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PDB: 413 results
4YMN
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BU of 4ymn by Molmil
Structure of human DNA polymerase beta complexed with N7BG in the template base paired with incoming non-hydrolyzable CTP
Descriptor: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine, DNA 10-mer (up-primer), DNA 16-mer (template), ...
Authors:Lee, S, Koag, M.-C.
Deposit date:2015-03-06
Release date:2016-03-09
Last modified:2024-02-28
Method:X-RAY DIFFRACTION (2.591 Å)
Cite:Structural and kinetic studies of the effect of guanine-N7 alkylation and metal cofactors on DNA replication.
Biochemistry, 2018
1TVA
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BU of 1tva by Molmil
HUMAN DNA POLYMERASE BETA COMPLEXED WITH NICKED DNA CONTAINING A MISMATCHED TEMPLATE THYMIDINE AND INCOMING CYTIDINE
Descriptor: 5'-D(*CP*CP*GP*AP*CP*TP*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:Krahn, J.M, Beard, W.A, Wilson, S.H.
Deposit date:2004-06-29
Release date:2004-11-23
Last modified:2024-02-14
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Structural insights into DNA polymerase Beta deterrents for misincorporation support an induced-fit mechanism for fidelity
Structure, 12, 2004
9ICX
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BU of 9icx by Molmil
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA (NON GAPPED DNA ONLY)
Descriptor: DNA (5'-D(*CP*AP*GP*AP*TP*G)-3'), DNA (5'-D(*CP*AP*TP*CP*TP*G)-3'), PROTEIN (DNA POLYMERASE BETA (E.C.2.7.7.7)), ...
Authors:Pelletier, H, Sawaya, M.R.
Deposit date:1996-10-24
Release date:1996-11-15
Last modified:2023-08-02
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Crystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, processivity, and fidelity
Biochemistry, 35, 1996
9ICW
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BU of 9icw by Molmil
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SIX BASE PAIRS OF DNA; NATIVE STRUCTURE
Descriptor: DNA (5'-D(*CP*AP*GP*AP*TP*G)-3'), DNA (5'-D(*CP*AP*TP*CP*TP*GP*T)-3'), PROTEIN (DNA POLYMERASE BETA (E.C.2.7.7.7)), ...
Authors:Pelletier, H, Sawaya, M.R.
Deposit date:1995-12-16
Release date:1996-11-15
Last modified:2023-08-02
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Crystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, processivity, and fidelity
Biochemistry, 35, 1996
6NKT
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BU of 6nkt by Molmil
Ternary complex crystal structure of K289M variant of DNA polymerase Beta with beta-gamma difluoro analogue of dGTP
Descriptor: 2'-DEOXY-5'-O-[({[DIFLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL}OXY)(HYDROXY)PHOSPHORYL]GUANOSINE, DNA (5'-D(*CP*CP*GP*AP*CP*CP*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:2019-01-07
Release date:2020-01-08
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Revealing an Internal Stabilization Deficiency in the DNA Polymerase beta K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography.
Biochemistry, 59, 2020
1BPZ
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BU of 1bpz by Molmil
HUMAN DNA POLYMERASE BETA COMPLEXED WITH NICKED DNA
Descriptor: DNA (5'-D(*CP*CP*GP*AP*CP*CP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*G)-3'), DNA (5'-D(*GP*TP*CP*GP*G)-3'), ...
Authors:Sawaya, M.R, Prasad, R, Wilson, S.H, Kraut, J, Pelletier, H.
Deposit date:1997-04-14
Release date:1997-06-16
Last modified:2023-08-02
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism.
Biochemistry, 36, 1997
3C2L
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BU of 3c2l by Molmil
Ternary complex of DNA POLYMERASE BETA with a C:DAPCPP mismatch in the active site
Descriptor: 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine, DNA (5'-D(*DCP*DCP*DGP*DAP*DCP*DCP*DGP*DCP*DGP*DCP*DAP*DTP*DCP*DAP*DGP*DC)-3'), DNA (5'-D(*DGP*DCP*DTP*DGP*DAP*DTP*DGP*DCP*DGP*DC)-3'), ...
Authors:Batra, V.K, Beard, W.A, Shock, D.D, Pedersen, L.C, Wilson, S.H.
Deposit date:2008-01-25
Release date:2008-05-20
Last modified:2023-08-30
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation.
Mol.Cell, 30, 2008
4PHP
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BU of 4php by Molmil
Structure of human DNA polymerase beta complexed with T in the template base paired with incoming non-hydrolyzable GTP and MANGANESE
Descriptor: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine, DNA (5'-D(*CP*CP*GP*AP*CP*TP*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:Koag, M.C, Lee, S.
