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3SQ5	Crystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodiesterase H432N Mutant Descriptor: Tyrosyl-DNA phosphodiesterase 1 Authors: Gajewski, S, White, S.W. Deposit date: 2011-07-04 Release date: 2011-12-28 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (2.3 Å) Cite: Analysis of the active-site mechanism of tyrosyl-DNA phosphodiesterase I: a member of the phospholipase D superfamily. J.Mol.Biol., 415, 2012
3SQ8	Crystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodiesterase 1 H432R Mutant (SCAN1 Mutant) Descriptor: Tyrosyl-DNA phosphodiesterase 1 Authors: Gajewski, S, White, S.W. Deposit date: 2011-07-05 Release date: 2011-12-28 Last modified: 2023-09-13 Method: X-RAY DIFFRACTION (2.1 Å) Cite: Analysis of the active-site mechanism of tyrosyl-DNA phosphodiesterase I: a member of the phospholipase D superfamily. J.Mol.Biol., 415, 2012
5W9Q	Zinc finger region of MBD1 in complex with CpG DNA Descriptor: Methyl-CpG-binding domain protein 1, UNKNOWN ATOM OR ION, ZINC ION, ... Authors: Liu, K, Xu, C, Tempel, W, Walker, J.R, Arrowsmith, C.H, Bountra, C, Edwards, A.M, Min, J, Structural Genomics Consortium (SGC) Deposit date: 2017-06-23 Release date: 2017-10-18 Last modified: 2023-10-04 Method: X-RAY DIFFRACTION (1.8 Å) Cite: DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants. Structure, 26, 2018
5ORQ	Crystal structure of designed cPPR-Telo1 in complex with ssDNA Descriptor: DNA (5'-D(P*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3'), cPPR-Telo1 Authors: Spahr, H, Rackham, O. Deposit date: 2017-08-16 Release date: 2018-06-20 Last modified: 2024-11-06 Method: X-RAY DIFFRACTION (1.95 Å) Cite: Modular ssDNA binding and inhibition of telomerase activity by designer PPR proteins. Nat Commun, 9, 2018
3UGM	Structure of TAL effector PthXo1 bound to its DNA target Descriptor: DNA-1, DNA-2, TAL effector AvrBs3/PthA Authors: Mak, A.N.S, Bradley, P, Cernadas, R.A, Bogdanove, A.J, Stoddard, B.L. Deposit date: 2011-11-02 Release date: 2012-01-04 Last modified: 2024-02-28 Method: X-RAY DIFFRACTION (3 Å) Cite: The Crystal Structure of TAL Effector PthXo1 Bound to Its DNA Target. Science, 335, 2012
5TH3	Restriction/modification system-Type II R.SwaI cleaved DNA complex Descriptor: 1,2-ETHANEDIOL, ACETATE ION, DNA (cleaved 25-MER, ... Authors: Shen, B.W, Stoddard, B.L. Deposit date: 2016-09-29 Release date: 2016-12-21 Last modified: 2024-10-30 Method: X-RAY DIFFRACTION (2.33 Å) Cite: DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target. Nucleic Acids Res., 45, 2017
1NOM	DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7), 31-KD DOMAIN; SOAKED IN THE PRESENCE OF MNCL2 (5 MILLIMOLAR) Descriptor: DNA POLYMERASE BETA, MANGANESE (II) ION Authors: Pelletier, H, Sawaya, M.R. Deposit date: 1996-04-19 Release date: 1996-11-15 Last modified: 2024-05-22 Method: X-RAY DIFFRACTION (3 Å) Cite: Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis. Biochemistry, 35, 1996
8HMW	Double methyl modification on guanosine promotes unusual structural distortion and conformational transition in Z-DNA Descriptor: DNA (5'-D(*CP*GP*CP*(SJO)P*CP*G)-3') Authors: Lee, J.-H, Oh, K.-I. Deposit date: 2022-12-06 Release date: 2023-04-26 Last modified: 2024-05-15 Method: SOLUTION NMR Cite: Entropy-driven conformational transition of flexible Z-DNA to a novel non-B helix by double-methylated guanosine J Mol Liq, 2023
3MFH	DNA Polymerase Eta in Complex With Undamaged DNA Descriptor: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, 5'-D(*GP*TP*CP*CP*TP*CP*CP*CP*CP*TP*(DOC))-3', 5'-D(*TP*AP*AP*TP*TP*GP*AP*GP*GP*GP*GP*AP*GP*GP*AP*C)-3', ... Authors: Silverstein, T.D, Johnson, R.E, Jain, R, Prakash, L, Prakash, S, Aggarwal, A.K. Deposit date: 2010-04-02 Release date: 2010-06-23 Last modified: 2023-09-06 Method: X-RAY DIFFRACTION (2 Å) Cite: Structural basis for the suppression of skin cancers by DNA polymerase eta. Nature, 465, 2010
