, 150-300 mM sodium acetate, 50 mM HEPES, 1 mM TECP
250uM protein with 300 uM DNA assembly mixed 1:1 with reagent
|
Resolution 1.80 Å R-free 0.202 |
| 9Y1G S180R human DNA polymerase beta, Binary complex templating dC Deposited 2025-08-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：S180R | NA SODIUM ION × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；13-16% PEG 3350, 150-300 mM sodium acetate, 50 mM HEPES, 1 mM TECP
250uM protein with 300 uM DNA assembly mixed 1:1 with reagent
|
Resolution 1.60 Å R-free 0.209 |
| 9Y1H S180R human DNA polymerase beta, Ternary complex dA:dUmpNpp Deposited 2025-08-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：S180R | NA SODIUM ION × 2 MG MAGNESIUM ION × 2 DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；13-16% PEG 3350, 150-300 mM sodium acetate, 50 mM HEPES, 1 mM TECP
250uM protein with 300 uM DNA assembly mixed 1:1 with reagent
|
Resolution 1.96 Å R-free 0.202 |
| 9Y1I S180R human DNA polymerase beta, Ternary complex dG:dCmpCpp Deposited 2025-08-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：S180R | NA SODIUM ION × 2 MG MAGNESIUM ION × 2 XC5 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；13-16% PEG 3350, 150-300 mM sodium acetate, 50 mM HEPES, 1 mM TECP
250uM protein with 300 uM DNA assembly mixed 1:1 with reagent
|
Resolution 2.15 Å R-free 0.213 |
| 9Y1J S180R human DNA polymerase beta, Ternary complex dT:dAmpCpp Deposited 2025-08-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：S180R | NA SODIUM ION × 2 MG MAGNESIUM ION × 2 F2A 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；13-16% PEG 3350, 150-300 mM sodium acetate, 50 mM HEPES, 1 mM TECP
250uM protein with 300 uM DNA assembly mixed 1:1 with reagent
|
Resolution 1.55 Å R-free 0.182 |
| 9Y1K S180R human DNA polymerase beta, Ternary complex dC:dGmpCpp Deposited 2025-08-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
1–335（335 aa）
|
Mutation：S180R | NA SODIUM ION × 2 MG MAGNESIUM ION × 2 1GC 2'-deoxy-5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；13-16% PEG 3350, 150-300 mM sodium acetate, 50 mM HEPES, 1 mM TECP
250uM protein with 300 uM DNA assembly mixed 1:1 with reagent
|
Resolution 1.70 Å R-free 0.217 |
431 other PDB entries and 433 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | DPOLB_HUMAN |
| Isoform | — |
| PDB entities | 4 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–335； UniProt 1–334 |
