4R15
 
 | | High-resolution crystal structure of Z-DNA in complex with Cr3+ cations | | Descriptor: | CHROMIUM ION, DNA (5'-D(*CP*GP*CP*GP*CP*G)-3') | | Authors: | Drozdzal, P, Gilski, M, Kierzek, R, Lomozik, L, Jaskolski, M. | | Deposit date: | 2014-08-04 | | Release date: | 2015-03-04 | | Last modified: | 2023-09-20 | | Method: | X-RAY DIFFRACTION (0.97 Å) | | Cite: | High-resolution crystal structure of Z-DNA in complex with Cr(3+) cations.
J.Biol.Inorg.Chem., 20, 2015
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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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2V4Q
 | | Post-insertion complex of the Y-family DNA polymerase Dpo4 with M1dG containing template DNA | | Descriptor: | 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*C)-3', 5'-D(*TP*CP*AP*C M1GP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3', ... | | Authors: | Eoff, R.L, Stafford, J.B, Szekely, J, Rizzo, C.J, Egli, M, Guengerich, F.P, Marnett, L.J. | | Deposit date: | 2008-09-26 | | Release date: | 2009-06-16 | | Last modified: | 2023-12-13 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Structural and Functional Analysis of Sulfolobus Solfataricus Y-Family DNA Polymerase Dpo4-Catalyzed Bypass of the Malondialdehyde-Deoxyguanosine Adduct.
Biochemistry, 48, 2009
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5SZT
 | | Crystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 7-(N-(10-hydroxydecanoyl)-aminopentenyl)-7-deaza-2'-dATP | | Descriptor: | 7-(N-(10-hydroxydecanoyl)-aminopentenyl)-7-deaza-2'-dATP, ACETATE ION, DNA (5'-D(*AP*AP*AP*TP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'), ... | | Authors: | Hottin, A, Betz, K, Marx, A. | | Deposit date: | 2016-08-15 | | Release date: | 2016-12-14 | | Last modified: | 2024-01-17 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structural Basis for the KlenTaq DNA Polymerase Catalysed Incorporation of Alkene- versus Alkyne-Modified Nucleotides.
Chemistry, 23, 2017
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7K5Q
 | | Bst DNA polymerase I time-resolved structure, 8 min post dATP addition | | Descriptor: | 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, DNA (5'-D(P*G*CP*GP*AP*TP*CP*AP*CP*GP*T)-3'), DNA (5'-D(P*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'), ... | | Authors: | Chim, N, Meza, R.A, Trinh, A.M, Chaput, J.C. | | Deposit date: | 2020-09-17 | | Release date: | 2021-03-03 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Following replicative DNA synthesis by time-resolved X-ray crystallography.
Nat Commun, 12, 2021
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7K5T
 | | Bst DNA polymerase I time-resolved structure, 25.5 hr post dATP and dCTP addition | | Descriptor: | 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE, DNA (5'-D(P*CP*GP*AP*TP*CP*AP*CP*GP*TP*A)-3'), DNA (5'-D(P*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*C)-3'), ... | | Authors: | Chim, N, Meza, R.A, Trinh, A.M, Chaput, J.C. | | Deposit date: | 2020-09-17 | | Release date: | 2021-03-03 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Following replicative DNA synthesis by time-resolved X-ray crystallography.
