134D
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171D
| SOLUTION STRUCTURE OF A DNA DODECAMER CONTAINING THE ANTI-NEOPLASTIC AGENT ARABINOSYLCYTOSINE: COMBINED USE OF NMR, RESTRAINED MOLECULAR DYNAMICS AND FULL RELAXATION MATRIX REFINEMENT | Descriptor: | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') | Authors: | Schweitzer, B.I, Mikita, T, Kellogg, G.W, Gardner, K.H, Beardsley, G.P. | Deposit date: | 1994-03-14 | Release date: | 1994-07-31 | Last modified: | 2024-05-22 | Method: | SOLUTION NMR | Cite: | Solution structure of a DNA dodecamer containing the anti-neoplastic agent arabinosylcytosine: combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement. Biochemistry, 33, 1994
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7TYR
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8TPK
| P6522 crystal form of C. crescentus DriD-ssDNA-DNA complex | Descriptor: | DNA (5'-D(*AP*TP*AP*CP*GP*AP*CP*AP*GP*TP*AP*AP*CP*TP*GP*TP*CP*GP*TP*AP*T)-3'), DNA (5'-D(*AP*TP*AP*CP*GP*AP*CP*AP*GP*TP*TP*AP*CP*TP*GP*TP*CP*GP*TP*AP*T)-3'), DNA (5'-D(P*GP*TP*C)-3'), ... | Authors: | Schumacher, M.A. | Deposit date: | 2023-08-04 | Release date: | 2023-11-29 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (3.46 Å) | Cite: | Structure of the WYL-domain containing transcription activator, DriD, in complex with ssDNA effector and DNA target site. Nucleic Acids Res., 52, 2024
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8TP8
| Structure of the C. crescentus WYL-activator, DriD, bound to ssDNA and cognate DNA | Descriptor: | DNA (5'-D(*AP*TP*AP*CP*GP*AP*CP*AP*GP*TP*AP*AP*CP*TP*GP*TP*CP*GP*TP*AP*T)-3'), DNA (5'-D(*AP*TP*AP*CP*GP*AP*CP*AP*GP*TP*TP*AP*CP*TP*GP*TP*CP*GP*TP*AP*T)-3'), DNA (5'-D(P*GP*TP*C)-3'), ... | Authors: | Schumacher, M.A. | Deposit date: | 2023-08-04 | Release date: | 2023-11-29 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.74 Å) | Cite: | Structure of the WYL-domain containing transcription activator, DriD, in complex with ssDNA effector and DNA target site. Nucleic Acids Res., 52, 2024
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1PUE
| PU.1 ETS DOMAIN-DNA COMPLEX | Descriptor: | DNA (5'-D(*AP*AP*AP*AP*AP*GP*GP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3'), DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*CP*CP*TP*TP*TP*T)-3'), PROTEIN (TRANSCRIPTION FACTOR PU.1 (TF PU.1)) | Authors: | Kodandapani, R, Pio, F, Ni, C.Z, Piccialli, G, Klemsz, M, McKercher, S, Maki, R.A, Ely, K.R. | Deposit date: | 1996-07-08 | Release date: | 1997-02-12 | Last modified: | 2024-02-14 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | A new pattern for helix-turn-helix recognition revealed by the PU.1 ETS-domain-DNA complex. Nature, 380, 1996
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7T23
| E. coli DnaB bound to two DnaG C-terminal domains, ssDNA, ADP and AlF4 | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'), DNA primase, ... | Authors: | Oakley, A.J, Xu, Z.Q. | Deposit date: | 2021-12-02 | Release date: | 2023-01-18 | Last modified: | 2023-05-31 | Method: | ELECTRON MICROSCOPY (4.2 Å) | Cite: | Sequence of conformation changes of DnaB helicase during DNA unwinding and priming in Escherichia coli To Be Published
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7T22
| E. coli DnaB bound to three DnaG C-terminal domains, ssDNA, ADP and AlF4 | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'), DNA primase, ... | Authors: | Oakley, A.J, Xu, Z.Q. | Deposit date: | 2021-12-02 | Release date: | 2023-01-18 | Last modified: | 2023-05-31 | Method: | ELECTRON MICROSCOPY (4.2 Å) | Cite: | Sequence of conformation changes of DnaB helicase during DNA unwinding and priming in Escherichia coli To Be Published
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7QVB
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1CMA
