3LK9
| DNA polymerase beta with a gapped DNA substrate and dTMP(CF2)P(CF2)P | Descriptor: | 5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl](difluoro)methyl}(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: | Zibinsky, M, Surya Prakash, G.K, Upton, T.G, Kashemirov, B.A, McKenna, C.E, Oertell, K, Goodman, M.F, Batra, V.K, Pedersen, L.C, Beard, W.A, Wilson, S.H. | Deposit date: | 2010-01-27 | Release date: | 2011-01-12 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Synthesis and biological evaluation of fluorinated deoxynucleotide analogs based on bis-(difluoromethylene)triphosphoric acid. Proc.Natl.Acad.Sci.USA, 107, 2010
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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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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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3JPO
| Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monochloromethylene 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 (2 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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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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4UB1
| DNA polymerase beta product complex with a templating adenine and 8-oxodGMP, 90 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 (2.341 Å) | Cite: | Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide. Nature, 517, 2015
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4UB2
| DNA polymerase beta product complex with a templating cytosine and 8-oxodGMP, 120 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 (2.51 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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4UB4
| DNA polymerase beta substrate complex with a templating cytosine and incoming dGTP, 0 s | Descriptor: | 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, 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', ... | 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 (1.954 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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4UB5
| DNA polymerase beta substrate complex with a templating cytosine, incoming 8-oxodGTP, and Mn2+, 5 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: | 2014-08-11 | Release date: | 2014-11-12 | Last modified: | 2023-09-27 | Method: | X-RAY DIFFRACTION (2.15 Å) | Cite: | Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide. Nature, 517, 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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3MBY
| Ternary complex of DNA Polymerase BETA with template base A and 8oxodGTP in the active site with a dideoxy terminated primer | Descriptor: | 8-OXO-2'-DEOXYGUANOSINE-5'-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, Hou, E.W, Pedersen, L.C, Prasad, R, Wilson, S.H. | Deposit date: | 2010-03-26 | Release date: | 2010-06-09 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Mutagenic conformation of 8-oxo-7,8-dihydro-2'-dGTP in the confines of a DNA polymerase active site. Nat.Struct.Mol.Biol., 17, 2010
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1ZJN
| 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
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1ZJM
| Human DNA Polymerase beta complexed with DNA containing an A-A mismatched primer terminus | Descriptor: | 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3', 5'-D(P*GP*TP*CP*GP*G)-3', DNA polymerase beta, ... | 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 (2.1 Å) | Cite: | Nucleotide-induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate. STRUCTURE, 13, 2005
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4F5O
| Open ternary complex of R283K DNA polymerase beta with a one metal bound 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: | 2012-05-13 | Release date: | 2012-12-12 | Last modified: | 2023-09-13 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly. Structure, 20, 2012
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4F5Q
| Closed ternary complex of R283K DNA polymerase beta | 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(P*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 (2.25 Å) | Cite: | Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly. Structure, 20, 2012
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4GFJ
| Crystal structure of Topo-78, an N-terminal 78kDa fragment of topoisomerase V | Descriptor: | GLYCEROL, Topoisomerase V, ZINC ION | Authors: | Rajan, R, Prasad, R, Taneja, B, Wilson, S.H, Mondragon, A. | Deposit date: | 2012-08-03 | Release date: | 2012-12-05 | Last modified: | 2023-09-13 | Method: | X-RAY DIFFRACTION (2.91 Å) | Cite: | Identification of one of the apurinic/apyrimidinic lyase active sites of topoisomerase V by structural and functional studies. Nucleic Acids Res., 41, 2013
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4F5N
| Open ternary complex of R283K DNA polymerase beta with a metal free 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*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 (1.8 Å) | Cite: | Structures of dNTP Intermediate States during DNA Polymerase Active Site Assembly. Structure, 20, 2012
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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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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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4GXK
| R283K DNA polymerase beta ternary complex with a templating 8OG and incoming dATP analog | Descriptor: | 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine, 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 (1.998 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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