3NIC	DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29kI inactive variant Y49F Descriptor: DNA (5'-D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C)-3'), DNA (5'-D(P*GP*CP*GP*GP*CP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*TP*CP*CP*CP*G)-3'), Eco29kIR, ... Authors: Mak, A.N.S, Lambert, A.R, Stoddard, B.L. Deposit date: 2010-06-15 Release date: 2010-09-08 Last modified: 2024-04-03 Method: X-RAY DIFFRACTION (2.8 Å) Cite: Folding, DNA Recognition, and Function of GIY-YIG Endonucleases: Crystal Structures of R.Eco29kI. Structure, 18, 2010
5CPK	Nucleosome containing methylated Sat2L DNA Descriptor: DNA (145-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... Authors: Osakabe, A, Arimura, Y, Adachi, F, Maehara, K, Ohkawa, Y, Kurumizaka, H. Deposit date: 2015-07-21 Release date: 2015-10-28 Last modified: 2023-11-08 Method: X-RAY DIFFRACTION (2.632 Å) Cite: Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA. Open Biology, 5, 2015
5CPI	Nucleosome containing unmethylated Sat2R DNA Descriptor: DNA (146-MER), Histone H2A type 1-B/E, Histone H2B type 1-J, ... Authors: Osakabe, A, Arimura, Y, Adachi, F, Maehara, K, Ohkawa, Y, Kurumizaka, H. Deposit date: 2015-07-21 Release date: 2015-10-28 Last modified: 2023-11-08 Method: X-RAY DIFFRACTION (2.902 Å) Cite: Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA. Open Biology, 5, 2015
8Y0D	Crystal structure of SauCas9 in complex with sgRNA and 20nt ssDNA target Descriptor: CRISPR-associated endonuclease Cas9, DNA (5'-D(P*GP*TP*AP*AP*AP*GP*TP*TP*AP*AP*AP*TP*AP*GP*CP*AP*GP*AP*C)-3'), RNA (73-MER) Authors: Chen, Y, Chen, J, Liu, L. Deposit date: 2024-01-22 Release date: 2025-01-01 Last modified: 2025-02-19 Method: X-RAY DIFFRACTION (3.92 Å) Cite: DNA target binding-induced pre-crRNA processing in type II and V CRISPR-Cas systems. Nucleic Acids Res., 53, 2025
9AU8	Ternary complex of human DNA polymerase theta polymerase domain with a mismatched T:T base pair Descriptor: DNA (5'-D(P*AP*GP*TP*GP*CP*TP*AP*CP*G)-3'), DNA (5'-D(P*CP*GP*TP*AP*GP*(DOC))-3'), DNA polymerase theta, ... Authors: Li, C, Gao, Y. Deposit date: 2024-02-28 Release date: 2025-03-05 Last modified: 2025-05-28 Method: ELECTRON MICROSCOPY (3.44 Å) Cite: Structural basis of error-prone DNA synthesis by DNA polymerase theta. Nat Commun, 16, 2025
5VAZ	Crystal structure of a DNA primase domain from Pseudomonas aeruginosa Descriptor: DNA primase, SULFATE ION Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) Deposit date: 2017-03-28 Release date: 2017-04-05 Last modified: 2023-10-04 Method: X-RAY DIFFRACTION (2.4 Å) Cite: Crystal structure of a DNA primase domain from Pseudomonas aeruginosa To Be Published
4P4O	Crystal structure of Leishmania infantum polymerase beta: Ternary gap complex Descriptor: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE, DNA (5'-D(*CP*AP*GP*TP*AP*T)-3'), DNA (5'-D(P*CP*GP*GP*CP*AP*AP*TP*AP*CP*TP*G)-3'), ... Authors: Mejia, E, Burak, M, Alonso, A, Larraga, V, Kunkel, T, Bebenek, K, Garcia-Diaz, M. Deposit date: 2014-03-12 Release date: 2014-08-06 Last modified: 2023-12-27 Method: X-RAY DIFFRACTION (2.3001 Å) Cite: Structures of the Leishmania infantum polymerase beta. DNA Repair (Amst.), 18, 2014
4ZT0	Crystal structure of catalytically-active Streptococcus pyogenes Cas9 in complex with single-guide RNA at 2.9 Angstrom resolution Descriptor: CRISPR-associated endonuclease Cas9, single-guide RNA Authors: Jiang, F, Doudna, J.A. Deposit date: 2015-05-14 Release date: 2015-07-08 Last modified: 2024-11-06 Method: X-RAY DIFFRACTION (2.9 Å) Cite: A Cas9-guide RNA complex preorganized for target DNA recognition. Science, 348, 2015