Deposit date:2014-05-06
Release date:2015-05-06
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:The spontaneous base substitution mechanisms of human DNA polymerase beta
To Be Published
6PH6
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BU of 6ph6 by Molmil
Ternary complex crystal structure of DNA polymerase Beta with 2nt-gap with dCTP bound downstream
Descriptor: 2'-DEOXYCYTIDINE-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*G)-3'), ...
Authors:Batra, V.K, Wilson, S.H.
Deposit date:2019-06-25
Release date:2019-12-11
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:DNA polymerase beta nucleotide-stabilized template misalignment fidelity depends on local sequence context.
J.Biol.Chem., 295, 2020
7MZ8
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BU of 7mz8 by Molmil
Structure of human DNA polymerase beta complexed with 3-deaza-3-methyladenine (3dMeA) at N-1 of the template base paired with incoming dTTP
Descriptor: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine, DNA (5'-D(*CP*CP*GP*AP*CP*GP*(DZM)P*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*T)-3'), ...
Authors:Koag, M.-C, Lee, S.
Deposit date:2021-05-24
Release date:2022-06-01
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Structure Of Human Dna Polymerase Beta Complexed With 8Oa As The Template Base In A 1-Nucleotide Gapped Dna
To Be Published
3ISD
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BU of 3isd by Molmil
Ternary complex of human DNA polymerase beta with an abasic site (THF): DAPCPP mismatch
Descriptor: 1,2-ETHANEDIOL, 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine, 5'-D(*CP*CP*GP*AP*CP*(3DR)P*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', ...
Authors:Beard, W.A, Shock, D.D, Batra, V.K, Pedersen, L.C, Wilson, S.H.
Deposit date:2009-08-25
Release date:2009-09-15
Last modified:2023-09-06
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:DNA polymerase beta substrate specificity: side chain modulation of the "A-rule".
J.Biol.Chem., 284, 2009
6N2T
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BU of 6n2t by Molmil
Ternary complex crystal structure of DNA polymerase Beta with 5-hydroxymethyl-dC (5-hmC) at the templating position
Descriptor: 2'-deoxy-5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine, DNA (5'-D(*CP*CP*GP*AP*CP*(5HC)P*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:Batra, V.K, Wilson, S.H.
Deposit date:2018-11-14
Release date:2019-03-27
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Molecular basis for the faithful replication of 5-methylcytosine and its oxidized forms by DNA polymerase beta.
J.Biol.Chem., 294, 2019
6PH5
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BU of 6ph5 by Molmil
Binary product complex crystal structure of DNA polymerase Beta with an extra-helical template base
Descriptor: DNA (5'-D(*CP*CP*GP*AP*CP*GP*CP*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'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ...
Authors:Batra, V.K, Wilson, S.H.
Deposit date:2019-06-25
Release date:2019-12-11
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (2.602 Å)
Cite:DNA polymerase beta nucleotide-stabilized template misalignment fidelity depends on local sequence context.
J.Biol.Chem., 295, 2020
1ZJN
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BU of 1zjn by Molmil
Human DNA Polymerase beta complexed with DNA containing an A-A mismatched primer terminus with dGTP
Descriptor: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3', 5'-D(P*GP*TP*CP*GP*G)-3', ...
Authors:Batra, V.K, Beard, W.A, Shock, D.D, Pedersen, L.C, Wilson, S.H.
Deposit date:2005-04-29
Release date:2005-08-16
Last modified:2023-08-23
Method:X-RAY DIFFRACTION (2.61 Å)
Cite:Nucleotide-induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate.
STRUCTURE, 13, 2005
5V1J
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BU of 5v1j by Molmil
DNA polymerase beta open product complex with 8-oxoG:C and inserted dCTP
Descriptor: DNA (5'-D(*CP*CP*GP*AP*CP*GP*CP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(8OG)P*C)-3'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ...
Authors:Freudenthal, B.D, Smith, M.R, Whitaker, A.M, Schaich, M.A.
Deposit date:2017-03-02
Release date:2017-05-10
Last modified:2024-03-06
Method:X-RAY DIFFRACTION (2.616 Å)
Cite:Capturing a mammalian DNA polymerase extending from an oxidized nucleotide.
Nucleic Acids Res., 45, 2017
8VFB
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BU of 8vfb by Molmil
Ternary 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 (2.64 Å)
Cite:Biochemical and structural characterization of Fapy•dG replication by Human DNA polymerase beta.
Nucleic Acids Res., 52, 2024
6E3X
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BU of 6e3x by Molmil
Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable ATP
Descriptor: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine, DNA (5'-D(*CP*CP*GP*AP*CP*(A38) 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:Koag, M.-C, Lee, S.
