PDB: 47011 resultsInfo pagesStatus searchChemie searchBIRD

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6M2V	Crystal structure of UHRF1 SRA complexed with fully-mCHG DNA. Descriptor: DNA (5'-D(*TP*CP*AP*CP*GP*(5CM)P*TP*GP*CP*GP*TP*GP*A)-3'), E3 ubiquitin-protein ligase UHRF1 Authors: Abhishek, S, Nakarakanti, N.K, Deeksha, W, Rajakumara, E. Deposit date: 2020-03-01 Release date: 2021-01-13 Last modified: 2023-11-29 Method: X-RAY DIFFRACTION (3 Å) Cite: Mechanistic insights into recognition of symmetric methylated cytosines in CpG and non-CpG DNA by UHRF1 SRA. Int.J.Biol.Macromol., 170, 2021
4XRH	Human DNA polymerase lambda- MgdTTP binary and complex with 6 paired DNA Descriptor: DNA (5'-D(*CP*AP*GP*TP*AP*C)-3'), DNA (5'-D(P*GP*TP*AP*CP*TP*G)-3'), DNA polymerase lambda, ... Authors: Liu, M.S, Tsai, M.D. Deposit date: 2015-01-21 Release date: 2016-02-24 Last modified: 2023-11-08 Method: X-RAY DIFFRACTION (3 Å) Cite: Structural Mechanism for the Fidelity Modulation of DNA Polymerase lambda J.Am.Chem.Soc., 138, 2016
5K5H	Homo sapiens CCCTC-binding factor (CTCF) ZnF4-7 and DNA complex structure Descriptor: DNA (5'-D(*CP*AP*GP*CP*AP*GP*GP*GP*GP*GP*CP*GP*C)-3'), DNA (5'-D(*CP*GP*CP*CP*CP*CP*CP*TP*GP*CP*TP*GP*G)-3'), Transcriptional repressor CTCF, ... Authors: Hashimoto, H, Cheng, X. Deposit date: 2016-05-23 Release date: 2017-05-24 Last modified: 2024-03-06 Method: X-RAY DIFFRACTION (3.108 Å) Cite: Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA. Mol. Cell, 66, 2017
1DCT	DNA (CYTOSINE-5) METHYLASE FROM HAEIII COVALENTLY BOUND TO DNA Descriptor: CALCIUM ION, DNA (5'-D(*AP*CP*CP*AP*GP*CP*AP*GP*GP*(C49)P*CP*AP*CP*CP*AP*GP*TP*G)-3'), DNA (5'-D(*TP*CP*AP*CP*TP*GP*GP*TP*GP*GP*(C5M)P*CP*TP*GP*CP*TP*GP*G)-3'), ... Authors: Reinisch, K.M, Chen, L, Verdine, G.L, Lipscomb, W.N. Deposit date: 1995-05-17 Release date: 1995-09-15 Last modified: 2024-10-09 Method: X-RAY DIFFRACTION (2.8 Å) Cite: The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing. Cell(Cambridge,Mass.), 82, 1995
1DNE	MOLECULAR STRUCTURE OF THE NETROPSIN-D(CGCGATATCGCG) COMPLEX: DNA CONFORMATION IN AN ALTERNATING AT SEGMENT; CONFORMATION 2 Descriptor: DNA (5'-D(*CP*GP*CP*GP*AP*TP*AP*TP*CP*GP*CP*G)-3'), NETROPSIN Authors: Coll, M, Aymami, J, Van Der Marel, G.A, Van Boom, J.H, Rich, A, Wang, A.H.-J. Deposit date: 1988-09-14 Release date: 1989-01-09 Last modified: 2024-02-07 Method: X-RAY DIFFRACTION (2.4 Å) Cite: Molecular structure of the netropsin-d(CGCGATATCGCG) complex: DNA conformation in an alternating AT segment. Biochemistry, 28, 1989
5GAT	SOLUTION NMR STRUCTURE OF THE WILD TYPE DNA BINDING DOMAIN OF AREA COMPLEXED TO A 13BP DNA CONTAINING A CGATA SITE, 35 STRUCTURES Descriptor: DNA (5'-D(*CP*AP*GP*CP*GP*AP*TP*AP*GP*AP*GP*AP*C)-3'), DNA (5'-D(*GP*TP*CP*TP*CP*TP*AP*TP*CP*GP*CP*TP*G)-3'), NITROGEN REGULATORY PROTEIN AREA, ... Authors: Clore, G.M, Starich, M, Wikstrom, M, Gronenborn, A.M. Deposit date: 1997-11-07 Release date: 1998-01-28 Last modified: 2024-05-22 Method: SOLUTION NMR Cite: The solution structure of a fungal AREA protein-DNA complex: an alternative binding mode for the basic carboxyl tail of GATA factors. J.Mol.Biol., 277, 1998
5KKQ	Homo sapiens CCCTC-binding factor (CTCF) ZnF3-7 and DNA complex structure Descriptor: DNA (5'-D(*GP*CP*CP*AP*GP*CP*AP*GP*GP*GP*GP*GP*CP*GP*CP*TP*A)-3'), DNA (5'-D(*TP*AP*GP*CP*GP*CP*CP*CP*CP*CP*TP*GP*CP*TP*GP*GP*C)-3'), Transcriptional repressor CTCF, ... Authors: Hashimoto, H, Wang, D, Cheng, X. Deposit date: 2016-06-22 Release date: 2017-05-24 Last modified: 2024-03-06 Method: X-RAY DIFFRACTION (1.744 Å) Cite: Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA. Mol. Cell, 66, 2017
8VX4	Human OGG1 bound to a 35-bp DNA with an 8-oxoG in the middle Descriptor: DNA (35-MER), N-glycosylase/DNA lyase Authors: You, Q, Li, H. Deposit date: 2024-02-03 Release date: 2024-10-09 Method: ELECTRON MICROSCOPY (3.7 Å) Cite: Human 8-oxoguanine glycosylase OGG1 binds nucleosome at the dsDNA ends and the super-helical locations. Commun Biol, 7, 2024
