7YGO
 
 | | DNA duplex containing 5OHU-Hg(II)-T base pairs | | Descriptor: | DNA (5'-D(*GP*GP*AP*CP*CP*TP*(6HU)P*GP*GP*TP*CP*C)-3'), MERCURY (II) ION | | Authors: | Kondo, J, Torigoe, H, Arakawa, F. | | Deposit date: | 2022-07-12 | | Release date: | 2023-05-24 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (2.403 Å) | | Cite: | Specific binding of Hg 2+ to mismatched base pairs involving 5-hydroxyuracil in duplex DNA.
J.Inorg.Biochem., 241, 2023
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7YGP
 | | DNA duplex containing 5OHU-T base pairs | | Descriptor: | COBALT (II) ION, COBALT HEXAMMINE(III), DNA (5'-D(*GP*GP*AP*CP*CP*TP*(OHU)P*GP*GP*TP*CP*C)-3') | | Authors: | Kondo, J, Torigoe, H, Arakawa, F. | | Deposit date: | 2022-07-12 | | Release date: | 2023-05-24 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1.997 Å) | | Cite: | Specific binding of Hg 2+ to mismatched base pairs involving 5-hydroxyuracil in duplex DNA.
J.Inorg.Biochem., 241, 2023
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4PWM
 | | Crystal structure of Dickerson Drew Dodecamer with 5-carboxycytosine | | Descriptor: | 5'-[CGCGAATT(5CC)GCG]-3' | | Authors: | Szulik, M.W, Pallan, P, Banerjee, S, Voehler, M, Egli, M, Stone, M.P. | | Deposit date: | 2014-03-20 | | Release date: | 2015-02-11 | | Last modified: | 2023-09-20 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Differential stabilities and sequence-dependent base pair opening dynamics of watson-crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine.
Biochemistry, 54, 2015
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4QC7
 | | Dodecamer structure of 5-formylcytosine containing DNA | | Descriptor: | short DNA strands | | Authors: | Szulik, M.W, Pallan, P, Egli, M, Stone, M.P. | | Deposit date: | 2014-05-09 | | Release date: | 2015-02-11 | | Last modified: | 2023-09-20 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Differential stabilities and sequence-dependent base pair opening dynamics of watson-crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine.
Biochemistry, 54, 2015
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4L6C
 | | Crystal structure of human mitochondrial deoxyribonucleotidase in complex with the inhibitor pib-t | | Descriptor: | 1,2-ETHANEDIOL, 1-{2-deoxy-3,5-O-[(4-iodophenyl)(phosphono)methylidene]-beta-D-threo-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione, 5'(3')-deoxyribonucleotidase, ... | | Authors: | Pachl, P, Brynda, J, Rezacova, P. | | Deposit date: | 2013-06-12 | | Release date: | 2014-09-10 | | Last modified: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Conformationally constrained nucleoside phosphonic acids - potent inhibitors of human mitochondrial and cytosolic 5'(3')-nucleotidases.
Org.Biomol.Chem., 12, 2014
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4MWO
 | | Crystal structure of human mitochondrial 5'(3')-deoxyribonucleotidase in complex with the inhibitor CPB-T | | Descriptor: | 1-{3,5-O-[(4-carboxyphenyl)(phosphono)methylidene]-2-deoxy-beta-D-threo-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione, 5'(3')-deoxyribonucleotidase, mitochondrial, ... | | Authors: | Pachl, P, Rezacova, P, Brynda, J. | | Deposit date: | 2013-09-25 | | Release date: | 2014-09-10 | | Last modified: | 2023-09-20 | | Method: | X-RAY DIFFRACTION (1.67 Å) | | Cite: | Conformationally constrained nucleoside phosphonic acids - potent inhibitors of human mitochondrial and cytosolic 5'(3')-nucleotidases.
Org.Biomol.Chem., 12, 2014
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2R8K
 | | Structure of the Eukaryotic DNA Polymerase eta in complex with 1,2-d(GpG)-cisplatin containing DNA | | Descriptor: | 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, 5'-D(*DGP*DTP*DGP*DGP*DTP*DGP*DAP*DGP*DC)-3', 5'-D(P*DGP*DGP*DCP*DTP*DCP*DAP*DCP*DCP*DAP*DC)-3', ... | | Authors: | Carell, T, Alt, A, Lammens, K. | | Deposit date: | 2007-09-11 | | Release date: | 2007-12-11 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (3.3 Å) | | Cite: | Bypass of DNA lesions generated during anticancer treatment with cisplatin by DNA polymerase eta
Science, 318, 2007
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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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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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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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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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3N4N
 | | Insights into the stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido[2,3-d]pyrimidin-2-one | | Descriptor: | 5'-D(*CP*GP*CP*GP*AP*A)-3', 5'-D(P*TP*TP*(B7C)P*GP*CP*G)-3' | | Authors: | Takenaka, A, Juan, E.C.M, Shimizu, S. | | Deposit date: | 2010-05-22 | | Release date: | 2010-08-11 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.92 Å) | | Cite: | Insights into the DNA stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido [2,3-d]pyrimidin-2-one.