4ZT9	Nuclease-inactive Streptococcus pyogenes Cas9 (D10A/H840A, dCas9) in complex with single-guide RNA at 3.1 Angstrom resolution Descriptor: CRISPR-associated endonuclease Cas9, single-guide RNA Authors: Jiang, F, Doudna, J.A. Deposit date: 2015-05-14 Release date: 2015-07-08 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (3.1 Å) Cite: A Cas9-guide RNA complex preorganized for target DNA recognition. Science, 348, 2015
5WJQ	mouseZFP568-ZnF2-11 in complex with DNA Descriptor: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, DNA (28-MER), ZINC ION, ... Authors: Patel, A, Cheng, X. Deposit date: 2017-07-24 Release date: 2018-03-07 Last modified: 2024-11-20 Method: X-RAY DIFFRACTION (2.794 Å) Cite: DNA Conformation Induces Adaptable Binding by Tandem Zinc Finger Proteins. Cell, 173, 2018
3MX4	DNA binding and cleavage by the GIY-YIG endonuclease R.Eco29KI inactive variant E142Q Descriptor: DNA (5'-D(P*CP*GP*GP*GP*AP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*GP*CP*CP*GP*C)-3'), DNA (5'-D(P*GP*CP*GP*GP*CP*GP*GP*CP*CP*CP*GP*CP*GP*GP*GP*CP*CP*TP*CP*CP*CP*G)-3'), Eco29kIR Authors: Mak, A.N.S, Lambert, A.R, Stoddard, B.L. Deposit date: 2010-05-06 Release date: 2010-09-08 Last modified: 2024-04-03 Method: X-RAY DIFFRACTION (2.5 Å) Cite: Folding, DNA Recognition, and Function of GIY-YIG Endonucleases: Crystal Structures of R.Eco29kI. Structure, 18, 2010
5TGX	Restriction/modification system-Type II R-SwaI complexed with partially cleaved DNA Descriptor: 1,2-ETHANEDIOL, ACETATE ION, CALCIUM ION, ... Authors: Shen, B.W, Stoddard, B.L. Deposit date: 2016-09-28 Release date: 2016-12-21 Last modified: 2024-11-20 Method: X-RAY DIFFRACTION (2.3 Å) Cite: DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target. Nucleic Acids Res., 45, 2017
2PV0	DNA methyltransferase 3 like protein (DNMT3L) Descriptor: DNA (cytosine-5)-methyltransferase 3-like, ZINC ION Authors: Cheng, X. Deposit date: 2007-05-09 Release date: 2007-08-14 Last modified: 2024-02-21 Method: X-RAY DIFFRACTION (3.3 Å) Cite: DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature, 448, 2007
4P4M	Crystal structure of Leishmania infantum polymerase beta: Ternary P/T complex Descriptor: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE, DNA (5'-D(*CP*AP*GP*TP*A)-3'), DNA (5'-D(P*AP*TP*AP*CP*TP*G)-3'), ... Authors: Mejia, E, Burak, M, Alonso, A, Larraga, V, Kunkel, T.A, Bebenek, K, Garcia-Diaz, M. Deposit date: 2014-03-12 Release date: 2014-08-06 Last modified: 2023-09-27 Method: X-RAY DIFFRACTION (1.9185 Å) Cite: Structures of the Leishmania infantum polymerase beta. DNA Repair (Amst.), 18, 2014
1JY1	CRYSTAL STRUCTURE OF HUMAN TYROSYL-DNA PHOSPHODIESTERASE (TDP1) Descriptor: TYROSYL-DNA PHOSPHODIESTERASE Authors: Davies, D.R, Interthal, H, Champoux, J.J, Hol, W.G.J. Deposit date: 2001-09-10 Release date: 2002-02-20 Last modified: 2024-10-16 Method: X-RAY DIFFRACTION (1.69 Å) Cite: The crystal structure of human tyrosyl-DNA phosphodiesterase, Tdp1. Structure, 10, 2002
5BT2	MeCP2 MBD domain (A140V) in complex with methylated DNA Descriptor: DNA (5'-D(*AP*TP*AP*GP*AP*AP*GP*AP*AP*TP*TP*CP*(5CM)P*GP*TP*TP*CP*CP*AP*G)-3'), DNA (5'-D(*TP*CP*TP*GP*GP*AP*AP*(5CM)P*GP*GP*AP*AP*TP*TP*CP*TP*TP*CP*TP*A)-3'), Methyl-CpG-binding protein 2 Authors: Ho, K.L, Chia, J.Y, Tan, W.S, Ng, C.L, Hu, N.J, Foo, H.L. Deposit date: 2015-06-02 Release date: 2016-08-17 Last modified: 2023-11-08 Method: X-RAY DIFFRACTION (2.2 Å) Cite: A/T Run Geometry of B-form DNA Is Independent of Bound Methyl-CpG Binding Domain, Cytosine Methylation and Flanking Sequence. Sci Rep, 6, 2016

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