| MET REPRESSOR/DNA COMPLEX + S-ADENOSYL-METHIONINE | Descriptor: | DNA (5'-D(*AP*GP*AP*CP*GP*TP*CP*TP*A)-3'), DNA (5'-D(*TP*TP*AP*GP*AP*CP*GP*TP*CP*T)-3'), PROTEIN (MET REPRESSOR), ... | Authors: | Somers, W.S, Phillips, S.E.V. | Deposit date: | 1992-08-24 | Release date: | 1993-10-31 | Last modified: | 2024-02-07 | Method: | X-RAY DIFFRACTION (2.8 Å) | Cite: | Crystal structure of the met repressor-operator complex at 2.8 A resolution reveals DNA recognition by beta-strands. Nature, 359, 1992
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7QA9
| 10bp DNA/DNA duplex | Descriptor: | DNA (5'-D(*CP*CP*AP*TP*TP*AP*TP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*TP*GP*G)-3') | Authors: | Li, Q, Trajkovski, M, Fan, C, Chen, J, Zhou, Y, Lu, K, Li, H, Su, X, Xi, Z, Plavec, J, Zhou, C. | Deposit date: | 2021-11-16 | Release date: | 2022-11-16 | Last modified: | 2024-06-19 | Method: | SOLUTION NMR | Cite: | 4'-SCF 3 -Labeling Constitutes a Sensitive 19 F NMR Probe for Characterization of Interactions in the Minor Groove of DNA. Angew.Chem.Int.Ed.Engl., 61, 2022
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7SJR
| Cryo-EM structure of AdnA-AdnB(W325A) in complex with DNA and AMPPNP | Descriptor: | DNA (70-MER), DNA helicase, IRON/SULFUR CLUSTER, ... | Authors: | Wang, J, Warren, G.M, Shuman, S, Patel, D.J. | Deposit date: | 2021-10-18 | Release date: | 2021-12-22 | Last modified: | 2024-06-05 | Method: | ELECTRON MICROSCOPY (3.8 Å) | Cite: | Structure-activity relationships at a nucleobase-stacking tryptophan required for chemomechanical coupling in the DNA resecting motor-nuclease AdnAB. Nucleic Acids Res., 50, 2022
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2ZKD
| Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA | Descriptor: | 1,2-ETHANEDIOL, ACETATE ION, DNA (5'-D(*DCP*DTP*DAP*DCP*DCP*DGP*DGP*DAP*DTP*DTP*DGP*DC)-3'), ... | Authors: | Arita, K, Ariyoshi, M, Tochio, H, Nakamura, Y, Shirakawa, M. | Deposit date: | 2008-03-19 | Release date: | 2008-09-09 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism Nature, 455, 2008
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1V9P
| Crystal Structure Of Nad+-Dependent DNA Ligase | Descriptor: | ADENOSINE MONOPHOSPHATE, DNA ligase, ZINC ION | Authors: | Lee, J.Y, Chang, C, Song, H.K, Moon, J, Yang, J.K, Kim, H.K, Kwon, S.K, Suh, S.W. | Deposit date: | 2004-01-27 | Release date: | 2004-03-30 | Last modified: | 2023-12-27 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications. Embo J., 19, 2000
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5U1J
| Structure of pNOB8 ParA bound to nonspecific DNA | Descriptor: | DNA (5'-D(*CP*GP*TP*GP*TP*AP*AP*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*A)-3'), DNA (5'-D(*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*AP*TP*GP*AP*CP*AP*CP*G)-3'), PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, ... | Authors: | Schumacher, M.A. | Deposit date: | 2016-11-28 | Release date: | 2017-04-19 | Last modified: | 2024-09-25 | Method: | X-RAY DIFFRACTION (2.95 Å) | Cite: | Structures of partition protein ParA with nonspecific DNA and ParB effector reveal molecular insights into principles governing Walker-box DNA segregation. Genes Dev., 31, 2017
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8AAN
| The nucleoprotein complex of Rep protein with iteron containing dsDNA and DUE ssDNA. | Descriptor: | DNA (5'-D(*AP*TP*TP*TP*TP*TP*AP*T)-3'), DNA (5'-D(*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*AP*GP*T)-3'), DNA (5'-D(*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*GP*GP*T)-3'), ... | Authors: | Nowacka, M, Wegrzyn, K. | Deposit date: | 2022-07-01 | Release date: | 2023-09-27 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.19 Å) | Cite: | Rep protein accommodates together dsDNA and ssDNA which enables a loop-back mechanism to plasmid DNA replication initiation. Nucleic Acids Res., 51, 2023
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170D
