1D6M
 
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2LB4
 | | DNA / RNA Hybrid containing a central stereo specific Sp borano phosphate linkage | | Descriptor: | DNA_(5'-D(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3')_, RNA_(5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3')_ | | Authors: | Johnson, C.N, Spring, A.M, Shaw, B.R, Germann, M.W. | | Deposit date: | 2011-03-22 | | Release date: | 2011-06-29 | | Last modified: | 2024-05-01 | | Method: | SOLUTION NMR | | Cite: | Structural Basis of the RNase H1 Activity on Stereo Regular Borano Phosphonate DNA/RNA Hybrids.
Biochemistry, 50, 2011
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4RHD
 | | DNA Duplex with Novel ZP Base Pair | | Descriptor: | DNA 9mer novel P nucleobase, DNA 9mer novel Z nucleobase, MAGNESIUM ION | | Authors: | Zhang, W, Zhang, L, Benner, S, Huang, Z. | | Deposit date: | 2014-10-01 | | Release date: | 2015-07-08 | | Last modified: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Evolution of functional six-nucleotide DNA.
J.Am.Chem.Soc., 137, 2015
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6RAS
 | | Pmar-Lig_Pre. | | Descriptor: | ADENOSINE MONOPHOSPHATE, ATP-dependent DNA ligase, DNA, ... | | Authors: | Leiros, H.K.S, Williamson, A. | | Deposit date: | 2019-04-07 | | Release date: | 2019-07-10 | | Last modified: | 2024-05-01 | | Method: | X-RAY DIFFRACTION (2.75 Å) | | Cite: | Structural intermediates of a DNA-ligase complex illuminate the role of the catalytic metal ion and mechanism of phosphodiester bond formation.
Nucleic Acids Res., 47, 2019
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6RAU
 | | PostS3_Pmar_lig4_WT | | Descriptor: | ADENOSINE MONOPHOSPHATE, ATP-dependent DNA ligase, DNA (5'-D(*AP*TP*TP*GP*CP*GP*AP*CP*CP*CP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*A)-3'), ... | | Authors: | Leiros, H.K.S, Williamson, A. | | Deposit date: | 2019-04-08 | | Release date: | 2019-07-10 | | Last modified: | 2024-05-01 | | Method: | X-RAY DIFFRACTION (1.99 Å) | | Cite: | Structural intermediates of a DNA-ligase complex illuminate the role of the catalytic metal ion and mechanism of phosphodiester bond formation.
Nucleic Acids Res., 47, 2019
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4GLH
 | | DNA dodecamer containing 5-hydroxymethyl cytosine | | Descriptor: | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(5HC)P*GP*CP*G)-3'), POTASSIUM ION | | Authors: | Spingler, B, Renciuk, D, Vorlickova, M. | | Deposit date: | 2012-08-14 | | Release date: | 2013-08-28 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (1.662 Å) | | Cite: | Crystal structures of B-DNA dodecamer containing the epigenetic modifications 5-hydroxymethylcytosine or 5-methylcytosine.
Nucleic Acids Res., 41, 2013
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4GLG
 | | DNA dodecamer containing 5-methyl cytosine | | Descriptor: | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(5CM)P*GP*CP*G)-3') | | Authors: | Spingler, B, Renciuk, D, Vorlickova, M. | | Deposit date: | 2012-08-14 | | Release date: | 2013-08-28 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (1.72 Å) | | Cite: | Crystal structures of B-DNA dodecamer containing the epigenetic modifications 5-hydroxymethylcytosine or 5-methylcytosine.
Nucleic Acids Res., 41, 2013
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4GLC
 | | DNA dodecamer containing 5-hydroxymethyl-cytosine | | Descriptor: | DNA (5'-D(*CP*GP*(5HC)P*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') | | Authors: | Spingler, B, Renciuk, D, Vorlickova, M. | | Deposit date: | 2012-08-14 | | Release date: | 2013-08-28 | | Last modified: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (1.831 Å) | | Cite: | Crystal structures of B-DNA dodecamer containing the epigenetic modifications 5-hydroxymethylcytosine or 5-methylcytosine.