Nucleic Acids Res., 2010
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3N4O
 | | Insights into the stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido[2,3-d]pyrimidin-2-one | | Descriptor: | 2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE, 5'-D(*CP*GP*CP*GP*AP*AP*TP*(B7C)P*CP*GP*CP*G)-3' | | Authors: | Takenaka, A, Juan, E.C.M, Shimizu, S. | | Deposit date: | 2010-05-22 | | Release date: | 2010-08-11 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Insights into the DNA stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido [2,3-d]pyrimidin-2-one.
Nucleic Acids Res., 2010
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3OPI
 | | 7-DEAZA-2'-DEOXYADENOSINE modification in B-FORM DNA | | Descriptor: | DNA (5'-D(*CP*GP*CP*GP*AP*(7DA)P*TP*TP*CP*GP*CP*G)-3'), MAGNESIUM ION, SODIUM ION | | Authors: | Kowal, E.A, Ganguly, M, Pallan, P.S, Marky, L.A, Gold, B, Egli, M, Stone, M.P. | | Deposit date: | 2010-09-01 | | Release date: | 2011-08-31 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (1.1 Å) | | Cite: | Altering the Electrostatic Potential in the Major Groove: Thermodynamic and Structural Characterization of 7-Deaza-2'-deoxyadenosine:dT Base Pairing in DNA.
J.Phys.Chem.B, 115, 2011
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4ASJ
 | | Pseudomonas aeruginosa RmlA in complex with allosteric inhibitor | | Descriptor: | CHLORIDE ION, GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE, N-(6-amino-1-benzyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-N-methylbenzenesulfonamide, ... | | Authors: | Alphey, M.S, Pirrie, L, Torrie, L.S, Gardiner, M, Westwood, N.J, Gray, D, Naismith, J.H. | | Deposit date: | 2012-05-01 | | Release date: | 2012-10-31 | | Last modified: | 2023-12-20 | | Method: | X-RAY DIFFRACTION (2.25 Å) | | Cite: | Allosteric competitive inhibitors of the glucose-1-phosphate thymidylyltransferase (RmlA) from Pseudomonas aeruginosa.
ACS Chem. Biol., 8, 2013
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3PF4
 | | Crystal structure of Bs-CspB in complex with r(GUCUUUA) | | Descriptor: | Cold shock protein cspB, MAGNESIUM ION, SODIUM ION, ... | | Authors: | Sachs, R, Max, K.E.A, Heinemann, U. | | Deposit date: | 2010-10-27 | | Release date: | 2011-09-21 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (1.38 Å) | | Cite: | RNA single strands bind to a conserved surface of the major cold shock protein in crystals and solution.
Rna, 18, 2012
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3PF5
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2L4L
 | | Structural insights into the cTAR DNA recognition by the HIV-1 Nucleocapsid protein: role of sugar deoxyriboses in the binding polarity of NC | | Descriptor: | 5'-D(*CP*TP*GP*G)-3', HIV-1 nucleocapsid protein NCp7, ZINC ION | | Authors: | Bazzi, A, Zargarian, L, Chaminade, F, Boudier, C, De Rocquigny, H, Rene, B, Mely, Y, Fosse, P, Mauffret, O. | | Deposit date: | 2010-10-08 | | Release date: | 2010-12-08 | | Last modified: | 2024-05-01 | | Method: | SOLUTION NMR | | Cite: | Structural insights into the cTAR DNA recognition by the HIV-1 nucleocapsid protein: role of sugar deoxyriboses in the binding polarity of NC.
Nucleic Acids Res., 39, 2011
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1X95
 | | Solution structure of the DNA-hexamer ATGCAT complexed with DNA Bis-intercalating Anticancer Drug XR5944 (MLN944) | | Descriptor: | 1-METHYL-9-[12-(9-METHYLPHENAZIN-10-IUM-1-YL)-12-OXO-2,11-DIAZA-5,8-DIAZONIADODEC-1-ANOYL]PHENAZIN-10-IUM, 5'-D(*AP*TP*GP*CP*AP*T)-3' | | Authors: | Dai, J, Punchihewa, C, Mistry, P, Ooi, A.T, Yang, D. | | Deposit date: | 2004-08-19 | | Release date: | 2004-09-28 | | Last modified: | 2024-05-01 | | Method: | SOLUTION NMR | | Cite: | Novel DNA bis-intercalation by MLN944, a potent clinical bisphenazine anticancer drug.