| SOLUTION STRUCTURE OF A DNA DODECAMER CONTAINING THE ANTI-NEOPLASTIC AGENT ARABINOSYLCYTOSINE: COMBINED USE OF NMR, RESTRAINED MOLECULAR DYNAMICS AND FULL RELAXATION MATRIX REFINEMENT | Descriptor: | DNA/RNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*T)-R(P*CAR)-D(P*GP*CP*G)-3') | Authors: | Schweitzer, B.I, Mikita, T, Kellogg, G.W, Gardner, K.H, Beardsley, G.P. | Deposit date: | 1994-03-14 | Release date: | 1994-07-31 | Last modified: | 2024-05-22 | Method: | SOLUTION NMR | Cite: | Solution structure of a DNA dodecamer containing the anti-neoplastic agent arabinosylcytosine: combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement. Biochemistry, 33, 1994
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190D
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7Q2X
| Cryo-EM structure of clamped S.cerevisiae condensin-DNA complex (Form I) | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, BERYLLIUM TRIFLUORIDE ION, Condensin complex subunit 1, ... | Authors: | Lee, B.-G, Rhodes, J, Lowe, J. | Deposit date: | 2021-10-26 | Release date: | 2022-03-23 | Last modified: | 2022-04-13 | Method: | ELECTRON MICROSCOPY (3 Å) | Cite: | Clamping of DNA shuts the condensin neck gate. Proc.Natl.Acad.Sci.USA, 119, 2022
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7Q2Y
| Cryo-EM structure of clamped S.cerevisiae condensin-DNA complex (form II) | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, BERYLLIUM TRIFLUORIDE ION, Condensin complex subunit 1, ... | Authors: | Lee, B.-G, Rhodes, J, Lowe, J. | Deposit date: | 2021-10-26 | Release date: | 2022-03-23 | Last modified: | 2023-09-13 | Method: | ELECTRON MICROSCOPY (3 Å) | Cite: | Clamping of DNA shuts the condensin neck gate. Proc.Natl.Acad.Sci.USA, 119, 2022
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7Q2Z
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5EEA
| Structure of HOXB13-DNA(CAA) complex | Descriptor: | DNA (5'-D(P*GP*GP*AP*CP*CP*CP*AP*AP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3'), DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*TP*TP*GP*GP*GP*TP*CP*C)-3'), Homeobox protein Hox-B13 | Authors: | Morgunova, E, Yin, Y, Jolma, A, Popov, A, Taipale, J. | Deposit date: | 2015-10-22 | Release date: | 2016-10-26 | Last modified: | 2024-01-10 | Method: | X-RAY DIFFRACTION (2.195 Å) | Cite: | Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima. Elife, 7, 2018
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7C0J
| Crystal structure of chimeric mutant of GH5 in complex with Z-DNA | Descriptor: | DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3'), Histone H5,Double-stranded RNA-specific adenosine deaminase | Authors: | Choi, H.J, Park, C.H. | Deposit date: | 2020-05-01 | Release date: | 2020-12-16 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.75 Å) | Cite: | Dual conformational recognition by Z-DNA binding protein is important for the B-Z transition process. Nucleic Acids Res., 48, 2020
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3Q5F
| Crystal structure of the Salmonella transcriptional regulator SlyA in complex with DNA | Descriptor: | DNA (5'-D(*AP*AP*TP*AP*AP*CP*TP*TP*AP*GP*CP*AP*AP*GP*CP*TP*AP*AP*TP*TP*AP*TP*A)-3'), DNA (5'-D(*TP*TP*AP*TP*AP*AP*TP*TP*AP*GP*CP*TP*TP*GP*CP*TP*AP*AP*GP*TP*TP*AP*T)-3'), Transcriptional regulator slyA | Authors: | Dolan, K.T, Duguid, E.M. | Deposit date: | 2010-12-28 | Release date: | 2011-05-04 | Last modified: | 2024-02-21 | Method: | X-RAY DIFFRACTION (2.96 Å) | Cite: | Crystal Structures of SlyA Protein, a Master Virulence Regulator of Salmonella, in Free and DNA-bound States. J.Biol.Chem., 286, 2011
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7T21
| E. coli DnaB bound to ssDNA and ADP-AlF4 | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'), MAGNESIUM ION, ... | Authors: | Oakley, A.J, Xu, Z.Q. | Deposit date: | 2021-12-02 | Release date: | 2023-01-18 | Last modified: | 2024-06-05 | Method: | ELECTRON MICROSCOPY (5.4 Å) | Cite: | Sequence of conformation changes of DnaB helicase during DNA unwinding and priming in Escherichia coli To Be Published
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