5ODJ
 
 | | Single-stranded DNA-binding protein from bacteriophage Enc34 | | Descriptor: | CHLORIDE ION, MAGNESIUM ION, Single-stranded DNA-binding protein | | Authors: | Cernooka, E, Rumnieks, J, Kazaks, A, Tars, K. | | Deposit date: | 2017-07-05 | | Release date: | 2017-10-25 | | Last modified: | 2017-11-29 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Structural Basis for DNA Recognition of a Single-stranded DNA-binding Protein from Enterobacter Phage Enc34.
Sci Rep, 7, 2017
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4FLY
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1JXL
 | | Crystal Structure of a Y-Family DNA Polymerase in a Ternary Complex with DNA Substrates and an Incoming Nucleotide | | Descriptor: | 1,2-ETHANEDIOL, 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*T)-3', ... | | Authors: | Ling, H, Boudsocq, F, Woodgate, R, Yang, W. | | Deposit date: | 2001-09-07 | | Release date: | 2001-10-05 | | Last modified: | 2023-08-16 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication.
Cell(Cambridge,Mass.), 107, 2001
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1JX4
 | | Crystal Structure of a Y-family DNA Polymerase in a Ternary Complex with DNA Substrates and an Incoming Nucleotide | | Descriptor: | 2',3'-DIDEOXYADENOSINE-5'-DIPHOSPHATE, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-3', 5'-D(*T*TP*CP*AP*TP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3', ... | | Authors: | Ling, H, Boudsocq, F, Woodgate, R, Yang, W. | | Deposit date: | 2001-09-05 | | Release date: | 2001-10-05 | | Last modified: | 2011-11-16 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication.
Cell(Cambridge,Mass.), 107, 2001
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1QTM
 | | DDTTP-TRAPPED CLOSED TERNARY COMPLEX OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS | | Descriptor: | 5'-D(*AP*AP*AP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3', 5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(2DT))-3', DNA POLYMERASE I, ... | | Authors: | Li, Y, Mitaxov, V, Waksman, G. | | Deposit date: | 1999-06-28 | | Release date: | 1999-08-16 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structure-based design of Taq DNA polymerases with improved properties of dideoxynucleotide incorporation.
Proc.Natl.Acad.Sci.USA, 96, 1999
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6S48
 | | AvaII RESTRICTION ENDONUCLEASE IN COMPLEX WITH PARTIALLY CLEAVED dsDNA | | Descriptor: | BETA-MERCAPTOETHANOL, CALCIUM ION, DNA (5'-D(*GP*AP*TP*G)-3'), ... | | Authors: | Kisiala, M, Kowalska, M, Korza, H, Czapinska, H, Bochtler, M. | | Deposit date: | 2019-06-26 | | Release date: | 2020-05-20 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation.
Nucleic Acids Res., 48, 2020
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6P4F
 | | Crystal structure of the XPB-Bax1-forked DNA ternary complex | | Descriptor: | CHLORIDE ION, DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*AP*AP*CP*AP*TP*CP*CP*TP*TP*TP*GP*CP*TP*AP*CP*AP*A)-3'), DNA (5'-D(P*TP*GP*TP*AP*GP*GP*TP*TP*TP*CP*CP*AP*TP*GP*TP*TP*GP*AP*GP*TP*CP*A)-3'), ... | | Authors: | He, F, Hilario, E, Fan, L. | | Deposit date: | 2019-05-27 | | Release date: | 2020-06-17 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (3.55 Å) | | Cite: | Structural basis of the XPB helicase-Bax1 nuclease complex interacting with the repair bubble DNA.
Nucleic Acids Res., 48, 2020
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3SPY
 | | RB69 DNA Polymerase(L415A/L561A/S565G/Y567A) Ternary Complex with dUpCpp Opposite dA | | Descriptor: | 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]uridine, 5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3', 5'-D(*TP*CP*GP*AP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3', ... | | Authors: | Xia, S, Konigsberg, W.H, Wang, J. | | Deposit date: | 2011-07-04 | | Release date: | 2011-10-12 | | Last modified: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (2.14 Å) | | Cite: | Structural Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase.
Biochemistry, 50, 2011
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3SI6
 | | RB69 DNA Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with dUpNpp and a Deoxy-terminated Primer in the presence of Mg2+ | | Descriptor: | 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE, 5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3', 5'-D(*TP*CP*AP*AP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3', ... | | Authors: | Wang, M, Wang, J, Konigsberg, W.H. | | Deposit date: | 2011-06-17 | | Release date: | 2011-10-12 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Structural Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase.
