DNA polymerase I, thermostable
Thermus aquaticus
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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain A； UniProt 290–832 | Not recorded | SO4 SULFATE ION × 10 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；0.1M HEPES pH7.5, 1.5M Lithium sulfate | Resolution 1.97 Å R-free 0.242 |
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 8XJR | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1BGX TAQ POLYMERASE IN COMPLEX WITH TP7, AN INHIBITORY FAB Deposited 1998-06-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain T
1–832（832 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；PROTEIN WAS CRYSTALLIZED FROM 22% PEG 3350, 200 MM TRIS/HCL, PH 7.4. COMPLEX WAS MADE AT A PROTEIN CONCENTRATION OF 0.5 MG/ML, LEFT FOR 2-3 DAYS AT 4 DEGREES CELSIUS, CONCENTRATED TO 5MG/ML PROTEIN AND CRYSTALLIZATION CARRIED OUT IN HANGING DROPS., vapor diffusion - hanging drop, temperature 277K
|
Resolution 2.30 Å R-free 0.253 |
| 1JXE STOFFEL FRAGMENT OF TAQ DNA POLYMERASE I Deposited 1996-10-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
293–832（540 aa）
Fragment：STOFFEL FRAGMENT, RESIDUES 290 - 832
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.85 Å |
| 1KTQ DNA POLYMERASE Deposited 1995-08-16 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
290–832（543 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.50 Å R-free 0.262 |
| 1QSS DDGTP-TRAPPED CLOSED TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS Deposited 1999-06-23 | 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
293–831（539 aa）
Fragment：KLENOW FRAGMENT
|
Mutation：A348E | MG MAGNESIUM ION × 2 DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；HEPES, SODIUM ACETATE, PEG 4000, MANGANESE CHLORIDE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
|
Resolution 2.30 Å R-free 0.285 |
| 1QSY DDATP-Trapped closed ternary complex of the large fragment of DNA Polymerase I from thermus aquaticus Deposited 1999-06-24 | 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
293–831（539 aa）
Fragment：KLENOW FRAGMENT
|
Mutation：A348E | MG MAGNESIUM ION × 2 DDS 2',3'-dideoxyadenosine triphosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；HEPES, SODIUM ACETATE, PEG 4000, MANGANESE CHLORIDE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
|
Resolution 2.30 Å R-free 0.276 |
| 1QTM DDTTP-TRAPPED CLOSED TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS Deposited 1999-06-28 | Different construct 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
293–831（539 aa）
Fragment：KLENOW FRAGMENT, RESIDUES 293-831
|
Not recorded | MG MAGNESIUM ION × 2 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；HEPES, SODIUM ACETATE, PEG 4000, MNCL2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
|
Resolution 2.30 Å R-free 0.280 |
| 1TAQ STRUCTURE OF TAQ DNA POLYMERASE Deposited 1996-06-04 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–832（832 aa）
|
Mutation：S575C, S576C, S577C | BGL 2-O-octyl-beta-D-glucopyranose × 1 ZN ZINC ION × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.40 Å R-free 0.323 |
| 1TAU TAQ POLYMERASE (E.C.2.7.7.7)/DNA/B-OCTYLGLUCOSIDE COMPLEX Deposited 1996-06-17 | Different construct 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
1–832（832 aa）
|
Not recorded | BGL 2-O-octyl-beta-D-glucopyranose × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 295.00K
|
Resolution 3.00 Å R-free 0.305 |
| 2KTQ OPEN TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS Deposited 1998-07-30 | Different construct 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
295–832（538 aa）
|
Not recorded | MG MAGNESIUM ION × 1 DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8；pH 8.0
|
Resolution 2.30 Å R-free 0.288 |
| 3KTQ CRYSTAL STRUCTURE OF AN ACTIVE TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS Deposited 1998-07-28 | Different construct 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
293–832（540 aa）
|
Not recorded | MG MAGNESIUM ION × 2 DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8；pH 8.0
|
Resolution 2.30 Å R-free 0.275 |
| 3LWL Structure of Klenow fragment of Taq polymerase in complex with an abasic site Deposited 2010-02-24 | Different construct 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
293–832（540 aa）
Fragment：KLENOW FRAGMENT, UNP residues 293-832
|
Not recorded | DDS 2',3'-dideoxyadenosine triphosphate × 1 MG MAGNESIUM ION × 1 ACT ACETATE ION × 5 GOL GLYCEROL × 7 NA SODIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.05M sodium cacodylate, 0.2M ammonium acetate, 0.01M magnesium acetate, 30% PEG 8000, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.25 Å R-free 0.234 |
| 3LWM Structure of the large fragment of thermus aquaticus DNA polymerase I in complex with a blunt-ended DNA and ddATP Deposited 2010-02-24 | Different construct 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
293–832（540 aa）
Fragment：KLENOW FRAGMENT, UNP residues 293-832
|
Not recorded | DDS 2',3'-dideoxyadenosine triphosphate × 1 ACT ACETATE ION × 4 GOL GLYCEROL × 5 MG MAGNESIUM ION × 1 NA SODIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；0.05M TRIS HCl, pH 8, 0.2M ammonium chloride, 0.01M calcium chloride and 35% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.19 Å R-free 0.228 |
