6CUA
 
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7MZ1
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5V1F
 | | DNA polymerase beta substrate complex with 8-oxoG at the primer terminus and incoming dCTP | | Descriptor: | 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, CALCIUM ION, DNA (5'-D(*CP*CP*GP*AP*CP*GP*CP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... | | Authors: | Freudenthal, B.D, Smith, M.R, Schaich, M.A, Whitaker, A.M. | | Deposit date: | 2017-03-02 | | Release date: | 2017-05-10 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (2.181 Å) | | Cite: | Capturing a mammalian DNA polymerase extending from an oxidized nucleotide.
Nucleic Acids Res., 45, 2017
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6CLY
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4RPZ
 | | Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dCTP soaked with MgCl2 for 60 s | | Descriptor: | 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*(8OG)P*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... | | Authors: | Vyas, R, Reed, A.J, Suo, Z. | | Deposit date: | 2014-10-31 | | Release date: | 2015-04-15 | | Last modified: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (2.19 Å) | | Cite: | Viewing Human DNA Polymerase beta Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography.
J.Am.Chem.Soc., 137, 2015
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4YMM
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2FMQ
 | | Sodium in active site of DNA Polymerase Beta | | Descriptor: | 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE, 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', ... | | Authors: | Batra, V.K, Beard, W.A, Shock, D.D, Krahn, J.M, Pedersen, L.C, Wilson, S.H. | | Deposit date: | 2006-01-09 | | Release date: | 2006-04-25 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Magnesium-induced assembly of a complete DNA polymerase catalytic complex.
Structure, 14, 2006
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4GXJ
 | | R283K DNA polymerase beta ternary complex with a templating 8OG and incoming dCTP analog | | Descriptor: | 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine, DNA (5'-D(*CP*CP*GP*AP*CP*(8OG)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3'), ... | | Authors: | Freudenthal, B.D, Beard, W.A, Wilson, S.H. | | Deposit date: | 2012-09-04 | | Release date: | 2013-01-16 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | DNA polymerase minor groove interactions modulate mutagenic bypass of a templating 8-oxoguanine lesion.
Nucleic Acids Res., 41, 2013
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6CTP
 | | Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CH2, beta, gamma dTTP analogue | | Descriptor: | CHLORIDE ION, 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*(DOC))-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 (2.2 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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2ISP
 | | Ternary complex of DNA Polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-methylene triphosphate | | Descriptor: | 2'-DEOXY-5'-O-(HYDROXY{[HYDROXY(PHOSPHONOMETHYL)PHOSPHORYL]OXY}PHOSPHORYL)GUANOSINE, 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', ... | | Authors: | Sucato, C.A, Upton, T.G, Kashemirov, B.A, Martinek, V, Xiang, Y, Beard, W.A. | | Deposit date: | 2006-10-18 | | Release date: | 2007-01-30 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Modifying the beta,gamma Leaving-Group Bridging Oxygen Alters Nucleotide Incorporation Efficiency, Fidelity, and the Catalytic Mechanism of DNA Polymerase beta.
Biochemistry, 46, 2007
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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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5J29
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5J0P
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7RBK
 | | Human DNA polymerase beta crosslinked complex, 40 s Ca to Mg exchange | | Descriptor: | 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, 2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol, DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*CP*C)-3'), ... | | Authors: | Kumar, A. | | Deposit date: | 2021-07-06 | | Release date: | 2022-03-09 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.2 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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5J2J
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4RQ2
 | | Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine (8-oxoG)and dCTP soaked with MnCl2 for 35 s | | Descriptor: | ACETATE ION, DNA (5'-D(*CP*CP*GP*AP*CP*(8OG)P*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: | Vyas, R, Reed, A.J, Suo, Z. | | Deposit date: | 2014-10-31 | | Release date: | 2015-04-15 | | Last modified: | 2023-09-20 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Viewing Human DNA Polymerase beta Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography.
J.Am.Chem.Soc., 137, 2015
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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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5VRX
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4F5R
 | | Open and closed ternary complex of R283K DNA polymerase beta with a dCTP analog in the same asymmetric unit | | Descriptor: | 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine, 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 (2.2 Å) | | Cite: | Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly.
Structure, 20, 2012
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4RQ0
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1BPY
 | | HUMAN DNA POLYMERASE BETA COMPLEXED WITH GAPPED DNA AND DDCTP | | Descriptor: | 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE, 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*DOC)-3'), ... | | Authors: | Sawaya, M.R, Pelletier, H, Prasad, R, Wilson, S.H, Kraut, J. | | Deposit date: | 1997-04-15 | | Release date: | 1997-06-16 | | Last modified: | 2023-08-02 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism.
Biochemistry, 36, 1997
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6BTE
 | | DNA Polymerase Beta I260Q Binary Complex | | Descriptor: | CHLORIDE ION, DNA Downstream Strand, DNA Primer Strand, ... | | Authors: | Eckenroth, B.E, Doublie, S. | | Deposit date: | 2017-12-06 | | Release date: | 2018-09-26 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | I260Q DNA polymerase beta highlights precatalytic conformational rearrangements critical for fidelity.
Nucleic Acids Res., 46, 2018
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3RJH
 | | Ternary complex of DNA Polymerase Beta with a gapped DNA containing (syn)8odG:dA at primer terminus and dG:dCMP(CF2)PPin the active site | | Descriptor: | 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]cytidine, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*GP*(8OG)P*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... | | Authors: | Batra, V.K, Beard, W.A, Wilson, S.H. | | Deposit date: | 2011-04-15 | | Release date: | 2012-01-18 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Binary complex crystal structure of DNA polymerase beta reveals multiple conformations of the templating 8-oxoguanine lesion
Proc.Natl.Acad.Sci.USA, 109, 2012
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5WNZ
 | | DNA polymerase beta substrate complex with incoming 5-FodCTP | | Descriptor: | 2'-deoxy-5-formylcytidine 5'-(tetrahydrogen triphosphate), CALCIUM ION, CHLORIDE ION, ... | | Authors: | Schaich, M.A, Smith, M.R, Cloud, A.S, Holloran, S.M, Freudenthal, B.D. | | Deposit date: | 2017-08-01 | | Release date: | 2017-09-13 | | Last modified: | 2023-10-04 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Structures of a DNA Polymerase Inserting Therapeutic Nucleotide Analogues.
Chem. Res. Toxicol., 30, 2017
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5DB7
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