Nat Commun, 12, 2021
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2ZHG
 | | Crystal structure of SoxR in complex with DNA | | Descriptor: | 2,3-DIHYDROXY-1,4-DITHIOBUTANE, DNA (5'-D(*DGP*DCP*DCP*DTP*DCP*DAP*DAP*DGP*DTP*DTP*DAP*DAP*DCP*DTP*DTP*DGP*DAP*DGP*DGP*DC)-3'), FE2/S2 (INORGANIC) CLUSTER, ... | | Authors: | Watanabe, S, Kita, A, Kobayashi, K, Miki, K. | | Deposit date: | 2008-02-05 | | Release date: | 2008-03-25 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Crystal structure of the [2Fe-2S] oxidative-stress sensor SoxR bound to DNA
Proc.Natl.Acad.Sci.Usa, 105, 2008
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4R55
 | | The crystal structure of a Cren7 mutant protein GR and dsDNA complex | | Descriptor: | Chromatin protein Cren7, DNA (5'-D(*GP*TP*GP*AP*TP*CP*AP*C)-3') | | Authors: | Zhang, Z.F, Gong, Y, Chen, Y.Y, Li, H.B, Huang, L. | | Deposit date: | 2014-08-20 | | Release date: | 2015-08-05 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Insights into the interaction between Cren7 and DNA: the role of loop beta 3-beta 4
Extremophiles, 19, 2015
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4R56
 | | Crystal structure of Sulfolobus Cren7-dsDNA(GTGATCAC) complex | | Descriptor: | Chromatin protein Cren7, DNA (5'-D(*GP*TP*GP*AP*TP*CP*AP*C)-3') | | Authors: | Zhang, Z.F, Gong, Y, Chen, Y.Y, Li, H.B, Huang, L. | | Deposit date: | 2014-08-20 | | Release date: | 2015-08-05 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Insights into the interaction between Cren7 and DNA: the role of loop beta 3-beta 4
Extremophiles, 19, 2015
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5K07
 | | Crystal structure of CREN7-DSDNA (GTAATTGC) complex | | Descriptor: | Chromatin protein Cren7, DNA (5'-D(*GP*TP*AP*AP*TP*TP*GP*C)-3') | | Authors: | Zhang, Z.F, Gong, Y. | | Deposit date: | 2016-05-17 | | Release date: | 2017-05-24 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Sequence-Dependent T:G Base Pair Opening in DNA Double Helix Bound by Cren7, a Chromatin Protein Conserved among Crenarchaea
PLoS ONE, 11, 2016
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5K17
 | | Crystal structure of CREN7-DSDNA (GTGATCGC) complex | | Descriptor: | Chromatin protein Cren7, DNA (5'-D(*GP*TP*GP*AP*TP*CP*GP*C)-3') | | Authors: | Zhang, Z.F, Gong, Y. | | Deposit date: | 2016-05-17 | | Release date: | 2017-05-24 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Sequence-Dependent T:G Base Pair Opening in DNA Double Helix Bound by Cren7, a Chromatin Protein Conserved among Crenarchaea
PLoS ONE, 11, 2016
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3LWM
 | | Structure of the large fragment of thermus aquaticus DNA polymerase I in complex with a blunt-ended DNA and ddATP | | Descriptor: | 2',3'-dideoxyadenosine triphosphate, ACETATE ION, DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(2DA))-3'), ... | | Authors: | Marx, A, Diederichs, K, Obeid, S. | | Deposit date: | 2010-02-24 | | Release date: | 2010-05-05 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.186 Å) | | Cite: | Replication through an abasic DNA lesion: structural basis for adenine selectivity
Embo J., 29, 2010
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6LMJ
 | | ASFV pA104R in complex with double-strand DNA | | Descriptor: | A104R, DNA (5'-D(*TP*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*A)-3') | | Authors: | Wang, H, Qi, J, Chai, Y, Gao, F, Liu, R. | | Deposit date: | 2019-12-25 | | Release date: | 2020-05-13 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | The structural basis of African swine fever virus pA104R binding to DNA and its inhibition by stilbene derivatives.
Proc.Natl.Acad.Sci.USA, 117, 2020
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2UVR
 | | Crystal structures of mutant Dpo4 DNA polymerases with 8-oxoG containing DNA template-primer constructs | | Descriptor: | 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*C)-3', 5'-D(*TP*CP*AP*CP*8OGP*GP*AP*AP*TP*CP *CP*TP*TP*CP*CP*CP*CP*C)-3', ... | | Authors: | Irimia, A, Egli, M. | | Deposit date: | 2007-03-13 | | Release date: | 2007-05-08 | | Last modified: | 2023-12-13 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Hydrogen Bonding of 7,8-Dihydro-8-Oxodeoxyguanosine with a Charged Residue in the Little Finger Domain Determines Miscoding Events in Sulfolobus Solfataricus DNA Polymerase Dpo4.