| 3M8R Crystal structure of the large fragment of DNA polymerase I from Thermus aquaticus in a closed ternary complex with trapped 4'-ethylated dTTP Deposited 2010-03-19 | Different construct 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
293–832（540 aa）
Fragment：Klenow Fragment
|
Not recorded | HXZ 4'-ethylthymidine 5'-(tetrahydrogen triphosphate) × 1 MG MAGNESIUM ION × 2 15P POLYETHYLENE GLYCOL (N=34) × 2 GOL GLYCEROL × 4 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；30% (w/v) PEG 8000, 0.2M ammonium acetate, 0.02M magnesium acetate, 0.05M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.00 Å R-free 0.221 |
| 3M8S Crystal structure of the large fragment of DNA polymerase I from Thermus aquaticus in a closed ternary complex with trapped 4'-methylated dTTP Deposited 2010-03-19 | Different construct 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
293–832（540 aa）
Fragment：KLENOW FRAGMENT
|
Not recorded | HXB 4'-methylthymidine 5'-(tetrahydrogen triphosphate) × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 3 PEG DI(HYDROXYETHYL)ETHER × 1 15P POLYETHYLENE GLYCOL (N=34) × 1 ACT ACETATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；30% (w/v) PEG 8000, 0.2M ammonium acetate, 0.02M magnesium acetate, 0.05M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.20 Å R-free 0.224 |
| 3OJS Snapshots of the large fragment of DNA polymerase I from Thermus Aquaticus processing C5 modified thymidines Deposited 2010-08-23 | Different construct 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
293–832（540 aa）
Fragment：unp residues 292-832
|
Not recorded | XJS 2'-deoxy-5-[9-(3-{[4-(diethylamino)-4-oxobutanoyl]amino}propyl)-18-ethyl-5,8,14,17-tetraoxo-4,9,13,18-tetraazaicos-1-yn-1-yl]uridine 5'-(tetrahydrogen triphosphate) × 1 GOL GLYCEROL × 8 MG MAGNESIUM ION × 2 PGE TRIETHYLENE GLYCOL × 4 ACT ACETATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.05M Na cacodylate ph 6.5, 0.2M NH4OAc, 0.01M Mg(OAc)2, 26% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.90 Å R-free 0.212 |
| 3OJU Snapshot of the large fragment of DNA polymerase I from Thermus Aquaticus processing c5 modified thymidies Deposited 2010-08-23 | Different construct 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
293–832（540 aa）
Fragment：unp residues 292-832
|
Not recorded | SSJ 2'-deoxy-5-[(1-hydroxy-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)ethynyl]uridine 5'-(tetrahydrogen triphosphate) × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 6 PGE TRIETHYLENE GLYCOL × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 9；291 K；0.05M Tris HCl ph 9, 0.2M NH4Cl, 0.01M CaCl2, 26% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.00 Å R-free 0.219 |
| 3PO4 Structure of a mutant of the large fragment of DNA polymerase I from Thermus aquaticus in complex with a blunt-ended DNA and ddATP Deposited 2010-11-22 | 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
293–832（540 aa）
Fragment：KLENOW FRAGMENT
|
Mutation：I614K, M747K | MG MAGNESIUM ION × 3 NA SODIUM ION × 1 GOL GLYCEROL × 1 DDS 2',3'-dideoxyadenosine triphosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.05M sodium cacodylate, 0.2M KCl, 0.1M Mg(OAc)2, 20% PEG 8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.80 Å R-free 0.194 |
| 3PO5 Structure of a mutant of the large fragment of DNA polymerase I from Thermus Auqaticus in complex with an abasic site and ddATP Deposited 2010-11-22 | 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
293–832（540 aa）
Fragment：Klenow Fragment
|
Mutation：I614K, M747K | MG MAGNESIUM ION × 1 PGE TRIETHYLENE GLYCOL × 2 DDS 2',3'-dideoxyadenosine triphosphate × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.8；291 K；0.05M Tris HCl, 0.2M NH4Cl, 0.01M CaCl2, 28% PEG 4000, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.39 Å R-free 0.266 |
| 3PY8 Crystal structure of a mutant of the large fragment of DNA polymerase I from thermus aquaticus in a closed ternary complex with DNA and ddCTP Deposited 2010-12-12 | 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
293–832（540 aa）
Fragment：DNA polymerase I large fragment
|
Mutation：I614K, M747K | DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 2 MN MANGANESE (II) ION × 5 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.1；291 K；0.1M Hepes, 20mM MnCl2, 0.1M Na-acetate, 12 % PEG 4000, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.74 Å R-free 0.199 |
| 3RR7 Binary Structure of the large fragment of Taq DNA polymerase bound to an abasic site Deposited 2011-04-29 | Different construct 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
293–832（540 aa）
Fragment：klenow fragment
|
Not recorded | FMT FORMIC ACID × 1 GOL GLYCEROL × 3 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M TRIS HCl pH 7.5, 0.2 M Magnesium Formate, 12% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.95 Å R-free 0.232 |
| 3RR8 Ternary Structure of the large fragment of Taq DNA polymerase bound to an abasic site and a ddGTP Deposited 2011-04-29 | Different construct 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
293–832（540 aa）
Fragment：klenow fragment
|
Not recorded | DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.05 M Na cacodylate pH 6.5, 0.2 M NH4OAc, 0.01 M Mg(OAc)2, 25% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.40 Å R-free 0.256 |