J.Biol.Chem., 279, 2004
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2MHZ
 | | Structure of Exocyclic S,S N6,N6-(2,3-Dihydroxy-1,4-butadiyl)-2'-Deoxyadenosine Adduct Induced by 1,2,3,4-Diepoxybutane in DNA | | Descriptor: | 5'-D(*CP*GP*GP*AP*CP*(SDE)P*AP*GP*AP*AP*G)-3', 5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3' | | Authors: | Kowal, E.A, Seneviratne, U, Wickramaratne, S, Doherty, K.E, Cao, X, Tretyakova, N, Stone, M.P. | | Deposit date: | 2013-12-05 | | Release date: | 2014-05-28 | | Last modified: | 2024-05-01 | | Method: | SOLUTION NMR | | Cite: | Structures of Exocyclic R,R- and S,S-N(6),N(6)-(2,3-Dihydroxybutan-1,4-diyl)-2'-Deoxyadenosine Adducts Induced by 1,2,3,4-Diepoxybutane.
Chem.Res.Toxicol., 27, 2014
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2M11
 | | Structure of perimidinone-derived synthetic nucleoside paired with guanine in DNA duplex | | Descriptor: | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(D3N)P*GP*CP*G)-3') | | Authors: | Kowal, E.A, Lad, R, Pallan, P.S, Muffly, E, Wawrzak, Z, Egli, M, Sturla, S.J, Stone, M.P. | | Deposit date: | 2012-11-09 | | Release date: | 2013-06-12 | | Last modified: | 2024-05-01 | | Method: | SOLUTION NMR | | Cite: | Recognition of O6-benzyl-2'-deoxyguanosine by a perimidinone-derived synthetic nucleoside: a DNA interstrand stacking interaction.
Nucleic Acids Res., 41, 2013
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2OJZ
 | | Anti-DNA antibody ED10 | | Descriptor: | Fab ED10 heavy chain, Fab ED10 light chain | | Authors: | Stanfield, R.L, Sanguineti, S, Wilson, I.A, de Prat-Gay, G. | | Deposit date: | 2007-01-15 | | Release date: | 2007-06-12 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (2.73 Å) | | Cite: | Specific recognition of a DNA immunogen by its elicited antibody
J.Mol.Biol., 370, 2007
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227D
 | | A CRYSTALLOGRAPHIC AND SPECTROSCOPIC STUDY OF THE COMPLEX BETWEEN D(CGCGAATTCGCG)2 AND 2,5-BIS(4-GUANYLPHENYL)FURAN, AN ANALOGUE OF BERENIL. STRUCTURAL ORIGINS OF ENHANCED DNA-BINDING AFFINITY | | Descriptor: | 2,5-BIS(4-GUANYLPHENYL)FURAN, DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') | | Authors: | Laughton, C.A, Tanious, F, Nunn, C.M, Boykin, D.W, Wilson, W.D, Neidle, S. | | Deposit date: | 1995-08-08 | | Release date: | 1995-11-11 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | A crystallographic and spectroscopic study of the complex between d(CGCGAATTCGCG)2 and 2,5-bis(4-guanylphenyl)furan, an analogue of berenil. Structural origins of enhanced DNA-binding affinity.
Biochemistry, 35, 1996
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289D
 | | TARGETING THE MINOR GROOVE OF DNA: CRYSTAL STRUCTURES OF TWO COMPLEXES BETWEEN FURAN DERIVATIVES OF BERENIL AND THE DNA DODECAMER D(CGCGAATTCGCG)2 | | Descriptor: | 2,5-BIS{[4-(N-CYCLOPROPYLDIAMINOMETHYL)PHENYL]}FURAN, DNA (5'-R(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') | | Authors: | Trent, J.O, Clark, G.R, Kumar, A, Wilson, W.D, Boykin, D.W, Hall, J.E, Tidwell, R.R, Blagburn, B.L, Neidle, S. | | Deposit date: | 1996-10-10 | | Release date: | 1996-12-17 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Targeting the minor groove of DNA: crystal structures of two complexes between furan derivatives of berenil and the DNA dodecamer d(CGCGAATTCGCG)2.
J.Med.Chem., 39, 1996
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206D
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