Biochemistry, 50, 2011
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3SQ1
 | | RB69 DNA Polymerase Ternary Complex with dUpCpp Opposite dA | | Descriptor: | 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE, 5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3', 5'-D(*TP*CP*GP*AP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3', ... | | Authors: | Xia, S, Konigsberg, W.H, Wang, J. | | Deposit date: | 2011-07-04 | | Release date: | 2011-10-12 | | Last modified: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (1.82 Å) | | Cite: | Structural Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase.
Biochemistry, 50, 2011
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5KK5
 | | AsCpf1(E993A)-crRNA-DNA ternary complex | | Descriptor: | CRISPR-associated endonuclease Cpf1, DNA (28-MER), DNA (8-mer), ... | | Authors: | Gao, P, Yang, H, Rajashankar, K.R, Huang, Z, Patel, D.J. | | Deposit date: | 2016-06-21 | | Release date: | 2016-08-10 | | Last modified: | 2024-03-06 | | Method: | X-RAY DIFFRACTION (3.289 Å) | | Cite: | Type V CRISPR-Cas Cpf1 endonuclease employs a unique mechanism for crRNA-mediated target DNA recognition.
Cell Res., 26, 2016
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3L9Q
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3SJJ
 | | RB69 DNA Polymerase Triple Mutant (L561A/S565G/Y567A) Ternary Complex with dUpNpp and a Deoxy-terminated Primer in the presence of Mn2+ | | Descriptor: | 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE, 5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3', 5'-D(*TP*CP*AP*AP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3', ... | | Authors: | Wang, M, Wang, J, Konigsberg, W.H. | | Deposit date: | 2011-06-21 | | Release date: | 2011-10-12 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (2.38 Å) | | Cite: | Structural Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase.
Biochemistry, 50, 2011
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1SKS
 | | Binary 3' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn thymine dimer on the template | | Descriptor: | 5'-D(*CP*CP*CP*(TTD)P*AP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3', 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*C*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*(2DT))-3', DNA polymerase, ... | | Authors: | Li, Y, Dutta, S, Doublie, S, Bdour, H.M, Taylor, J.S, Ellenberger, T. | | Deposit date: | 2004-03-05 | | Release date: | 2004-07-06 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7.
Nat.Struct.Mol.Biol., 11, 2004
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1SL1
 | | Binary 5' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn thymine dimer on the template | | Descriptor: | 5'-D(*CP*CP*C*(TTD)P*AP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3', 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*TP*(2DA))-3', DNA polymerase, ... | | Authors: | Li, Y, Dutta, S, Doublie, S, Bdour, H.M, Taylor, J.S, Ellenberger, T. | | Deposit date: | 2004-03-05 | | Release date: | 2004-07-06 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7.
Nat.Struct.Mol.Biol., 11, 2004
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1SKR
 | | T7 DNA Polymerase Complexed To DNA Primer/Template and ddATP | | Descriptor: | 2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE, 5'-D(*CP*CP*CP*TP*TP*TP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3', 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*C*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*AP*(2DA))-3', ... | | Authors: | Li, Y, Dutta, S, Doublie, S, Bdour, H.M, Taylor, J.S, Ellenberger, T. | | Deposit date: | 2004-03-05 | | Release date: | 2004-07-06 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7.
Nat.Struct.Mol.Biol., 11, 2004
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1SL2
 | | Ternary 5' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn thymine dimer on the template and an incoming nucleotide | | Descriptor: | 2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE, 5'-D(*CP*CP*CP*(TTD)P*AP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3', 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*TP*(2DA))-3', ... | | Authors: | Li, Y, Dutta, S, Doublie, S, Bdour, H.M, Taylor, J.S, Ellenberger, T. | | Deposit date: | 2004-03-05 | | Release date: | 2004-07-06 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7.
Nat.Struct.Mol.Biol., 11, 2004
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1SKW
 | | Binary 3' complex of T7 DNA polymerase with a DNA primer/template containing a disordered cis-syn thymine dimer on the template | | Descriptor: | 5'-D(*CP*CP*CP*(TTD)P*AP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3', 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*C*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*(2DT))-3', DNA polymerase, ... | | Authors: | Li, Y, Dutta, S, Doublie, S, Bdour, H.M, Taylor, J.S, Ellenberger, T. | | Deposit date: | 2004-03-05 | | Release date: | 2004-07-06 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7.