| 3RRG Ternary Structure of the large fragment of Taq DNA polymerase bound to an abasic site and a ddGTP Deposited 2011-04-29 | Different construct 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
293–832（540 aa）
Fragment：klenow fragment
|
Not recorded | DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 NA SODIUM ION × 1 GOL GLYCEROL × 2 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.05 M Na cacodylate pH 6.5, 0.2 M NH4OAc, 0.01 M Mg(OAc)2, 28% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.30 Å R-free 0.250 |
| 3RRH Ternary Structure of the large fragment of Taq DNA polymerase bound to an abasic site and a ddTTP Deposited 2011-04-29 | Different construct 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
293–832（540 aa）
Fragment：klenow fragment
|
Not recorded | TTP THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 4 PGE TRIETHYLENE GLYCOL × 2 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.05 M Na cacodylate pH 6.5, 0.2 M NH4OAc, 0.01 M Mg(OAc)2, 28% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.80 Å R-free 0.201 |
| 3RTV Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with natural primer/template DNA Deposited 2011-05-04 | Different construct 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
293–832（540 aa）
Fragment：Klenow Fragment
|
Not recorded | DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 3 GOL GLYCEROL × 6 ACT ACETATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.05M sodium cacodylate, 0.2M ammonium acetate, 0.01M magnesium acetate, 30% PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.90 Å R-free 0.202 |
| 3SV3 Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with the artificial base pair dNaM-d5SICSTP Deposited 2011-07-12 | Different construct 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
293–832（540 aa）
Fragment：Klenow Fragment, UNP residues 293-832
|
Not recorded | 5SI 2-{2-deoxy-5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-6-methylisoquinoline-1(2H)-thione × 2 MG MAGNESIUM ION × 5 GOL GLYCEROL × 4 FMT FORMIC ACID × 16 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；13% PEG 8000, 100mM NH4Cl, 0.1M MgFormate, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.10 Å R-free 0.215 |
| 3SV4 Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dT as templating nucleobase Deposited 2011-07-12 | Different construct 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
293–832（540 aa）
Fragment：Klenow Fragment, UNP residues 293-832
|
Not recorded | FMT FORMIC ACID × 9 MG MAGNESIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；18% PEG 8000, 0.2M MgFormate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.99 Å R-free 0.216 |
| 3SYZ Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dNaM as templating nucleobase Deposited 2011-07-18 | Different construct 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
293–832（540 aa）
Fragment：Klenow Fragment, UNP residues 293-832
|
Not recorded | FMT FORMIC ACID × 6 GOL GLYCEROL × 10 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；11% PEG 8000, 0.2M MgFormate, 0.1M Tris, 20mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.95 Å R-free 0.201 |
| 3SZ2 Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dG as templating nucleobase Deposited 2011-07-18 | Different construct 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
293–832（540 aa）
Fragment：Klenow Fragment, UNP residues 293-832
|
Not recorded | FMT FORMIC ACID × 6 MG MAGNESIUM ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；15% PEG 8000, 0.2M MgFormate, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.15 Å R-free 0.237 |
| 3T3F Ternary Structure of the large fragment of Taq DNA polymerase bound to an abasic site and dNITP Deposited 2011-07-25 | Different construct 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
293–832（540 aa）
Fragment：klenow fragment (UNP residues 293-832)
|
Not recorded | GOL GLYCEROL × 13 MG MAGNESIUM ION × 4 NA SODIUM ION × 1 N5P 1-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-5-NITRO -1H-INDOLE × 1 FMT FORMIC ACID × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.1 M TRIS HCl, 0.2 M MgFormate, 18% PEG 8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.90 Å R-free 0.206 |
| 4BWJ KlenTaq mutant in complex with DNA and ddCTP Deposited 2013-07-03 | 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
293–832（540 aa）
Fragment：KLENOW FRAGMENT, RESIDUES 293-832
|
Mutation：YES | DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP. 100MM TRIS PH 7.5, 200MM MG-FORMATE, 15% PEG 8K
|
Resolution 1.55 Å R-free 0.201 |
| 4BWM KlenTaq mutant in complex with a RNA/DNA hybrid Deposited 2013-07-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: trimeric |
Chain A
293–832（540 aa）
Fragment：KLENOW FRAGMENT, RESIDUES 293-832
|
Mutation：YES | DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1 CL CHLORIDE ION × 2 MG MAGNESIUM ION × 3 FMT FORMIC ACID × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；HANGING DROP. 100MM TRIS PH8.5, 200MM MG-FORMATE, 20% PEG 8K MICROSEEDED
|
Resolution 1.75 Å R-free 0.208 |
| 4C8K Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a partially closed complex with the artificial base pair d5SICS-dNaMTP Deposited 2013-10-01 | Different construct 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