J.Biol.Chem., 282, 2007
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2V9W
 | | Complex structure of Sulfolobus solfataricus DPO4 and DNA duplex containing a hydrophobic thymine isostere 2,4-difluorotoluene nucleotide in the template strand | | Descriptor: | 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *CP*TP*G)-3', 5'-D(*TP*TP*CP*AP*GP*DFTP*AP*GP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3', ... | | Authors: | Irimia, A, Pallan, P.S, Egli, M. | | Deposit date: | 2007-08-27 | | Release date: | 2007-10-30 | | Last modified: | 2023-12-13 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Structure and Activity of Y-Class DNA Polymerase Dpo4 from Sulfolobus Solfataricus with Templates Containing the Hydrophobic Thymine Analog 2,4-Difluorotoluene.
J.Biol.Chem., 282, 2007
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2UVV
 | | Crystal structures of mutant Dpo4 DNA polymerases with 8-oxoG containing DNA template-primer constructs | | Descriptor: | 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*C)-3', 5'-D(*TP*CP*AP*CP*8OGP*GP*AP*AP*TP*CP *CP*TP*TP*CP*CP*CP*CP*C)-3', ... | | Authors: | Irimia, A, Egli, M. | | Deposit date: | 2007-03-14 | | Release date: | 2007-05-08 | | Last modified: | 2023-12-13 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Hydrogen Bonding of 7,8-Dihydro-8-Oxodeoxyguanosine with a Charged Residue in the Little Finger Domain Determines Miscoding Events in Sulfolobus Solfataricus DNA Polymerase Dpo4.
J.Biol.Chem., 282, 2007
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2UVW
 | | Crystal structures of mutant Dpo4 DNA polymerases with 8-oxoG containing DNA template-primer constructs | | Descriptor: | 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*A)-3', 5'-D(*TP*CP*AP*CP*8OGP*GP*AP*AP*TP*CP *CP*TP*TP*CP*CP*CP*CP*C)-3', ... | | Authors: | Irimia, A, Egli, M. | | Deposit date: | 2007-03-14 | | Release date: | 2007-05-08 | | Last modified: | 2023-12-13 | | Method: | X-RAY DIFFRACTION (2.09 Å) | | Cite: | Hydrogen Bonding of 7,8-Dihydro-8-Oxodeoxyguanosine with a Charged Residue in the Little Finger Domain Determines Miscoding Events in Sulfolobus Solfataricus DNA Polymerase Dpo4.
J.Biol.Chem., 282, 2007
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2VA3
 | | Complex structure of Sulfolobus solfataricus DPO4 and DNA duplex containing a hydrophobic thymine isostere 2,4-difluorotoluene nucleotide in the template strand | | Descriptor: | 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *CP*TP*A)-3', 5'-D(*TP*TP*CP*AP*DFTP*TP*AP*GP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3', ... | | Authors: | Irimia, A, Pallan, P.S, Egli, M. | | Deposit date: | 2007-08-28 | | Release date: | 2007-10-30 | | Last modified: | 2023-12-13 | | Method: | X-RAY DIFFRACTION (2.98 Å) | | Cite: | Structure and Activity of Y-Class DNA Polymerase Dpo4 from Sulfolobus Solfataricus with Templates Containing the Hydrophobic Thymine Analog 2,4-Difluorotoluene.
J.Biol.Chem., 282, 2007
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7P5Z
 | | Structure of a DNA-loaded MCM double hexamer engaged with the Dbf4-dependent kinase | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, ADENOSINE-5'-TRIPHOSPHATE, Cell division control protein 7, ... | | Authors: | Greiwe, J.F, Miller, T.C.R, Martino, F, Costa, A. | | Deposit date: | 2021-07-15 | | Release date: | 2022-02-02 | | Last modified: | 2024-07-17 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | Structural mechanism for the selective phosphorylation of DNA-loaded MCM double hexamers by the Dbf4-dependent kinase.