Nucleic Acids Res., 41, 2013
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2LAR
 | | DNA / RNA Hybrid containing a central stereo specific Rp borano phosphate linkage | | Descriptor: | DNA_(5'-D(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3')_, RNA_(5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3')_ | | Authors: | Johnson, C.N, Spring, A.M, Shaw, B.R, Germann, M.W. | | Deposit date: | 2011-03-18 | | Release date: | 2011-10-12 | | Last modified: | 2024-05-01 | | Method: | SOLUTION NMR | | Cite: | Structural basis of the RNase H1 activity on stereo regular borano phosphonate DNA/RNA hybrids.
Biochemistry, 50, 2011
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1IPP
 | | HOMING ENDONUCLEASE/DNA COMPLEX | | Descriptor: | CADMIUM ION, DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*AP*GP*TP*CP*A)-3'), INTRON-ENCODED ENDONUCLEASE I-PPOI, ... | | Authors: | Flick, K.E, Jurica, M.S, Monnat Jr, R.J, Stoddard, B.L. | | Deposit date: | 1998-03-19 | | Release date: | 1998-09-02 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI.
Nature, 394, 1998
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4RTK
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6ZT5
 | | Complex between a homodimer of Mycobacterium smegmatis MfpA and a single copy of the N-terminal 47 kDa fragment of the Mycobacterium smegmatis DNA Gyrase B subunit | | Descriptor: | DNA gyrase subunit B, Pentapeptide repeat protein MfpA, SULFATE ION | | Authors: | Feng, L, Mundy, J.E.A, Stevenson, C.E.M, Mitchenall, L.A, Lawson, D.M, Mi, K, Maxwell, A. | | Deposit date: | 2020-07-17 | | Release date: | 2021-03-03 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | The pentapeptide-repeat protein, MfpA, interacts with mycobacterial DNA gyrase as a DNA T-segment mimic.
Proc.Natl.Acad.Sci.USA, 118, 2021
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4RTS
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9CIH
 | | Crystal structure of human polymerase eta with incoming dCMPnPP nucleotide across O4-methyl threofuranosyl thymidine in DNA template at extension stage | | Descriptor: | 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine, DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*A)-3'), DNA (5'-D(*CP*AP*TP*GP*(A1A0L)P*TP*GP*AP*CP*GP*CP*T)-3'), ... | | Authors: | Tomar, R, Stone, M.P, Egli, M. | | Deposit date: | 2024-07-03 | | Release date: | 2024-09-18 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (2.15 Å) | | Cite: | DNA Replication across alpha-l-(3'-2')-Threofuranosyl Nucleotides Mediated by Human DNA Polymerase eta.
Biochemistry, 63, 2024
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9CHW
 | | Crystal structure of human polymerase eta with incoming dAMPnPP nucleotide opposite threofuranosyl thymidine in DNA template | | Descriptor: | 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine, DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3'), DNA (5'-D(*CP*AP*TP*(TFT)P*AP*TP*GP*AP*CP*GP*CP*T)-3'), ... | | Authors: | Tomar, R, Stone, M.P, Egli, M. | | Deposit date: | 2024-07-02 | | Release date: | 2024-09-18 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (2.16 Å) | | Cite: | DNA Replication across alpha-l-(3'-2')-Threofuranosyl Nucleotides Mediated by Human DNA Polymerase eta.
Biochemistry, 63, 2024
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9CJ9
 | | Crystal structure of human polymerase eta with incoming dAMPnPP nucleotide opposite O4-methyl threofuranosyl thymidine in DNA template at insertion stage | | Descriptor: | 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine, DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3'), DNA (5'-D(*CP*AP*TP*(TFT)P*AP*TP*GP*AP*CP*GP*CP*T)-3'), ... | | Authors: | Tomar, R, Stone, M.P, Egli, M. | | Deposit date: | 2024-07-05 | | Release date: | 2024-09-18 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (2.98 Å) | | Cite: | DNA Replication across alpha-l-(3'-2')-Threofuranosyl Nucleotides Mediated by Human DNA Polymerase eta.
