3GDX
| Dna polymerase beta with a gapped DND substrate and dTMP(CF2)PP | Descriptor: | 5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... | Authors: | Wilson, S.H, Batra, V.K, Pedersen, L.C. | Deposit date: | 2009-02-24 | Release date: | 2009-05-05 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Alpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates: a convenient synthesis of useful probes for DNA polymerase beta structure and function Org.Lett., 11, 2009
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5TZV
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5DFF
| Human APE1 product complex | Descriptor: | 1,2-ETHANEDIOL, CHLORIDE ION, DI(HYDROXYETHYL)ETHER, ... | Authors: | Freudenthal, B.D, Wilson, S.H. | Deposit date: | 2015-08-26 | Release date: | 2015-10-14 | Last modified: | 2024-03-06 | Method: | X-RAY DIFFRACTION (1.57 Å) | Cite: | Capturing snapshots of APE1 processing DNA damage. Nat.Struct.Mol.Biol., 22, 2015
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5DFH
| Human APE1 mismatch product complex | Descriptor: | 1,2-ETHANEDIOL, DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*T)-3'), DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... | Authors: | Freudenthal, B.D, Wilson, S.H. | Deposit date: | 2015-08-26 | Release date: | 2015-10-14 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (1.949 Å) | Cite: | Capturing snapshots of APE1 processing DNA damage. Nat.Struct.Mol.Biol., 22, 2015
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5DFJ
| Human APE1 E96Q/D210N mismatch substrate complex | Descriptor: | 1,2-ETHANEDIOL, CHLORIDE ION, DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), ... | Authors: | Freudenthal, B.D, Wilson, S.H. | Deposit date: | 2015-08-26 | Release date: | 2015-10-14 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.85 Å) | Cite: | Capturing snapshots of APE1 processing DNA damage. Nat.Struct.Mol.Biol., 22, 2015
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6PH5
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4R64
| Binary complex crystal structure of E295K mutant of DNA polymerase Beta | Descriptor: | DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ... | Authors: | Batra, V.K, Beard, W.A, Wilson, S.H. | Deposit date: | 2014-08-22 | Release date: | 2014-10-08 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Substrate-induced DNA Polymerase beta Activation. J.Biol.Chem., 289, 2014
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4R66
| Ternary complex crystal structure of E295K mutant of DNA polymerase Beta | Descriptor: | 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... | Authors: | Batra, V.K, Beard, W.A, Wilson, S.H. | Deposit date: | 2014-08-22 | Release date: | 2014-10-08 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (2.25 Å) | Cite: | Substrate-induced DNA Polymerase beta Activation. J.Biol.Chem., 289, 2014
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6CRB
| Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CF2, beta, gamma dATP analogue | Descriptor: | 9-{2-deoxy-5-O-[(S)-{[(S)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D-erythro-pentofuranosyl}-9H-purin-6-amine, DNA polymerase beta, Downstream Primer Strand, ... | Authors: | Batra, V.K, Wilson, S.H. | Deposit date: | 2018-03-16 | Release date: | 2018-07-18 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (2.151 Å) | Cite: | Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs. Biochemistry, 57, 2018
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6CR7
| Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHF, beta, gamma dATP analogue | Descriptor: | 9-{2-deoxy-5-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D-erythro-pentofuranosyl}-9H-purin-6-amine, CHLORIDE ION, DNA polymerase beta, ... | Authors: | Batra, V.K, Wilson, S.H. | Deposit date: | 2018-03-16 | Release date: | 2018-07-04 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (2.29 Å) | Cite: | Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs. Biochemistry, 57, 2018
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6CR4
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6CTL
| Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCL-R/S isomers, beta, gamma dTTP analogue | Descriptor: | 5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... | Authors: | Batra, V.K, Wilson, S.H. | Deposit date: | 2018-03-23 | Release date: | 2018-06-20 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs. Biochemistry, 57, 2018
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6CR3
| Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CBr2, beta, gamma dATP analogue | Descriptor: | 2'-deoxy-5'-O-[(R)-{[(R)-[dibromo(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*TP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... | Authors: | Batra, V.K, Wilson, S.H. | Deposit date: | 2018-03-16 | Release date: | 2018-06-27 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs. Biochemistry, 57, 2018
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6CTJ
| Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCH3, beta, gamma dTTP analogue | Descriptor: | 5'-O-[(R)-hydroxy({(R)-hydroxy[(1S)-1-phosphonoethyl]phosphoryl}oxy)phosphoryl]thymidine, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... | Authors: | Batra, V.K, Wilson, S.H. | Deposit date: | 2018-03-23 | Release date: | 2018-06-20 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs. Biochemistry, 57, 2018
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6CTT
| Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCL (R & S isomers, beta, gamma dCTP analogue | Descriptor: | 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE, 5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxycytidine, 5'-O-[(R)-{[(R)-[(S)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxycytidine, ... | Authors: | Batra, V.K, Wilson, S.H. | Deposit date: | 2018-03-23 | Release date: | 2018-06-20 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs. Biochemistry, 57, 2018
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6CTW
| Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CCL2, beta, gamma dCTP analogue | Descriptor: | 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE, 4-amino-1-{2-deoxy-5-O-[(R)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-L-threo-pentofuranosyl}pyrimidin-2(1H)-one, CHLORIDE ION, ... | Authors: | Batra, V.K, Wilson, S.H. | Deposit date: | 2018-03-23 | Release date: | 2018-06-20 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (1.981 Å) | Cite: | Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs. Biochemistry, 57, 2018
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6CTM
| Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCL(R-isomer), beta, gamma dTTP analogue | Descriptor: | 5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... | Authors: | Batra, V.K, Wilson, S.H. | Deposit date: | 2018-03-23 | Release date: | 2018-06-20 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (2.101 Å) | Cite: | Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs. Biochemistry, 57, 2018
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6CR5
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4RT3
| Ternary complex crystal structure of DNA polymerase Beta with (alpha, beta)-NH-(beta,gamma)-CH2-dTTP | Descriptor: | 2'-deoxy-5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]amino}phosphoryl]-3,4-dihydrothymidine, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... | Authors: | Batra, V.K, Wilson, S.H. | Deposit date: | 2014-11-12 | Release date: | 2015-07-01 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (1.92 Å) | Cite: | Two Scaffolds from Two Flips: (alpha, beta)/(beta, gamma) CH2/NH "Met-Im" Analogues of dTTP. Org.Lett., 17, 2015
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4RT2
| Ternary complex crystal structure of DNA polymerase Beta with (alpha,beta)-CH2-(beta,gamma)-NH-dTTP | Descriptor: | 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]methyl}phosphoryl]-3,4-dihydrothymidine, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... | Authors: | Batra, V.K, Wilson, S.H. | Deposit date: | 2014-11-12 | Release date: | 2015-07-01 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (1.92 Å) | Cite: | Two Scaffolds from Two Flips: (alpha, beta)/(beta, gamma) CH2/NH "Met-Im" Analogues of dTTP. Org.Lett., 17, 2015
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4UBC
| DNA polymerase beta substrate complex with a templating cytosine and incoming 8-oxodGTP, 0 s | Descriptor: | 5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... | Authors: | Freudenthal, B.D, Wilson, S.H, Beard, W.A. | Deposit date: | 2014-08-12 | Release date: | 2014-11-12 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide. Nature, 517, 2015
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4UAZ
| DNA polymerase beta reactant complex with a templating adenine and incoming 8-oxodGTP, 20 s | Descriptor: | 5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*(8OG))-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... | Authors: | Freudenthal, B.D, Wilson, S.H, Beard, W.A. | Deposit date: | 2014-08-11 | Release date: | 2014-11-12 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (1.88 Å) | Cite: | Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide. Nature, 517, 2015
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4UB3
| DNA polymerase beta closed product complex with a templating cytosine and 8-oxodGMP, 60 s | Descriptor: | 5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*(8OG))-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... | Authors: | Freudenthal, B.D, Wilson, S.H, Beard, W.A. | Deposit date: | 2014-08-11 | Release date: | 2014-11-12 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (2.06 Å) | Cite: | Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide. Nature, 517, 2015
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4UBB
| DNA polymerase beta reactant complex with a templating cytosine and incoming 8-oxodGTP, 40 s | Descriptor: | 5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*(8OG))-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... | Authors: | Freudenthal, B.D, Wilson, S.H, Beard, W.A. | Deposit date: | 2014-08-12 | Release date: | 2014-11-12 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide. Nature, 517, 2015
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4UAY
| DNA polymerase beta product complex with a templating adenine and inserted 8-oxodGMP, 40 s | Descriptor: | 5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*(8OG))-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... | Authors: | Freudenthal, B.D, Wilson, S.H, Beard, W.A. | Deposit date: | 2014-08-11 | Release date: | 2014-11-12 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (1.984 Å) | Cite: | Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide. Nature, 517, 2015
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