293–832（540 aa）
Fragment：KLENOW FRAGMENT, RESIDUES 293-832
|
Not recorded | GOL GLYCEROL × 2 BMR ((2R,3S,5R)-3-hydroxy-5-(3-methoxynaphthalen-2-yl)methyl-tetrahydrogen-triphosphate × 1 MG MAGNESIUM ION × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；15% W/V PEG 8000, 100MM TRIS PH 7.0, 200MM MAGNESIUM FORMIAT
|
Resolution 2.17 Å R-free 0.221 |
| 4C8L Binary complex of the large fragment of DNA polymerase I from Thermus Aquaticus with the artificial base pair dNaM-d5SICS at the postinsertion site (sequence context 1) Deposited 2013-10-01 | Different construct 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
293–832（540 aa）
Fragment：KLENOW FRAGMENT, RESIDUES 293-832
|
Not recorded | GOL GLYCEROL × 5 SO4 SULFATE ION × 4 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；0.2M AMMONIUM SULFATE, 0.1M MES PH 6.5, 28% W/V PEG 5000MME
|
Resolution 1.70 Å R-free 0.214 |
| 4C8M Binary complex of the large fragment of DNA polymerase I from Thermus Aquaticus with the aritificial base pair d5SICS-dNaM at the postinsertion site (sequence context 2) Deposited 2013-10-01 | Different construct 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
293–832（540 aa）
Fragment：KLENOW FRAGMENT, RESIDUES 293-832
|
Not recorded | SO4 SULFATE ION × 3 GOL GLYCEROL × 5 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；0.2M AMMONIUM SULFATE, 0.1M MES PH 6.5, 30% (W/V) PEG 5000MME
|
Resolution 1.57 Å R-free 0.207 |
| 4C8N Binary complex of the large fragment of DNA polymerase I from Thermus Aquaticus with the aritificial base pair dNaM-d5SICS at the postinsertion site (sequence context 3) Deposited 2013-10-01 | Different construct 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
293–832（540 aa）
Fragment：KLENOW FRAGMENT, RESIDUES 293-832
|
Not recorded | SO4 SULFATE ION × 5 PGE TRIETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；1.2M LITHIUM SULFATE, 2% W/V PEG 1000, 50MM HEPES PH 7.5
|
Resolution 1.88 Å R-free 0.232 |
| 4C8O Binary complex of the large fragment of DNA polymerase I from Thermus Aquaticus with the aritificial base pair dNaM-d5SICS at the postinsertion site (sequence context 2) Deposited 2013-10-01 | Different construct 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
293–832（540 aa）
Fragment：KLENOW FRAGMENT, RESIDUES 293-832
|
Not recorded | SO4 SULFATE ION × 7 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；0.2M AMMONIUM SULFATE, 0.1M MES PH 6.5, 30% W/V PEG 5000MME
|
Resolution 1.75 Å R-free 0.212 |
| 4CCH Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with d5SICS as templating nucleotide Deposited 2013-10-23 | Different construct 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
293–832（540 aa）
Fragment：KLENOW FRAGMENT, RESIDUES 293-832
|
Not recorded | FMT FORMIC ACID × 4 MG MAGNESIUM ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8；20% W/V PEG 8000, 0.1M TRIS PH 8.0, 0.2M MAGNESIUM FORMATE, 20% GLYCEROL
|
Resolution 2.55 Å R-free 0.261 |
| 4DF4 Crystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 7-(N-(10-hydroxydecanoyl)-aminopentinyl)-7-deaza-2 -dATP Deposited 2012-01-23 | Different construct 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
293–832（540 aa）
Fragment：Klenow Fragment
|
Not recorded | MG MAGNESIUM ION × 5 0L3 7-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-5-{5-[(10-hydroxydecanoyl)amino]pent-1-yn-1-yl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；18% PEG 8000, 200mM Mg-Formate, 100 mMTris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.20 Å R-free 0.227 |
| 4DF8 Crystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with aminopentinyl-7-deaza-2-dATP Deposited 2012-01-23 | Different construct 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
293–832（540 aa）
Fragment：Klenow Fragment
|
Not recorded | 0L4 5-(5-aminopent-1-yn-1-yl)-7-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine × 1 MG MAGNESIUM ION × 3 EDO 1,2-ETHANEDIOL × 4 FMT FORMIC ACID × 4 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；18% PEG 8000, 200mM Mg-Formate, 100 mMTris pH 8.0 , VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.00 Å R-free 0.234 |
| 4DFJ Crystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 5-(aminopentinyl)-dTTP Deposited 2012-01-23 | Different construct 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
293–832（540 aa）
Fragment：Klenow Fragment
|
Not recorded | MG MAGNESIUM ION × 8 0KL 5-(5-aminopent-1-yn-1-yl)-2'-deoxyuridine 5'-(tetrahydrogen triphosphate) × 1 FMT FORMIC ACID × 6 EDO 1,2-ETHANEDIOL × 4 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；18% PEG 8000, 200mM Mg-Formate, 100 mMTris pH 8.0 , VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.90 Å R-free 0.204 |
| 4DFK large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 5-(N-(10-hydroxydecanoyl)-aminopentinyl)-2-dUTP Deposited 2012-01-24 | Different construct 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
293–832（540 aa）
Fragment：Klenow Fragment
|
Not recorded | 0L5 2'-deoxy-5-{5-[(10-hydroxydecanoyl)amino]pent-1-yn-1-yl}uridine 5'-(tetrahydrogen triphosphate) × 1 MG MAGNESIUM ION × 6 EDO 1,2-ETHANEDIOL × 3 FMT FORMIC ACID × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；18% PEG 8000, 200mM Mg-Formate, 100 mMTris pH 8.0 , VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.65 Å R-free 0.195 |