8VX6	Human OGG1 bound at the nucleosomal DNA entry site Descriptor: DNA (167-MER), Histone H2A, Histone H2B 1.1, ... Authors: You, Q, Li, H. Deposit date: 2024-02-03 Release date: 2024-10-09 Method: ELECTRON MICROSCOPY (3.2 Å) Cite: Human 8-oxoguanine glycosylase OGG1 binds nucleosome at the dsDNA ends and the super-helical locations. Commun Biol, 7, 2024
5DB8	Structure of human DNA polymerase beta Host-Guest complex with the N7MG base paired with a dA Descriptor: DNA (5'-D(*CP*CP*GP*AP*CP*GP*TP*CP*GP*CP*AP*TP*AP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*(FMG)P*AP*TP*GP*CP*GP*A)-3'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ... Authors: Koag, M.C, Lee, S. Deposit date: 2015-08-21 Release date: 2015-11-11 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (2.547 Å) Cite: N7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex DNA. J.Am.Chem.Soc., 137, 2015
7UXD	Crystal structure of APOBEC3G Catalytic domain complex with ssDNA containing 2'-deoxy Zebularine. Descriptor: DNA (5'-D(*AP*AP*TP*CP*CP*(DDN)P*AP*AP*A)-3'), DNA dC->dU-editing enzyme APOBEC-3G, ZINC ION Authors: Maiti, A, Matsuo, H. Deposit date: 2022-05-05 Release date: 2022-12-14 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (1.5 Å) Cite: Structure of the catalytically active APOBEC3G bound to a DNA oligonucleotide inhibitor reveals tetrahedral geometry of the transition state. Nat Commun, 13, 2022
5DB6	Structure of human DNA polymerase beta Host-Guest complex with the N7MG base paired with a dC Descriptor: DNA (5'-D(*CP*CP*GP*AP*CP*GP*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*(FMG)P*AP*TP*GP*CP*GP*A)-3'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ... Authors: Koag, M.C, Lee, S. Deposit date: 2015-08-20 Release date: 2015-11-11 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (2.83 Å) Cite: N7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex DNA. J.Am.Chem.Soc., 137, 2015
5DBC	Structure of human DNA polymerase beta Host-Guest complex with the dG base paired with a dG Descriptor: DNA (5'-D(*CP*CP*GP*AP*CP*GP*TP*CP*GP*CP*AP*TP*GP*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: Koag, M.C, Lee, S. Deposit date: 2015-08-21 Release date: 2015-11-11 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (2.402 Å) Cite: N7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex DNA. J.Am.Chem.Soc., 137, 2015
5DB7	Structure of human DNA polymerase beta Host-Guest complex with the N7MG base paired with a dT Descriptor: DNA (5'-D(*CP*CP*GP*AP*CP*GP*TP*CP*GP*CP*AP*TP*TP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*(FMG)P*AP*TP*GP*CP*GP*A)-3'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ... Authors: Koag, M.C, Lee, S. Deposit date: 2015-08-21 Release date: 2015-11-11 Last modified: 2024-03-13 Method: X-RAY DIFFRACTION (2.209 Å) Cite: N7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex DNA. J.Am.Chem.Soc., 137, 2015
7UI4	Crystal structure of the DNA preQ0 insertase DpdA Descriptor: DNA-guanine transglycosylase, ZINC ION Authors: Hung, S.-H, Swairjo, M.A. Deposit date: 2022-03-28 Release date: 2023-02-22 Last modified: 2024-05-22 Method: X-RAY DIFFRACTION (2.51 Å) Cite: 7-Deazaguanines in DNA: functional and structural elucidation of a DNA modification system. Nucleic Acids Res., 51, 2023
8E86	Human DNA polymerase eta-DNA-rC-ended primer-dGMPNPP ternary mismatch complex with Mn2+ Descriptor: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine, DNA (5'-D(*CP*AP*TP*TP*GP*TP*GP*AP*CP*GP*CP*T)-3'), DNA polymerase eta, ... Authors: Chang, C, Gao, Y. Deposit date: 2022-08-25 Release date: 2023-02-01 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (1.78 Å) Cite: Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase eta and reduces DNA synthesis fidelity. J.Biol.Chem., 299, 2023
8E8B	Human DNA polymerase eta-DNA-rU-ended primer ternary mismatch complex:ground state at pH7.0 (K+ MES) with 1 Ca2+ ion Descriptor: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, CALCIUM ION, DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3'), ... Authors: Chang, C, Gao, Y. Deposit date: 2022-08-25 Release date: 2023-02-01 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (2.2 Å) Cite: Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase eta and reduces DNA synthesis fidelity. J.Biol.Chem., 299, 2023