Nat.Struct.Mol.Biol., 29, 2022
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2UVU
 | | Crystal structures of mutant Dpo4 DNA polymerases with 8-oxoG containing DNA template-primer constructs | | Descriptor: | 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*CP*A)-3', 5'-D(*TP*CP*AP*CP*8OGP*GP*AP*AP*TP*CP *CP*TP*TP*CP*CP*CP*CP*C)-3', ... | | Authors: | Irimia, A, Egli, M. | | Deposit date: | 2007-03-14 | | Release date: | 2007-05-08 | | Last modified: | 2023-12-13 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Hydrogen Bonding of 7,8-Dihydro-8-Oxodeoxyguanosine with a Charged Residue in the Little Finger Domain Determines Miscoding Events in Sulfolobus Solfataricus DNA Polymerase Dpo4.
J.Biol.Chem., 282, 2007
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6DSW
 | | Bst DNA polymerase I pre-chemistry (n) structure | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*G)-3'), DNA (5'-D(P*AP*CP*GP*TP*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'), ... | | Authors: | Chim, N, Jackson, L.N, Chaput, J.C. | | Deposit date: | 2018-06-14 | | Release date: | 2018-10-31 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (1.589 Å) | | Cite: | Crystal structures of DNA polymerase I capture novel intermediates in the DNA synthesis pathway.
Elife, 7, 2018
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6DSU
 | | Bst DNA polymerase I pre-insertion complex structure | | Descriptor: | 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine, DNA (5'-D(*GP*CP*GP*AP*TP*CP*AP*CP*GP*T)-3'), DNA (5'-D(P*AP*CP*GP*TP*GP*AP*TP*CP*GP*CP*A)-3'), ... | | Authors: | Chim, N, Jackson, L.N, Chaput, J.C. | | Deposit date: | 2018-06-14 | | Release date: | 2018-10-31 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.98 Å) | | Cite: | Crystal structures of DNA polymerase I capture novel intermediates in the DNA synthesis pathway.
Elife, 7, 2018
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3BQ1
 | | Insertion ternary complex of Dbh DNA polymerase | | Descriptor: | 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE, CALCIUM ION, DNA (5'-D(*DGP*DAP*DAP*DGP*DCP*DCP*DGP*DGP*DCP*DG)-3'), ... | | Authors: | Pata, J.D, Wilson, R.C. | | Deposit date: | 2007-12-19 | | Release date: | 2008-04-08 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Structural insights into the generation of single-base deletions by the Y family DNA polymerase dbh.
Mol.Cell, 29, 2008
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1WTO
 | | Hyperthermophile chromosomal protein SAC7D double mutant V26F/M29F in complex with DNA GCGATCGC | | Descriptor: | 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3', DNA-binding proteins 7a/7b/7d | | Authors: | Chen, C.-Y, Ko, T.-P, Lin, T.-W, Chou, C.-C, Chen, C.-J, Wang, A.H.-J. | | Deposit date: | 2004-11-29 | | Release date: | 2005-02-22 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d
NUCLEIC ACIDS RES., 33, 2005
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1WTX
 | | Hyperthermophile chromosomal protein SAC7D single mutant V26A in complex with DNA GTAATTAC | | Descriptor: | 5'-D(*GP*TP*AP*AP*TP*TP*AP*C)-3', DNA-binding proteins 7a/7b/7d | | Authors: | Chen, C.-Y, Ko, T.-P, Lin, T.-W, Chou, C.-C, Chen, C.-J, Wang, A.H.-J. | | Deposit date: | 2004-11-29 | | Release date: | 2005-02-22 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d
NUCLEIC ACIDS RES., 33, 2005
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