| 4DFM Crystal structure of the large fragment of DNA polymerase I from Thermus aquaticus in ternary complex with 5-(aminopentinyl)-2-dCTP Deposited 2012-01-24 | Different construct 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
293–832（540 aa）
Fragment：Klenow Fragment
|
Not recorded | 0L6 5-(5-aminopent-1-yn-1-yl)-2'-deoxycytidine 5'-(tetrahydrogen triphosphate) × 1 MG MAGNESIUM ION × 4 FMT FORMIC ACID × 1 EDO 1,2-ETHANEDIOL × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；18% PEG 8000, 200mM Mg-Formate, 100 mM Tris pH 8.0 , VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.89 Å R-free 0.216 |
| 4DFP Crystal structure of the large fragment of DNA Polymerase I from Thermus aqauticus in a ternary complex with 7-(aminopentinyl)-7-deaza-dGTP Deposited 2012-01-24 | Different construct 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
293–832（540 aa）
Fragment：Klenow Fragment, UNP residues 293-831
|
Not recorded | MG MAGNESIUM ION × 5 EDO 1,2-ETHANEDIOL × 5 FMT FORMIC ACID × 7 0L7 2-amino-5-(5-aminopent-1-yn-1-yl)-7-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；18% PEG 8000, 200mM Mg-Formate, 100 mM Tris pH 8.0 , VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.00 Å R-free 0.224 |
| 4DLE Ternary Structure of the large Fragment of Taq DNA Polymerase: 4-Fluoroproline Variant Deposited 2012-02-06 | 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
293–832（540 aa）
Fragment：UNP RESIDUES 293-832
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 1 GOL GLYCEROL × 2 DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1 MN MANGANESE (II) ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.1 M HEPES, 20 mM MnCl2, 0.1 M NH4(OAc), 15% PEG 4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 2.44 Å R-free 0.282 |
| 4DLG Ternary Structure of the large Fragment of Taq DNA polymerase Deposited 2012-02-06 | Different construct 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
293–832（540 aa）
Fragment：UNP residues 293-832
|
Not recorded | DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 ACT ACETATE ION × 3 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；50 mM Na cacodylate, 0.2 M NH4(OAc), 10 mM Mg(OAc)2, 15% PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
|
Resolution 1.89 Å R-free 0.252 |
| 4ELT Snapshot of the large fragment of DNA polymerase I from Thermus Aquaticus processing modified pyrimidines Deposited 2012-04-11 | Different construct 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
293–832（540 aa）
|
Not recorded | 0R5 2'-deoxy-5-[(4-ethynylphenyl)ethynyl]uridine 5'-(tetrahydrogen triphosphate) × 1 MG MAGNESIUM ION × 3 GOL GLYCEROL × 9 ACT ACETATE ION × 3 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；50 mM Na cacodylate pH=6.5, 0.2 M NH4(OAc), 10 mM Mg(OAc)2, 28% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.20 Å R-free 0.209 |
| 4ELU Snapshot of the large fragment of DNA polymerase I from Thermus Aquaticus processing modified pyrimidines Deposited 2012-04-11 | Different construct 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
293–832（540 aa）
Fragment：UNP RESIDUES 293-832
|
Not recorded | 0R6 2'-deoxy-5-[(4-ethynylphenyl)ethynyl]cytidine 5'-(tetrahydrogen triphosphate) × 1 MG MAGNESIUM ION × 3 GOL GLYCEROL × 11 PGE TRIETHYLENE GLYCOL × 2 ACT ACETATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；50 mM Na cacodylate pH=6.5, 0.2 M NH4(OAc), 10 mM Mg(OAc)2, 28% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.80 Å R-free 0.182 |
| 4ELV Snapshot of the large fragment of DNA polymerase I from Thermus Aquaticus processing modified pyrimidines Deposited 2012-04-11 | Different construct 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
293–832（540 aa）
Fragment：UNP RESIDUES 293-832
|
Not recorded | MG MAGNESIUM ION × 3 0R7 [[(2S,5R)-5-[4-azanyl-5-[2-(4-ethynylphenyl)ethynyl]-2-oxidanylidene-pyrimidin-1-yl]oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 GOL GLYCEROL × 4 PGE TRIETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 2 CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.4；291 K；50 mM Tris HCl pH=8.4, 0.2 M NH4Cl, 10 mM CaCl2, 34% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.90 Å R-free 0.216 |
| 4KTQ BINARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM T. AQUATICUS BOUND TO A PRIMER/TEMPLATE DNA Deposited 1998-09-09 | Different construct 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
294–832（539 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；pH 7.5
|
Resolution 2.50 Å R-free 0.298 |
| 4N56 Binary complex structure of Klenow fragment of Taq DNA polymerase I707L mutant (Cs3C KlenTaq) with DNA Deposited 2013-10-09 | 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
281–832（552 aa）
Fragment：Klenow fragment (UNP residues 281-832)
|
Mutation：I707L | MN MANGANESE (II) ION × 1 GOL GLYCEROL × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M HEPES, pH 7.5, 20 mM manganese chloride, 0.1 M sodium acetate, 10% w/v PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 2.20 Å R-free 0.273 |
| 4N5S Ternary complex structure of Klenow fragment of Taq DNA polymerase I707L mutant (Cs3C KlenTaq) with DNA and ddCTP Deposited 2013-10-10 | 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
281–832（552 aa）
Fragment：Klenow fragment (UNP residues 281-832)