Biochemistry, 63, 2024
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9CI9
 | | Crystal structure of human polymerase eta with incoming dCMPnPP nucleotide across threofuranosyl thymidine in DNA template at extension stage | | Descriptor: | 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine, DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*A)-3'), DNA (5'-D(*CP*AP*TP*GP*(TFT)P*TP*GP*AP*CP*GP*CP*T)-3'), ... | | Authors: | Tomar, R, Stone, M.P, Egli, M. | | Deposit date: | 2024-07-02 | | Release date: | 2024-09-18 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (2.09 Å) | | Cite: | DNA Replication across alpha-l-(3'-2')-Threofuranosyl Nucleotides Mediated by Human DNA Polymerase eta.
Biochemistry, 63, 2024
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8YO4
 | | structure of phage T4 topoisomerase II central domain bound with DNA | | Descriptor: | DNA (5'-D(P*AP*TP*AP*TP*AP*TP*GP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*CP*AP*CP*AP*T)-3'), DNA (5'-D(P*TP*GP*TP*GP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*CP*AP*TP*AP*TP*AP*TP*A)-3'), DNA topoisomerase medium subunit, ... | | Authors: | Chen, Y.T, Xin, Y.H, Xian, R.Q. | | Deposit date: | 2024-03-12 | | Release date: | 2024-09-25 | | Method: | ELECTRON MICROSCOPY (3.2 Å) | | Cite: | structure of phage T4 topoisomerase II central domain bound with DNA
To be published
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8YON
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8YO7
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8YLU
 | | structure of phage T6 topoisomerase II central domain bound with DNA | | Descriptor: | DNA (5'-D(P*TP*AP*TP*AP*TP*GP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*CP*AP*CP*A)-3'), DNA topoisomerase (ATP-hydrolyzing), DNA topoisomerase medium subunit, ... | | Authors: | Chen, Y.T, Xin, Y.H. | | Deposit date: | 2024-03-06 | | Release date: | 2024-09-25 | | Method: | ELECTRON MICROSCOPY (2.8 Å) | | Cite: | structure of phage T6 topoisomerase II central domain bound with DNA
To be published
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5JJ4
 | | Crystal Structure of a Variant Human Activation-induced Deoxycytidine Deaminase as an MBP fusion protein | | Descriptor: | CALCIUM ION, Maltose-binding periplasmic protein,Single-stranded DNA cytosine deaminase, ZINC ION, ... | | Authors: | Pedersen, L.C, Goodman, M.F, Pham, P, Afif, S.A. | | Deposit date: | 2016-04-22 | | Release date: | 2016-06-29 | | Last modified: | 2023-09-27 | | Method: | X-RAY DIFFRACTION (2.807 Å) | | Cite: | Structural analysis of the activation-induced deoxycytidine deaminase required in immunoglobulin diversification.
DNA Repair (Amst.), 43, 2016
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8A2Q
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8GH5
 | | Implementing Logic Gates in DNA Crystal Engineering | | Descriptor: | DNA (5'-D(*AP*GP*AP*CP*G)-3'), DNA (5'-D(*CP*TP*AP*CP*G)-3'), DNA (5'-D(P*CP*GP*TP*GP*GP*A)-3'), ... | | Authors: | Zhang, C, Paluzzi, V.E, Sha, R, Jonoska, N, Mao, C. | | Deposit date: | 2023-03-09 | | Release date: | 2023-06-07 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.64 Å) | | Cite: | Implementing Logic Gates by DNA Crystal Engineering.
Adv Mater, 35, 2023
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5L06
 | | Solution Structure of a DNA Dodecamer with 5-methylcytosine at the 3rd Position | | Descriptor: | DNA (5'-D(*CP*GP*(5CM)P*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') | | Authors: | Miears, H.L, Hoppins, J.J, Gruber, D.R, Kasymov, R.D, Zharkov, D.O, Smirnov, S.L. | | Deposit date: | 2016-07-26 | | Release date: | 2016-12-21 | | Last modified: | 2024-05-01 | | Method: | SOLUTION NMR | | Cite: | Oxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation.
Nucleic Acids Res., 46, 2018
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