4F5P
 
 | | Open ternary mismatch complex of R283K DNA polymerase beta with a dATP analog | | Descriptor: | 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine, DNA (5'-D(*CP*CP*GP*AP*CP*GP*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'), ... | | Authors: | Freudenthal, B.D, Beard, W.A, Wilson, S.H. | | Deposit date: | 2012-05-13 | | Release date: | 2012-12-12 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly.
Structure, 20, 2012
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4KLF
 | | DNA polymerase beta matched reactant complex with Mg2+, 20 s | | Descriptor: | 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, 5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3', ... | | Authors: | Freudenthal, B.D, Beard, W.A, Shock, D.D, Wilson, S.H. | | Deposit date: | 2013-05-07 | | Release date: | 2013-07-17 | | Last modified: | 2023-09-20 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Observing a DNA polymerase choose right from wrong.
Cell(Cambridge,Mass.), 154, 2013
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5TBC
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6CTR
 | | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHF (R & S isomers), beta, gamma dCTP analogue | | Descriptor: | 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE, 2'-deoxy-5'-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine, 2'-deoxy-5'-O-[(R)-{[(R)-[(S)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine, ... | | 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 (1.85 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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5U9H
 | | DNA polymerase beta product complex with inserted Sp-isomer of dCTP-alpha-S | | Descriptor: | DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*(C7R))-3'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ... | | Authors: | Freudenthal, B.D, Wilson, S.H, Beard, W.A. | | Deposit date: | 2016-12-16 | | Release date: | 2017-02-08 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Revealing the role of the product metal in DNA polymerase beta catalysis.
Nucleic Acids Res., 45, 2017
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4R63
 | | Binary complex crystal structure of R258A 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 (1.85 Å) | | Cite: | Substrate-induced DNA Polymerase beta Activation.
J.Biol.Chem., 289, 2014
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7S9P
 | | Ternary complex of DNA Polymerase Beta with Template Fapy-dG and an incoming dCTP analog | | Descriptor: | 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*(FAP)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... | | Authors: | Freudenthal, B.D, Ryan, B.J, Smith, M.R. | | Deposit date: | 2021-09-21 | | Release date: | 2022-08-03 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (1.86 Å) | | Cite: | Structural Dynamics of a Common Mutagenic Oxidative DNA Lesion in Duplex DNA and during DNA Replication.
J.Am.Chem.Soc., 144, 2022
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6CTQ
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5VS4
 | | Human DNA polymerase beta 8-oxoG:dA extension with dTTP after 120 s | | Descriptor: | ACETATE ION, DNA (5'-D(*CP*CP*GP*AP*CP*AP*(8OG)P*GP*CP*GP*CP*AP*TP*CP*AP*G)-3'), DNA (5'-D(*CP*TP*GP*AP*TP*GP*CP*GP*CP*AP*T)-3'), ... | | Authors: | Reed, A.J, Suo, Z. | | Deposit date: | 2017-05-11 | | Release date: | 2017-07-19 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (1.87 Å) | | Cite: | Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta.
J. Am. Chem. Soc., 139, 2017
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4KLH
 | | DNA polymerase beta matched product complex with Mn2+, 40 s | | Descriptor: | 5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... | | Authors: | Freudenthal, B.D, Beard, W.A, Shock, D.D, Wilson, S.H. | | Deposit date: | 2013-05-07 | | Release date: | 2013-07-17 | | Last modified: | 2023-09-20 | | Method: | X-RAY DIFFRACTION (1.876 Å) | | Cite: | Observing a DNA polymerase choose right from wrong.
Cell(Cambridge,Mass.), 154, 2013
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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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6BEM
 | | Ternary complex crystal structure of DNA polymerase Beta with S-isomer of beta-gamma-CHCL-dCTP | | Descriptor: | 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE, 5'-O-[(R)-{[(R)-[(S)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxycytidine, CHLORIDE ION, ... | | Authors: | Batra, V.K, Wilson, S.H. | | Deposit date: | 2017-10-25 | | Release date: | 2018-10-31 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (1.88 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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7RBE
 | | Human DNA polymerase beta crosslinked binary complex - A | | Descriptor: | 2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol, CITRIC ACID, DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... | | Authors: | Reed, A.J, Kumar, A. | | Deposit date: | 2021-07-06 | | Release date: | 2022-03-09 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (1.89 Å) | | Cite: | Interlocking activities of DNA polymerase beta in the base excision repair pathway.