Nat.Struct.Mol.Biol., 11, 2004
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7OLB
 | | Crystal structure of Pab-AGOG, an 8-oxoguanine DNA glycosylase from Pyrococcus abyssi | | Descriptor: | 1,2-ETHANEDIOL, CHLORIDE ION, CITRIC ACID, ... | | Authors: | Coste, F, Goffinont, S, Flament, D, Castaing, B. | | Deposit date: | 2021-05-19 | | Release date: | 2022-06-01 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (1.1 Å) | | Cite: | Structural and functional determinants of the archaeal 8-oxoguanine-DNA glycosylase AGOG for DNA damage recognition and processing.
Nucleic Acids Res., 50, 2022
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3SCX
 | | RB69 DNA Polymerase Triple Mutant(L561A/S565G/Y567A) Ternary Complex with dUpNpp and a Deoxy-terminated Primer in the Presence of Ca2+ | | Descriptor: | 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE, 5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3', 5'-D(*TP*CP*AP*AP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3', ... | | Authors: | Wang, M, Wang, J, Konigsberg, W.H. | | Deposit date: | 2011-06-08 | | Release date: | 2011-10-12 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (2.35 Å) | | Cite: | Structural Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase.
Biochemistry, 50, 2011
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7OU3
 | | Crystal structure of Tga-AGOG, an 8-oxoguanine DNA glycosylase from Thermococcus gammatolerans | | Descriptor: | CHLORIDE ION, GLYCEROL, N-glycosylase/DNA lyase | | Authors: | Coste, F, Confalonieri, F, Castaing, B. | | Deposit date: | 2021-06-11 | | Release date: | 2022-06-22 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (1.49 Å) | | Cite: | Structural and functional determinants of the archaeal 8-oxoguanine-DNA glycosylase AGOG for DNA damage recognition and processing.
Nucleic Acids Res., 50, 2022
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1SL0
 | | Ternary 3' complex of T7 DNA polymerase with a DNA primer/template containing a disordered cis-syn thymine dimer on the template and an incoming nucleotide | | Descriptor: | 2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE, 5'-D(*CP*CP*CP*(TTD)P*AP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP*CP*G)-3', 5'-D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*(2DT))-3', ... | | Authors: | Li, Y, Dutta, S, Doublie, S, Bdour, H.M, Taylor, J.S, Ellenberger, T. | | Deposit date: | 2004-03-05 | | Release date: | 2004-07-06 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Nucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7.
Nat.Struct.Mol.Biol., 11, 2004
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3UIQ
 | | RB69 DNA Polymerase Ternary Complex containing dUpNpp | | Descriptor: | 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE, 5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*C)-3', 5'-D(*TP*CP*GP*AP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3', ... | | Authors: | Xia, S, Konigsberg, W.H, Wang, J. | | Deposit date: | 2011-11-05 | | Release date: | 2012-04-18 | | Last modified: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (1.879 Å) | | Cite: | Bidentate and tridentate metal-ion coordination states within ternary complexes of RB69 DNA polymerase.
Protein Sci., 21, 2012
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7TVE
 | | ATP and DNA bound SMC5/6 core complex | | Descriptor: | ADENOSINE-5'-TRIPHOSPHATE, DNA (68-MER), DNA (78-MER), ... | | Authors: | Yu, Y, Patel, D.J. | | Deposit date: | 2022-02-04 | | Release date: | 2022-06-22 | | Last modified: | 2024-02-21 | | Method: | ELECTRON MICROSCOPY (3.8 Å) | | Cite: | Cryo-EM structure of DNA-bound Smc5/6 reveals DNA clamping enabled by multi-subunit conformational changes.
Proc.Natl.Acad.Sci.USA, 119, 2022
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4DFM
 | | Crystal structure of the large fragment of DNA polymerase I from Thermus aquaticus in ternary complex with 5-(aminopentinyl)-2-dCTP | | Descriptor: | 1,2-ETHANEDIOL, 5'-d(AAAGCGCGCCGTGGTC)-3', 5'-d(GACCACGGCGC ddG)-3', ... | | Authors: | Bergen, K, Steck, A, Struett, S, Baccaro, A, Welte, W, Diederichs, K, Marx, A. | | Deposit date: | 2012-01-24 | | Release date: | 2012-05-16 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (1.886 Å) | | Cite: | Structures of KlenTaq DNA Polymerase Caught While Incorporating C5-Modified Pyrimidine and C7-Modified 7-Deazapurine Nucleoside Triphosphates.
J.Am.Chem.Soc., 134, 2012
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