|
Mutation：I707L | MN MANGANESE (II) ION × 6 MG MAGNESIUM ION × 1 DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 ACT ACETATE ION × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M HEPES, pH 7.5, 20 mM manganese chloride, 0.1 M sodium acetate, 10% w/v PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 289K
|
Resolution 1.67 Å R-free 0.192 |
| 4XIU Binary complex structure of Klenow fragment of Taq DNA polymerase I707L mutant with DNA containing TTT overhang Deposited 2015-01-07 | 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
294–832（539 aa）
Fragment：Klenow fragment of DNA polymerase I from Thermus aquatics
|
Mutation：I707L | MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；PEG4000
|
Resolution 2.50 Å R-free 0.286 |
| 5E41 Crystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 5-(N-(10-hydroxydecanoyl)-aminopentenyl)-2'-deoxyuridine-triphosphate Deposited 2015-10-05 | Different construct 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
293–832（540 aa）
|
Not recorded | MG MAGNESIUM ION × 2 AUL 2'-deoxy-5-{(1E)-5-[(10-hydroxydecanoyl)amino]pent-1-en-1-yl}uridine 5'-(tetrahydrogen triphosphate) × 1 GOL GLYCEROL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.05M Sodium cacodylate pH 6.5, 0.01M Magnesium acetate, 0.2M Ammonium acetate, 30% PEG 4000
|
Resolution 1.80 Å R-free 0.236 |
| 5KTQ LARGE FRAGMENT OF TAQ DNA POLYMERASE BOUND TO DCTP Deposited 1998-09-22 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
290–832（543 aa）
|
Not recorded | DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 9；pH 9.0
|
Resolution 2.50 Å R-free 0.280 |
| 5NKL Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a closed ternary complex with the artificial base pair dDs-dPxTP Deposited 2017-03-31 | Different construct 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
293–832（540 aa）
|
Not recorded | MG MAGNESIUM ION × 2 ACT ACETATE ION × 1 91T [[(2~{R},3~{S},5~{R})-5-[4-[(4~{R})-4,5-bis(oxidanyl)pent-1-ynyl]-2-nitro-pyrrol-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 91R [[(2~{R},3~{S},5~{R})-5-[4-[(4~{S})-4,5-bis(oxidanyl)pent-1-ynyl]-2-nitro-pyrrol-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；100mM TRIS pH 8.5, 0.2M Sodium acetate, 30% PEG 4000
|
Resolution 1.70 Å R-free 0.237 |
| 5O7T Crystal structure of KlenTaq mutant M747K in a closed ternary complex with a dG:dCTP base pair Deposited 2017-06-09 | 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
293–832（540 aa）
|
Mutation：M747K | MG MAGNESIUM ION × 3 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；20% PEG 3350, 0 .1M Magnesiumacetate
|
Resolution 1.80 Å R-free 0.235 |
| 5OXJ Crystal structure of KlenTaq mutant M747K in a closed ternary complex with a O6-MeG:BenziTP base pair Deposited 2017-09-06 | 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
293–832（540 aa）
|
Mutation：M747K | MN MANGANESE (II) ION × 2 NZI [(2~{R},3~{S},5~{R})-3-oxidanyl-5-(2-oxidanylidene-3~{H}-benzimidazol-1-yl)oxolan-2-yl]methyl [oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate × 1 ACT ACETATE ION × 3 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；22% PEG3350 + 0.1M Mg(OAc)2 + 0.1M HEPES pH 7.5
|
Resolution 2.00 Å R-free 0.257 |
| 5SZT Crystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 7-(N-(10-hydroxydecanoyl)-aminopentenyl)-7-deaza-2'-dATP Deposited 2016-08-15 | Different construct 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
293–832（540 aa）
|
Not recorded | MG MAGNESIUM ION × 3 GOL GLYCEROL × 2 ACT ACETATE ION × 4 72J 7-(N-(10-hydroxydecanoyl)-aminopentenyl)-7-deaza-2'-dATP × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.05 M sodium cacodylate pH 6.5, 0.01 M magnesium acetate, 0.2 M ammonium acetate, 30% PEG 4000
|
Resolution 1.80 Å R-free 0.230 |
| 5W6K Structure of mutant Taq Polymerase incorporating unnatural base pairs Z:P Deposited 2017-06-16 | Different construct 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
293–832（540 aa）
Fragment：UNP residues 293-831
|
Not recorded | A5J (1R)-1-[6-amino-5-(dihydroxyamino)-2-hydroxypyridin-3-yl]-1,4-anhydro-2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-D-erythro-pentitol × 1 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.16 K；19 % PEG 4000,
0.2 M ammonium acetate,
0.01 M magnesium acetate,
0.05 M sodium cacodylate pH 6.5
|
Resolution 2.34 Å R-free 0.275 |
| 5W6Q Structural basis for recognition of artificial DNA by an evolved KlenTaq variant Deposited 2017-06-16 | Different construct 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
293–832（540 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277.15 K；14 % PEG 8000,
0.2 M Mg formate,
0.1 M MES pH 6.0
|
Resolution 2.66 Å R-free 0.247 |
| 5W6Q Structural basis for recognition of artificial DNA by an evolved KlenTaq variant Deposited 2017-06-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain C
293–832（540 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277.15 K；14 % PEG 8000,
0.2 M Mg formate,
0.1 M MES pH 6.0
|
Resolution 2.66 Å R-free 0.247 |
| 5W6Q Structural basis for recognition of artificial DNA by an evolved KlenTaq variant Deposited 2017-06-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric |
Chain G
293–832（540 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277.15 K；14 % PEG 8000,
