3RJF
 
 | | Ternary complex of DNA Polymerase Beta with a gapped DNA containing (syn)8odG at template position paired with non-hydrolyzable dATP analog (dApCPP) | | Descriptor: | 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine, CHLORIDE ION, DNA (5'-D(*CP*CP*GP*AP*CP*(8OG)P*TP*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 (2.3 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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5TVP
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4DQQ
 | | Ternary complex of Bacillus DNA Polymerase I Large Fragment E658A, DNA duplex, and rCTP (paired with dG of template) in presence of Mg2+ | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, CYTIDINE-5'-TRIPHOSPHATE, ... | | Authors: | Wang, W, Beese, L.S. | | Deposit date: | 2012-02-16 | | Release date: | 2012-06-06 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (1.595 Å) | | Cite: | Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides.
J.Biol.Chem., 287, 2012
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4DQS
 | | Binary complex of Bacillus DNA Polymerase I Large Fragment and duplex DNA with rC in primer terminus paired with dG of template | | Descriptor: | CYTIDINE-5'-TRIPHOSPHATE, DNA (5'-D(*GP*A*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'), DNA polymerase, ... | | Authors: | Wang, W, Beese, L.S. | | Deposit date: | 2012-02-16 | | Release date: | 2012-06-06 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (1.66 Å) | | Cite: | Structural factors that determine selectivity of a high fidelity DNA polymerase for deoxy-, dideoxy-, and ribonucleotides.
J.Biol.Chem., 287, 2012
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1UA0
 | | Aminofluorene DNA adduct at the pre-insertion site of a DNA polymerase | | Descriptor: | 2-AMINOFLUORENE, DNA polymerase I, DNA primer strand, ... | | Authors: | Hsu, G.W, Kiefer, J.R, Becherel, O.J, Fuchs, R.P.P, Beese, L.S. | | Deposit date: | 2004-08-11 | | Release date: | 2004-09-28 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Observing translesion synthesis of an aromatic amine DNA adduct by a high-fidelity DNA polymerase
J.Biol.Chem., 279, 2004
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6ISF
 | | Structure of 9N-I DNA polymerase incorporation with dT in the active site | | Descriptor: | CALCIUM ION, DNA (5'-D(*AP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3'), DNA (5'-D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*T)-3'), ... | | Authors: | Linwu, S.W, Maestre-Reyna, M, Tsai, M.D, Tu, Y.H, Chang, W.H. | | Deposit date: | 2018-11-16 | | Release date: | 2019-08-28 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Thermococcus sp. 9°N DNA polymerase exhibits 3'-esterase activity that can be harnessed for DNA sequencing.
Commun Biol, 2, 2019
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6ISH
 | | Structure of 9N-I DNA polymerase incorporation with 3'-AL in the active site | | Descriptor: | CALCIUM ION, DNA (5'-D(*AP*CP*TP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*C)-3'), DNA (5'-D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*(DAL))-3'), ... | | Authors: | Linwu, S.W, Maestre-Reyna, M, Tsai, M.D, Tu, Y.H, Chang, W.H. | | Deposit date: | 2018-11-16 | | Release date: | 2019-08-28 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (3.3 Å) | | Cite: | Thermococcus sp. 9°N DNA polymerase exhibits 3'-esterase activity that can be harnessed for DNA sequencing.
Commun Biol, 2, 2019
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3EYZ
 | | Cocrystal structure of Bacillus fragment DNA polymerase I with duplex DNA (open form) | | Descriptor: | 5'-D(*DAP*DTP*DGP*DCP*DGP*DAP*DGP*DTP*DCP*DAP*DGP*DGP*DA)-3', 5'-D(*DCP*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DGP*DC)-3', DNA polymerase I, ... | | Authors: | Warren, J.J, Wu, E.Y, Golosov, A.A, Karplus, M, Beese, L.S. | | Deposit date: | 2008-10-22 | | Release date: | 2009-11-10 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | The Mechanism of the Translocation Step in DNA Replication by DNA Polymerase I: A Computer Simulation Analysis.
