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
|
|
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
|
|
4GXI
| R283K DNA polymerase beta binary complex with a templating 8OG | Descriptor: | 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'), DNA (5'-D(P*GP*TP*CP*GP*G)-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 (1.949 Å) | Cite: | DNA polymerase minor groove interactions modulate mutagenic bypass of a templating 8-oxoguanine lesion. Nucleic Acids Res., 41, 2013
|
|
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
|
|
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
|
|
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
|
|
4KLT
| DNA polymerase beta mismatched product complex with Mn2+, 30 min | 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*A)-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 (1.979 Å) | Cite: | Observing a DNA polymerase choose right from wrong. Cell(Cambridge,Mass.), 154, 2013
|
|
4KLL
| DNA polymerase beta matched product complex with Mg2+, 45 min | 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 (1.841 Å) | Cite: | Observing a DNA polymerase choose right from wrong. Cell(Cambridge,Mass.), 154, 2013
|
|
4KLU
| DNA polymerase beta mismatched product complex with Mn2+, 15 h | 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*A)-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 (1.97 Å) | Cite: | Observing a DNA polymerase choose right from wrong. Cell(Cambridge,Mass.), 154, 2013
|
|
4KLJ
| DNA polymerase beta matched product complex with Mg2+, 5 min | 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 (1.799 Å) | Cite: | Observing a DNA polymerase choose right from wrong. Cell(Cambridge,Mass.), 154, 2013
|
|
4KLQ
| Observing a DNA polymerase choose right from wrong. | Descriptor: | 2'-DEOXYADENOSINE 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*A)-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 (1.999 Å) | Cite: | Observing a DNA polymerase choose right from wrong. Cell(Cambridge,Mass.), 154, 2013
|
|
4KLD
| DNA polymerase beta matched substrate complex with Ca2+, 0 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*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 (1.916 Å) | Cite: | Observing a DNA polymerase choose right from wrong. Cell(Cambridge,Mass.), 154, 2013
|
|
4KLE
| DNA polymerase beta matched reactant complex with Mg2+, 10 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 (1.97 Å) | Cite: | Observing a DNA polymerase choose right from wrong. Cell(Cambridge,Mass.), 154, 2013
|
|
4KLO
| DNA polymerase beta matched nick complex with Mg2+ and PPi, 30 min | 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 (1.845 Å) | Cite: | Observing a DNA polymerase choose right from wrong. Cell(Cambridge,Mass.), 154, 2013
|
|
4KLS
| DNA polymerase beta mismatched reactant complex with Mn2+, 10 min | Descriptor: | 2'-DEOXYADENOSINE 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*A)-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 (1.978 Å) | Cite: | Observing a DNA polymerase choose right from wrong. Cell(Cambridge,Mass.), 154, 2013
|
|
4KLG
| DNA polymerase beta matched product complex with Mg2+, 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 (1.701 Å) | Cite: | Observing a DNA polymerase choose right from wrong. Cell(Cambridge,Mass.), 154, 2013
|
|
4KLM
| DNA polymerase beta matched product complex with Mg2+, 11 h | 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 (1.747 Å) | Cite: | Observing a DNA polymerase choose right from wrong. Cell(Cambridge,Mass.), 154, 2013
|
|
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
|
|
4KLI
| DNA polymerase beta matched product complex with Mg2+, 90 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 (1.597 Å) | Cite: | Observing a DNA polymerase choose right from wrong. Cell(Cambridge,Mass.), 154, 2013
|
|
4LVS
| DNA polymerase beta mismatched substrate complex with Mn2+, 2.5 min | Descriptor: | 2'-DEOXYADENOSINE 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*C)-3'), ... | Authors: | Freudenthal, B.D, Beard, W.A, Shock, D.D, Wilson, S.H. | Deposit date: | 2013-07-26 | Release date: | 2013-09-04 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (2.002 Å) | Cite: | Observing a DNA polymerase choose right from wrong. Cell(Cambridge,Mass.), 154, 2013
|
|
6DIA
| DNA polymerase beta substrate complex with templating cytosine and incoming Fapy-dGTP analog | Descriptor: | 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, DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), ... | Authors: | Freudenthal, B.D, Smith, M.R, Wilson, S.H, Beard, W.A. | Deposit date: | 2018-05-23 | Release date: | 2019-01-30 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (1.969 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
|
|
6DIC
| D276G DNA polymerase beta substrate complex with templating cytosine and incoming Fapy-dGTP analog | Descriptor: | 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, CHLORIDE ION, ... | Authors: | Freudenthal, B.D, Smith, M.R, Wilson, S.H, Beard, W.A. | Deposit date: | 2018-05-23 | Release date: | 2019-01-30 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (1.992 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
|
|
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
|
|
6MR7
| 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 (2.144 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
|
|
7LPH
| APE1 Mn-bound product complex with abasic ribonucleotide DNA | Descriptor: | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-R(P*N)-D(P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), ... | Authors: | Freudenthal, B.D, Hoitsma, N.M. | Deposit date: | 2021-02-11 | Release date: | 2021-08-04 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (1.99 Å) | Cite: | Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker. Comput Struct Biotechnol J, 19, 2021
|
|