8E87	Human DNA polymerase eta-DNA-rA-ended primer-dGMPNPP ternary mismatch complex with Mg2+ Descriptor: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine, DNA (5'-D(*CP*AP*TP*TP*TP*TP*GP*AP*CP*GP*CP*T)-3'), DNA polymerase eta, ... Authors: Chang, C, Gao, Y. Deposit date: 2022-08-25 Release date: 2023-02-01 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (2.19 Å) Cite: Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase eta and reduces DNA synthesis fidelity. J.Biol.Chem., 299, 2023
8E8J	Human DNA polymerase eta-DNA-rG-ended primer-dGMPNPP ternary mismatch complex with Mg2+ Descriptor: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine, DNA (5'-D(*CP*AP*TP*TP*CP*TP*GP*AP*CP*GP*CP*T)-3'), DNA polymerase eta, ... Authors: Chang, C, Gao, Y. Deposit date: 2022-08-25 Release date: 2023-02-01 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (2.4 Å) Cite: Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase eta and reduces DNA synthesis fidelity. J.Biol.Chem., 299, 2023
8E8G	Human DNA polymerase eta-DNA-rU-ended primer ternary mismatch complex:reaction with 10 mM Mn2+ for 180s Descriptor: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, DIPHOSPHATE, DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3'), ... Authors: Chang, C, Gao, Y. Deposit date: 2022-08-25 Release date: 2023-02-01 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (2.13 Å) Cite: Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase eta and reduces DNA synthesis fidelity. J.Biol.Chem., 299, 2023
8E3E	ZBTB7A Zinc Finger Domain Bound to DNA Duplex Containing CAST sequence (#10) Descriptor: DNA (5'-D(*CP*TP*TP*TP*GP*GP*GP*GP*AP*GP*GP*GP*GP*TP*CP*TP*TP*TP*TP*AP*C)-3'), DNA (5'-D(*GP*GP*TP*AP*AP*AP*AP*GP*AP*CP*CP*CP*CP*TP*CP*CP*CP*CP*AP*AP*A)-3'), ZINC ION, ... Authors: Horton, J.R, Ren, R, Cheng, X. Deposit date: 2022-08-17 Release date: 2023-02-08 Last modified: 2024-10-09 Method: X-RAY DIFFRACTION (2.99 Å) Cite: Structural basis for transcription factor ZBTB7A recognition of DNA and effects of ZBTB7A somatic mutations that occur in human acute myeloid leukemia. J.Biol.Chem., 299, 2023
8E8D	Human DNA polymerase eta-DNA-rU-ended primer ternary mismatch complex:reaction with 10 mM Mn2+ for 60s Descriptor: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3'), DNA polymerase eta, ... Authors: Chang, C, Gao, Y. Deposit date: 2022-08-25 Release date: 2023-02-01 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (2.09 Å) Cite: Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase eta and reduces DNA synthesis fidelity. J.Biol.Chem., 299, 2023
8E85	Human DNA polymerase eta-DNA-rG-ended primer-dGMPNPP ternary mismatch complex with Mn2+ Descriptor: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine, DNA (5'-D(*CP*AP*TP*TP*CP*TP*GP*AP*CP*GP*CP*T)-3'), DNA polymerase eta, ... Authors: Chang, C, Gao, Y. Deposit date: 2022-08-25 Release date: 2023-02-01 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (1.72 Å) Cite: Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase eta and reduces DNA synthesis fidelity. J.Biol.Chem., 299, 2023
8E8F	Human DNA polymerase eta-DNA-rU-ended primer ternary mismatch complex:reaction with 10 mM Mn2+ for 120s Descriptor: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, DIPHOSPHATE, DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3'), ... Authors: Chang, C, Gao, Y. Deposit date: 2022-08-25 Release date: 2023-02-01 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (2.14 Å) Cite: Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase eta and reduces DNA synthesis fidelity. J.Biol.Chem., 299, 2023
8E8C	Human DNA polymerase eta-DNA-rU-ended primer ternary mismatch complex:reaction with 10 mM Mn2+ for 30s Descriptor: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE, DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3'), DNA polymerase eta, ... Authors: Chang, C, Gao, Y. Deposit date: 2022-08-25 Release date: 2023-02-01 Last modified: 2023-10-25 Method: X-RAY DIFFRACTION (2.25 Å) Cite: Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase eta and reduces DNA synthesis fidelity. J.Biol.Chem., 299, 2023

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