0.2 M Mg formate,
0.1 M MES pH 6.0
|
Resolution 2.66 Å R-free 0.247 |
| 5YTC Large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with the unnatural base M-fC pair with dATP in the active site Deposited 2017-11-17 | Different construct 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
294–832（539 aa）
Fragment：large fragment
|
Not recorded | DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 8.5；293.15 K；0.2 M Mg(HCOO)2, 0.1 M Tris HCl (pH 8.5), 18% PEG 8000
|
Resolution 2.28 Å R-free 0.258 |
| 5YTD large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with the natural base pair 5fC:dGTP Deposited 2017-11-17 | Different construct 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
294–832（539 aa）
|
Not recorded | DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 7；293.15 K；0.05 M sodium cacodylate (pH 7.0), 0.2 M ammonium acetate, 0.01 M magnesium acetate, 30% PEG 8000
|
Resolution 2.00 Å R-free 0.239 |
| 5YTE Large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with with natural dT:dATP base pair Deposited 2017-11-17 | Different construct 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
294–832（539 aa）
|
Not recorded | DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 7；293.15 K；0.05 M sodium cacodylate (pH 7.0), 0.2 M ammonium acetate, 0.01 M magnesium acetate, 30% PEG 8000
|
Resolution 2.21 Å R-free 0.238 |
| 5YTF Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest complex with the unnatural base M-fC pair with dA Deposited 2017-11-17 | Different construct 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
294–832（539 aa）
Fragment：large fragment
|
Not recorded | MG MAGNESIUM ION × 3 DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 7；293.15 K；0.05 M sodium cacodylate (pH 7.0), 0.2 M ammonium acetate, 0.01 M magnesium acetate, 30% PEG 8000
|
Resolution 1.98 Å R-free 0.233 |
| 5YTG Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest complex with the unnatural base I-fC pair with dA Deposited 2017-11-17 | Different construct 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
294–832（539 aa）
|
Not recorded | DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 3 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 7；293.15 K；0.05 M sodium cacodylate (pH 7.0), 0.2 M ammonium acetate, 0.01 M magnesium acetate, 30% PEG 8000
|
Resolution 2.07 Å R-free 0.252 |
| 5YTH Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest complex with the unnatural base M-fC pair with dG Deposited 2017-11-17 | Different construct 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
294–832（539 aa）
Fragment：large fragment
|
Not recorded | DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 7；293.15 K；0.05 M sodium cacodylate (pH 7.0), 0.2 M ammonium acetate, 0.01 M magnesium acetate, 30% PEG 8000
|
Resolution 2.53 Å R-free 0.275 |
| 5Z3N Structure of large fragment of DNA Polymerase I from Thermus aquaticus Host-Guest complex with the unnatural base 5fC pair with dA Deposited 2018-01-08 | Different construct 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
294–832（539 aa）
|
Not recorded | MG MAGNESIUM ION × 3 DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 7；293.15 K；0.05 M sodium cacodylate (pH 7.0), 0.2 M ammonium acetate, 0.01 M magnesium acetate, 24% PEG 8000
|
Resolution 1.91 Å R-free 0.229 |
| 6FBC KlenTaq DNA polymerase processing a modified primer - bearing the modification at the 3'-terminus of the primer. Deposited 2017-12-19 | Different construct 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
293–832（540 aa）
|
Not recorded | XG4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine × 1 EDO 1,2-ETHANEDIOL × 2 MN MANGANESE (II) ION × 2 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；291 K；14 % PEG 4000, 0.1 M HEPES, 20 mM manganese(II) chloride, 0.1 M sodium actetate
|
Resolution 1.54 Å R-free 0.208 |
| 6FBD KlenTaq DNA polymerase processing a modified primer - bearing the modification upstream at the second primer nucleotide. Deposited 2017-12-19 | Different construct 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
293–832（540 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 XG4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine × 1 MG MAGNESIUM ION × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；291 K；16 % PEG 4000, 0.1 M HEPES, 25 mM manganese(II) chloride, 0.1 M sodium acetate
|
Resolution 2.10 Å R-free 0.233 |
| 6FBE KlenTaq DNA polymerase processing a modified primer - bearing the modification upstream at the third primer nucleotide. Deposited 2017-12-19 | Different construct 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
293–832（540 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 EDO 1,2-ETHANEDIOL × 2 XG4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；291 K；20 % PEG 4000, 0.1 M HEPES, 20 mM manganese(II) chloride, 0.1 M sodium acetate
|
Resolution 1.59 Å R-free 0.203 |
| 6FBF KlenTaq DNA polymerase processing a modified primer - bearing the modification upstream at the fourth primer nucleotide. Deposited 2017-12-19 | Different construct 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
293–832（540 aa）
|
Not recorded | MN MANGANESE (II) 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；pH 6；291 K；16 % PEG 4000, 20 mM manganese(II) chloride, 0.1 M TRIS, 0.1 M sodium acetate
