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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

Method: X-RAY DIFFRACTION Dmax: 80.8 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA POLYMERASE I, THERMOSTABLE

THERMUS AQUATICUS

UniProt P19821

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 2 PDB declaration: trimeric（3） Consistent with all polymer counts Chain A； UniProt 293–832 Fragment：KLENOW FRAGMENT, RESIDUES 293-832 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*C*DOC)-3' × 1 5'-D(*AP*AP*C*LHOP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3' × 1 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

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 4C8K 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 oligomeric state 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 construct Different oligomeric state 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 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 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 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 oligomeric state 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 mutation/modification 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 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
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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 construct Different oligomeric state 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
8XJR Apo form 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 monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 290–832（543 aa）
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
8XK7 binary complex of DNA polymerase SFM4-3 recognizing C2 methyoxy nucleotide Deposited 2023-12-22 Different construct 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 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 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 1–540； UniProt 293–832

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 4c8k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4c8k
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4c8k
Deposition date deposition_date2013-10-01
Structure title titleCrystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a partially closed complex with the artificial base pair d5SICS-dNaMTP
Keywords keywordsTRANSFERASE-DNA COMPLEX, UNNATURAL NUCLEOTIDE, ARTIFICIAL NUCLEOTIDE, BINARY COMPLEX, KLENTAQ; TRANSFERASE/DNA
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier26.05 Å
Radius of gyration Rg (electron density) rg_electron25.34 Å
Forward intensity I(0) i090325100.00
Molecular weight molecular_weight69706.0 kDa
Excluded volume excluded_volume85224 ų
Envelope volume envelope_volume105010 ų
Hydration-shell volume shell_volume33715 ų
Envelope diameter envelope_diameter83.7 Å
Shell Rg shell_rg33.47 Å
Envelope Rg envelope_rg25.33 Å
Shape Rg shape_rg25.37 Å
Total Rg total_rg26.01 Å
Total atoms total_atoms9558
Residues n_residues564
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax80.8 Å
Rg (real space) rg_real25.90 Å
Rg uncertainty (real space) rg_real_error0.42 Å
I(0) (real space) i0_real9.0330e+07
I(0) uncertainty (real space) i0_real_error1.1700e+06
Rg (reciprocal space) rg_reciprocal25.95 Å
I(0) (reciprocal space) i0_reciprocal90330000.0000
Solution quality estimate total_estimate0.9023
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.1 Å
Skewness Skewness skewness0.163
Kurtosis Kurtosis kurtosis-0.423
Angular range angular_range— – 0.3050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13220000.0000
Real-space data points n_real_points62
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.986
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id4c8kA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id4c8kA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1060 — Taq DNA Polymerase; Chain T, domain 4
Homologous superfamily homologous superfamily10 — Taq DNA Polymerase; Chain T, domain 4
Domain ID domain_id4c8kA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily370 —
Domain ID domain_id4c8kA04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily20 — 5' to 3' exonuclease, C-terminal subdomain
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8. Citations (1)

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9. Files and Curves (10)