Proc.Natl.Acad.Sci.USA, 119, 2022
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6MR8
 | | D276G DNA polymerase beta substrate complex with templating adenine and incoming Fapy-dGTP analog | | Descriptor: | 1,2-ETHANEDIOL, 1-[2-amino-5-(formylamino)-6-oxo-1,6-dihydropyrimidin-4-yl]-2,5-anhydro-1,3-dideoxy-6-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-D-ribo-hexitol, CALCIUM ION, ... | | Authors: | Freudenthal, B.D, Smith, M.R, Wilson, S.H, Beard, W.A. | | Deposit date: | 2018-10-11 | | Release date: | 2019-01-30 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (1.897 Å) | | Cite: | A guardian residue hinders insertion of a Fapy•dGTP analog by modulating the open-closed DNA polymerase transition.
Nucleic Acids Res., 47, 2019
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5UGO
 | | DNA polymerase beta nick complex with imidodiphosphate | | Descriptor: | CALCIUM ION, DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3'), ... | | Authors: | Freudenthal, B.D, Wilson, S.H, Beard, W.A. | | Deposit date: | 2017-01-09 | | Release date: | 2017-07-26 | | Last modified: | 2024-03-06 | | Method: | X-RAY DIFFRACTION (1.897 Å) | | Cite: | Modulating the DNA polymerase beta reaction equilibrium to dissect the reverse reaction.
Nat. Chem. Biol., 13, 2017
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6BEL
 | | Ternary complex crystal structure of DNA polymerase Beta with R-isomer of beta-gamma-CHF-dCTP | | Descriptor: | 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE, 2'-deoxy-5'-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine, CHLORIDE ION, ... | | Authors: | Batra, V.K, Wilson, S.H. | | Deposit date: | 2017-10-25 | | Release date: | 2018-10-31 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (1.898 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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8VF9
 | | Binary DNA Polymerase Beta bound to DNA containing primer terminal dA base-paired with FapydG | | Descriptor: | DNA (5'-D(*CP*CP*GP*AP*CP*CP*(FAP)P*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ... | | Authors: | Oden, P.N, Ryan, B.J, Freudenthal, B.D. | | Deposit date: | 2023-12-21 | | Release date: | 2024-05-08 | | Last modified: | 2024-06-05 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Biochemical and structural characterization of Fapy•dG replication by Human DNA polymerase beta.
Nucleic Acids Res., 52, 2024
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6CTU
 | | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CFCL, beta, gamma dCTP analogue | | Descriptor: | 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE, 4-amino-1-{5-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2-deoxy-alpha-L-threo-pentofuranosyl}pyrimidin-2(1H)-one, 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 (1.9 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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4RPX
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6NKU
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4RPY
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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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4UAW
 | | DNA polymerase beta substrate complex with a templating adenine and incoming 8-oxodGTP, 0 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*C)-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... | | Authors: | Freudenthal, B.D, Wilson, S.H, Beard, W.A. | | Deposit date: | 2014-08-11 | | Release date: | 2014-11-12 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide.
Nature, 517, 2015
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3JPQ
 | | Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monoBromo methylene triphosphate | | 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*(DOC))-3', 5'-D(P*GP*TP*CP*GP*G)-3', ... | | Authors: | Batra, V.K, Upton, J, Kashmerov, B, Beard, W.A, Wilson, S.H, Goodman, M.F, McKenna, C.E. | | Deposit date: | 2009-09-04 | | Release date: | 2010-06-02 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Halogenated beta,gamma-Methylene- and Ethylidene-dGTP-DNA Ternary Complexes with DNA Polymerase beta: Structural Evidence for Stereospecific Binding of the Fluoromethylene Analogues.
J.Am.Chem.Soc., 132, 2010
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5VRY
 | | Human DNA polymerase beta 8-oxoG:dC extension with dTTP after 20 s | | Descriptor: | CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*AP*(8OG)P*GP*CP*GP*CP*AP*TP*CP*AP*G)-3'), DNA (5'-D(*CP*TP*GP*AP*TP*GP*CP*GP*CP*CP*T)-3'), ... | | Authors: | Reed, A.J, Suo, Z. | | Deposit date: | 2017-05-11 | | Release date: | 2017-07-19 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Time-Dependent Extension from an 8-Oxoguanine Lesion by Human DNA Polymerase Beta.
J. Am. Chem. Soc., 139, 2017
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