Structure, 18, 2010
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7OXQ
 | | Crystal structure of HIV-1 reverse transcriptase with a double stranded DNA in complex with fragment 048 at the transient P-pocket. | | Descriptor: | 2-(4-bromanylpyrazol-1-yl)-~{N}-cyclopropyl-~{N}-methyl-ethanamide, CADMIUM ION, DNA (28-MER), ... | | Authors: | Martinez, S.E, Singh, A.K, Das, K. | | Deposit date: | 2021-06-22 | | Release date: | 2021-12-08 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (3.3 Å) | | Cite: | Sliding of HIV-1 reverse transcriptase over DNA creates a transient P pocket - targeting P-pocket by fragment screening.
Nat Commun, 12, 2021
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7OZ5
 | | Crystal structure of HIV-1 reverse transcriptase with a double stranded DNA in complex with fragment 166 at the transient P-pocket. | | Descriptor: | (1~{R},2~{R})-2-phenyl-~{N}-(1,3-thiazol-2-yl)cyclopropane-1-carboxamide, CADMIUM ION, DNA (28-MER), ... | | Authors: | Martinez, S.E, Singh, A.K, Das, K. | | Deposit date: | 2021-06-25 | | Release date: | 2021-12-08 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (3.37 Å) | | Cite: | Sliding of HIV-1 reverse transcriptase over DNA creates a transient P pocket - targeting P-pocket by fragment screening.
Nat Commun, 12, 2021
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7OZ2
 | | Crystal structure of HIV-1 reverse transcriptase with a double stranded DNA showing a transient P-pocket | | Descriptor: | CADMIUM ION, DNA (28-MER), DNA (5'-D(*AP*CP*AP*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*CP*G)-3'), ... | | Authors: | Martinez, S.E, Singh, A.K, Das, K. | | Deposit date: | 2021-06-25 | | Release date: | 2021-12-08 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (2.85 Å) | | Cite: | Sliding of HIV-1 reverse transcriptase over DNA creates a transient P pocket - targeting P-pocket by fragment screening.
Nat Commun, 12, 2021
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6IPF
 | | Post-catalytic Complex of Human DNA Polymerase Mu with Templating Cytosine and Mn-8oxodGMP | | Descriptor: | 1,2-ETHANEDIOL, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, CHLORIDE ION, ... | | Authors: | Chang, Y.K, Wu, W.J, Tsai, M.D. | | Deposit date: | 2018-11-03 | | Release date: | 2019-05-29 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.77 Å) | | Cite: | Human DNA Polymerase mu Can Use a Noncanonical Mechanism for Multiple Mn2+-Mediated Functions.
J.Am.Chem.Soc., 141, 2019
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6IPD
 | | Post-catalytic Complex of Human DNA Polymerase Mu with Templating Adenine and Mn-8oxodGMP | | Descriptor: | 1,2-ETHANEDIOL, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3'), ... | | Authors: | Chang, Y.K, Wu, W.J, Tsai, M.D. | | Deposit date: | 2018-11-03 | | Release date: | 2019-05-29 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Human DNA Polymerase mu Can Use a Noncanonical Mechanism for Multiple Mn2+-Mediated Functions.
J.Am.Chem.Soc., 141, 2019
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1AL9
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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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1AMD
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3T3F
 | | Ternary Structure of the large fragment of Taq DNA polymerase bound to an abasic site and dNITP | | Descriptor: | 1-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-5-NITRO -1H-INDOLE, 5'-D(*AP*AP*AP*(3DR)P*GP*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*(DOC))-3', ... | | Authors: | Marx, A, Diederichs, K, Obeid, S. | | Deposit date: | 2011-07-25 | | Release date: | 2012-02-15 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Amino acid templating mechanisms in selection of nucleotides opposite abasic sites by a family a DNA polymerase.
J.Biol.Chem., 287, 2012
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6CST
 | | Structure of human DNA polymerase kappa with DNA | | Descriptor: | 1,2-ETHANEDIOL, 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine, CHLORIDE ION, ... | | Authors: | Jha, V, Ling, H. | | Deposit date: | 2018-03-21 | | Release date: | 2019-01-30 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | 2.0 angstrom resolution crystal structure of human pol kappa reveals a new catalytic function of N-clasp in DNA replication.