Deposit date:2018-07-15
Release date:2019-04-03
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (2.65 Å)
Cite:Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable ATP
To Be Published
4Z6C
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BU of 4z6c by Molmil
Structure of human DNA polymerase beta 279NA mutant complexed with G in the template base paired with incoming non-hydrolyzable CTP
Descriptor: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine, DNA (5'-D(*CP*CP*GP*AP*CP*GP*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:Koag, M.-C, Lee, S.
Deposit date:2015-04-04
Release date:2016-04-13
Last modified:2023-09-27
Method:X-RAY DIFFRACTION (2.677 Å)
Cite:Insights into the effect of minor groove interactions and metal cofactors on mutagenic replication by human DNA polymerase beta.
Biochem. J., 475, 2018
4NLZ
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BU of 4nlz by Molmil
Structure of human DNA polymerase beta complexed with nicked DNA containing a mismatched template 8BrG and incoming GTP
Descriptor: 5'-D(*CP*CP*GP*AP*CP*(BGM)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3', 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*AP*G)-3', 5'-D(P*GP*TP*CP*GP*G)-3', ...
Authors:Koag, M.-C, Min, K, Monzingo, A.F, Lee, S.
Deposit date:2013-11-14
Release date:2014-01-22
Last modified:2024-02-28
Method:X-RAY DIFFRACTION (2.683 Å)
Cite:Structural basis for promutagenicity of 8-halogenated Guanine.
J.Biol.Chem., 289, 2014
9ICK
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BU of 9ick by Molmil
DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF ARTIFICIAL MOTHER LIQUOR
Descriptor: DNA (5'-D(*CP*AP*GP*AP*TP*G)-3'), DNA (5'-D(*CP*AP*TP*CP*TP*GP*T)-3'), PROTEIN (DNA POLYMERASE BETA (E.C.2.7.7.7)), ...
Authors:Pelletier, H, Sawaya, M.R.
Deposit date:1995-12-16
Release date:1996-11-15
Last modified:2023-08-02
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta
Biochemistry, 35, 1996
9ICV
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BU of 9icv by Molmil
DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX + 2'-DEOXYADENOSINE-5'-TRIPHOSPHATE, SOAKED IN THE PRESENCE OF DATP AND ZNCL2
Descriptor: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*A)-3'), DNA (5'-D(*TP*CP*TP*AP*AP*TP*GP*A)-3'), ...
Authors:Pelletier, H, Sawaya, M.R.
Deposit date:1995-12-16
Release date:1996-11-15
Last modified:2023-08-02
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta
Biochemistry, 35, 1996
4RQ1
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BU of 4rq1 by Molmil
Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine(8-oxoG) and dCTP soaked with MgCl2 for 1hr
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, Suo, Z.
Deposit date:2014-10-31
Release date:2015-04-15
Last modified:2023-09-20
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Viewing Human DNA Polymerase beta Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography.
J.Am.Chem.Soc., 137, 2015
1ZQI
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BU of 1zqi by Molmil
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF KCL (150 MILLIMOLAR)
Descriptor: DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*A)-3'), DNA (5'-D(*TP*CP*TP*AP*AP*TP*G)-3'), POTASSIUM ION, ...
Authors:Pelletier, H, Sawaya, M.R.
Deposit date:1996-04-12
Release date:1996-11-15
Last modified:2023-08-02
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis.
Biochemistry, 35, 1996
8ICO
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BU of 8ico by Molmil
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF AZT-TP (1 MILLIMOLAR) AND MNCL2 (5 MILLIMOLAR)
Descriptor: 3'-AZIDO-3'-DEOXYTHYMIDINE-5'-TRIPHOSPHATE, DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*A)-3'), DNA (5'-D(*TP*CP*TP*AP*AP*TP*G)-3'), ...
Authors:Pelletier, H, Sawaya, M.R.
Deposit date:1995-12-15
Release date:1996-11-15
Last modified:2023-08-02
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta.
Biochemistry, 35, 1996
8ICK
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BU of 8ick by Molmil
DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR), MGCL2 (5 MILLIMOLAR), AND MNCL2 (5 MILLIMOLAR)
Descriptor: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, DNA (5'-D(*CP*AP*TP*TP*AP*GP*AP*A)-3'), DNA (5'-D(*TP*CP*TP*AP*AP*TP*GP*A)-3'), ...
Authors:Pelletier, H, Sawaya, M.R.
Deposit date:1996-04-19
Release date:1996-11-15
Last modified:2023-08-02
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta.
Biochemistry, 35, 1996

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