|
Resolution 2.00 Å R-free 0.226 |
| 6FBG KlenTaq DNA polymerase processing a modified primer - bearing the modification upstream at the fifth primer nucleotide. Deposited 2017-12-19 | Different construct 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
293–832（540 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 EDO 1,2-ETHANEDIOL × 6 XG4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；291 K；15 % PEG 4000, 0.1 M HEPES, 20 mM manganese(II) chloride, 0.1 M sodium acetate
|
Resolution 1.70 Å R-free 0.217 |
| 6FBH KlenTaq DNA polymerase processing a modified primer - bearing the modification upstream at the sixth primer nucleotide. Deposited 2017-12-19 | Different construct 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
293–832（540 aa）
|
Not recorded | MN MANGANESE (II) ION × 2 EDO 1,2-ETHANEDIOL × 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；pH 7；291 K；29 % PEG 4000, 0.05 M TRIS, 20 mM manganese(II) chloride, 0.2 M ammonium chloride
|
Resolution 1.80 Å R-free 0.223 |
| 6FBI KlenTaq DNA polymerase in a closed, ternary complex with dGpNHpp bound in the active site Deposited 2017-12-19 | Different construct 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
293–832（540 aa）
|
Not recorded | XG4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine × 1 MN MANGANESE (II) ION × 2 EDO 1,2-ETHANEDIOL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；(A) 16 % PEG 4000, 0.1 M sodium acetate, 20 mM manganese(II) chloride, 0.1 M MES
(B) 17 % PEG 4000, 0.1 M ammonium acetate, 0.1 M HEPES, 20 mM manganese(II) chloride
(C) 15 % PEG 4000, 0.1 M sodium acetate, 20 mM manganese(II) chloride, 0.1 M MES
|
Resolution 1.90 Å R-free 0.235 |
| 6Q4U KlenTaq DNA pol in a closed ternary complex with 7-deaza-7-(2-(2-hydroxyethoxy)-N-(prop-2-yn-1-yl)acetamide)-2-dATP Deposited 2018-12-06 | Different construct 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
293–832（540 aa）
|
Not recorded | MG MAGNESIUM ION × 2 MN MANGANESE (II) ION × 1 HHZ [[(2~{R},3~{S},5~{R})-5-[4-azanyl-5-[3-[2-(2-hydroxyethyloxy)ethanoylamino]prop-1-ynyl]pyrrolo[2,3-d]pyrimidin-7-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；14 % PEG 8000, 0.1 M Tris pH 8.0, 0.2 M magnesium formate, 10 % glycerol
|
Resolution 2.00 Å R-free 0.220 |
| 6Q4V KlenTaq DNA polymerase in complex with dATP Deposited 2018-12-06 | Different construct 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
293–832（540 aa）
|
Not recorded | DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；27 % PEG 4000, 0.2 M ammonium acetate, 0.01 M magnesium (II) acetate, 0.1 M MES pH 6.5
|
Resolution 2.01 Å R-free 0.219 |
| 7OWF KlenTaq DNA polymerase in a ternary complex with primer/template and the fluorescent nucleotide analog BFdUTP Deposited 2021-06-18 | Different construct 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
293–832（540 aa）
|
Not recorded | MG MAGNESIUM ION × 3 2IU [[(2R,3S,5R)-5-[5-(1-benzofuran-2-yl)-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291.15 K；16% PEG 6000, 0.1M Tris pH 8.0, 0.2M magnesium formate
|
Resolution 1.91 Å R-free 0.241 |
| 8XK7 binary complex of DNA polymerase SFM4-3 recognizing C2 methyoxy nucleotide Deposited 2023-12-22 | Different construct 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
294–832（539 aa）
|
Not recorded | PO4 PHOSPHATE ION × 2 SO4 SULFATE ION × 3 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.2 M lithium sulfate monohydrate, 0.1 M HEPES pH 7.5, and 28% PEG 3350
|
Resolution 2.00 Å R-free 0.231 |
| 8XK9 ternary complex of DNA polymerase SFM4-3 recognizing C2 methyoxy nucleotide Deposited 2023-12-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric |
Chain A
294–832（539 aa）
Chain D
294–832（539 aa）
|
Not recorded | MG MAGNESIUM ION × 6 A1LWE [[(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 2 PEG DI(HYDROXYETHYL)ETHER × 2 PO4 PHOSPHATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.1 M HEPES pH 7.5, 10% propanol, and 20% PEG 4000
|
Resolution 2.40 Å R-free 0.218 |
| 9FM3 KlenTaq DNA polymerase in a ternary complex with primer/template and a selenophene-modified dUTP (SedUTP) Deposited 2024-06-05 | Different construct 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
293–832（540 aa）
|
Not recorded | A1IDZ [[(2~{R},3~{S},5~{R})-5-[2,4-bis(oxidanylidene)-5-selenophen-2-yl-pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 1 DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；JBScreen Nuc-Pro HTS condition F12:
1M di-Sodium tartrate, 50 mM TRIS pH 7.5, 30 mM Magnesium chloride
|
Resolution 2.59 Å R-free 0.245 |
| 9FMF KlenTaq DNA polymerase in a ternary complex with primer/template and a fluorobenzofuran-modified dUTP (FBFdUTP) Deposited 2024-06-06 | Different construct 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
293–832（540 aa）
|
Not recorded | MG MAGNESIUM ION × 1 A1IDW [[(2~{R},3~{S},5~{R})-5-[5-(5-fluoranyl-1-benzofuran-2-yl)-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；Nextal Nucleix Suite condition D12: 0.2 M Ammonium chloride, 0.01 M Calcium chloride, 0.05 M TRIS HCl pH 8.5, 20% (w/v) PEG 4000
|
Resolution 2.10 Å R-free 0.233 |
81 other PDB entries and 83 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | DPO1_THEAQ |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 6–548； UniProt 290–832 |