Sci Rep, 8, 2018
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207D
 | | SOLUTION STRUCTURE OF MITHRAMYCIN DIMERS BOUND TO PARTIALLY OVERLAPPING SITES ON DNA | | Descriptor: | 1,2-HYDRO-1-OXY-3,4-HYDRO-3-(1-METHOXY-2-OXY-3,4-DIHYDROXYPENTYL)-8,9-DIHYROXY-7-METHYLANTHRACENE, 2,6-dideoxy-3-C-methyl-beta-D-ribo-hexopyranose-(1-3)-2,6-dideoxy-beta-D-galactopyranose-(1-3)-beta-D-Olivopyranose, DNA (5'-D(*TP*AP*GP*CP*TP*AP*GP*CP*TP*A)-3'), ... | | Authors: | Sastry, M, Fiala, R, Patel, D.J. | | Deposit date: | 1995-04-20 | | Release date: | 1995-09-15 | | Last modified: | 2024-05-01 | | Method: | SOLUTION NMR | | Cite: | Solution structure of mithramycin dimers bound to partially overlapping sites on DNA.
J.Mol.Biol., 251, 1995
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6BS1
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1AXV
 | | SOLUTION NMR STRUCTURE OF THE [BP]DA ADDUCT OPPOSITE DT IN A DNA DUPLEX, 6 STRUCTURES | | Descriptor: | 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE, DNA DUPLEX D(CTCTC-[BP]A-CTTCC)D(GGAAGTGAGAG) | | Authors: | Mao, B, Gu, Z, Gorin, A.A, Chen, J, Hingerty, B.E, Amid, S, Broyde, S, Geacintov, N.E, Patel, D.J. | | Deposit date: | 1997-10-21 | | Release date: | 1998-07-01 | | Last modified: | 2024-05-22 | | Method: | SOLUTION NMR | | Cite: | Solution structure of the (+)-cis-anti-benzo[a]pyrene-dA ([BP]dA) adduct opposite dT in a DNA duplex.
Biochemistry, 38, 1999
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6ISI
 | | Structure of 9N-I DNA polymerase incorporation with 3'-CL in the active site | | Descriptor: | 3-[2-[2-(2-azanylethoxy)ethoxy]ethoxy]propanoic acid, CALCIUM ION, DNA (5'-D(P*AP*CP*GP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3'), ... | | Authors: | Linwu, S.W, Maestre-Reyna, M, Tsai, M.D, Tu, Y.H, Chang, W.H. | | Deposit date: | 2018-11-16 | | Release date: | 2019-08-28 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Thermococcus sp. 9°N DNA polymerase exhibits 3'-esterase activity that can be harnessed for DNA sequencing.
Commun Biol, 2, 2019
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6IPG
 | | Post-catalytic Complex of Human DNA Polymerase Mu with Templating Cytosine and Mg-8oxodGMP | | Descriptor: | 1,2-ETHANEDIOL, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, DNA (5'-D(*CP*GP*GP*CP*CP*TP*AP*CP*G)-3'), ... | | Authors: | Chang, Y.K, Wu, W.J, Tsai, M.D. | | Deposit date: | 2018-11-03 | | Release date: | 2019-05-29 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.62 Å) | | Cite: | Human DNA Polymerase mu Can Use a Noncanonical Mechanism for Multiple Mn2+-Mediated Functions.
J.Am.Chem.Soc., 141, 2019
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6ISG
 | | Structure of 9N-I DNA polymerase incorporation with dG in the active site | | Descriptor: | CALCIUM ION, DNA (5'-D(*GP*AP*CP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*G)-3'), DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*G)-3'), ... | | Authors: | Linwu, S.W, Maestre-Reyna, M, Tsai, M.D, Tu, Y.H, Chang, W.H. | | Deposit date: | 2018-11-16 | | Release date: | 2019-08-28 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (3.401 Å) | | Cite: | Thermococcus sp. 9°N DNA polymerase exhibits 3'-esterase activity that can be harnessed for DNA sequencing.
Commun Biol, 2, 2019
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8TLF
 | | CDCA7 (Mouse) Binds Non-B-form DNA oligo 36-mer (sg C2-Form 2) | | Descriptor: | 1,2-ETHANEDIOL, Cell division cycle-associated protein 7, GLYCEROL, ... | | Authors: | Horton, J.R, Ren, R, Cheng, X. | | Deposit date: | 2023-07-26 | | Release date: | 2024-08-21 | | Last modified: | 2024-08-28 | | Method: | X-RAY DIFFRACTION (1.64 Å) | | Cite: | The ICF syndrome protein CDCA7 harbors a unique DNA-binding domain that recognizes a CpG dyad in the context of a non-B DNA.
Biorxiv, 2023
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