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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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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3GJH
 | | Crystal structure of a DNA duplex containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one | | Descriptor: | 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(B7C)P*GP*CP*G)-3', 6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE | | Authors: | Takenaka, A, Juan, E.C.M, Shimizu, S, Haraguchi, T, Xiao, M, Kurose, T. | | Deposit date: | 2009-03-09 | | Release date: | 2010-03-31 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Insights into the stabilizing contributions of bicyclic cytosine analogues: crystal structures of DNA duplexes containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one
To be Published
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3GJJ
 | | crystal structure of a DNA duplex containing 7,8-dihydropyridol[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, Haraguchi, T, Xiao, M, Kurose, T, Ohkubo, A, Sekine, M, Shibata, T, Millington, C.L, Williams, D.M. | | Deposit date: | 2009-03-09 | | Release date: | 2010-03-31 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Insights into the stabilizing contributions of bicyclic cytosine analogues: crystal structures of DNA duplexes containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one
To be Published
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3GJK
 | | crystal structure of a DNA duplex containing 7,8-dihydropyridol[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', POTASSIUM ION | | Authors: | Takenaka, A, Juan, E.C.M, Shimizu, S, Haraguchi, T, Xiao, M, Kurose, T, Ohkubo, A, Sekine, M, Shibata, T, Millington, C.L, Williams, D.M. | | Deposit date: | 2009-03-09 | | Release date: | 2010-03-31 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Insights into the stabilizing contributions of bicyclic cytosine analogues: crystal structures of DNA duplexes containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one
To be Published
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3GJL
 | | crystal structure of a DNA duplex containing 7,8-dihydropyridol[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', SODIUM ION | | Authors: | Takenaka, A, Juan, E.C.M, Shimizu, S, Haraguchi, T, Xiao, M, Kurose, T, Ohkubo, A, Sekine, M, Shibata, T, Millington, C.L, Williams, D.M. | | Deposit date: | 2009-03-09 | | Release date: | 2010-03-31 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.92 Å) | | Cite: | Insights into the stabilizing contributions of bicyclic cytosine analogues: crystal structures of DNA duplexes containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one
To be Published
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456D
 | | MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGMO6AATCCGCG): THE WATSON-CRICK TYPE N6-METHOXYADENOSINE/CYTIDINE BASE-PAIRS IN B-DNA | | Descriptor: | DNA (5'-D(*CP*GP*CP*GP*(A47)P*AP*TP*CP*CP*GP*CP*G)-3'), MAGNESIUM ION | | Authors: | Chatake, T, Ono, A, Ueno, Y, Matsuda, A, Takenaka, A. | | Deposit date: | 1999-03-06 | | Release date: | 2000-01-01 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Crystallographic studies on damaged DNAs. I. An N(6)-methoxyadenine residue forms a Watson-Crick pair with a cytosine residue in a B-DNA duplex.
J.Mol.Biol., 294, 1999
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2FZA
 | | Crystal structure of d(GCGGGAGC): the base-intercalated duplex | | Descriptor: | 5'-D(*GP*(CBR)P*GP*GP*GP*AP*GP*C)-3', CALCIUM ION, SODIUM ION | | Authors: | Kondo, J, Ciengshin, T, Juan, E.C.M, Mitomi, K, Takenaka, A. | | Deposit date: | 2006-02-09 | | Release date: | 2007-01-23 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (3.6 Å) | | Cite: | Crystal structure of d(gcGXGAgc) with X=G: a mutation at X is possible to occur in a base-intercalated duplex for multiplex formation
Nucleosides Nucleotides Nucleic Acids, 25, 2006
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2GOT
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5B4V
 | | Crystal structure of D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis complexed with NAD+ and an inhibitor methylmalonate | | Descriptor: | 3-hydroxybutyrate dehydrogenase, CHLORIDE ION, METHYLMALONIC ACID, ... | | Authors: | Kanazawa, H, Tsunoda, M, Hoque, M.M, Suzuki, K, Yamamoto, T, Takenaka, A. | | Deposit date: | 2016-04-19 | | Release date: | 2016-08-17 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Structural insights into the catalytic reaction trigger and inhibition of D-3-hydroxybutyrate dehydrogenase
Acta Crystallogr.,Sect.F, 72, 2016
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5B4T
 | | Crystal structure of D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis complexed with NAD+ and a substrate D-3-hydroxybutyrate | | Descriptor: | (3R)-3-hydroxybutanoic acid, 3-hydroxybutyrate dehydrogenase, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... | | Authors: | Kanazawa, H, Tsunoda, M, Hoque, M.M, Suzuki, K, Yamamoto, T, Takenaka, A. | | Deposit date: | 2016-04-19 | | Release date: | 2016-08-17 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.19 Å) | | Cite: | Structural insights into the catalytic reaction trigger and inhibition of D-3-hydroxybutyrate dehydrogenase
Acta Crystallogr.,Sect.F, 72, 2016
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5B4U
 | | Crystal structure of D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis complexed with NAD+ and an inhibitor malonate | | Descriptor: | 3-hydroxybutyrate dehydrogenase, CHLORIDE ION, MALONIC ACID, ... | | Authors: | Kanazawa, H, Tsunoda, M, Hoque, M.M, Suzuki, K, Yamamoto, T, Takenaka, A. | | Deposit date: | 2016-04-19 | | Release date: | 2016-08-17 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Structural insights into the catalytic reaction trigger and inhibition of D-3-hydroxybutyrate dehydrogenase
Acta Crystallogr.,Sect.F, 72, 2016
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4IJ0
 | | Structures of DNA duplexes containing O6-carboxymethylguanine, a lesion associated with gastrointestinal cancer, reveal a mechanism for inducing transition mutation | | Descriptor: | 2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE, DNA (5'-D(*CP*GP*CP*(C6G)P*AP*AP*TP*TP*CP*GP*CP*G)-3'), STRONTIUM ION | | Authors: | Zhang, F, Suzuki, K, Tsunoda, M, Wilkinson, O, Millington, C.L, Williams, D.M, Morishita, E.C, Takenaka, A. | | Deposit date: | 2012-12-20 | | Release date: | 2013-05-08 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.54 Å) | | Cite: | Structures of DNA duplexes containing O6-carboxymethylguanine, a lesion associated with gastrointestinal cancer, reveal a mechanism for inducing pyrimidine transition mutations
Nucleic Acids Res., 41, 2013
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4ITD
 | | Structures of DNA duplexes containing O6-carboxymethylguanine, a lesion associated with gastrointestinal cancer, reveal a mechanism for inducing transition mutation | | Descriptor: | 2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE, DNA (5'-D(*CP*GP*CP*GP*(C6G)P*AP*TP*TP*CP*GP*CP*G)-3'), MAGNESIUM ION | | Authors: | Zhang, F, Suzuki, K, Tsunoda, M, Wilkinson, O, Millington, C.L, Williams, D.M, Morishita, E.C, Takenaka, A. | | Deposit date: | 2013-01-18 | | Release date: | 2013-05-08 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.94 Å) | | Cite: | Structures of DNA duplexes containing O6-carboxymethylguanine, a lesion associated with gastrointestinal cancer, reveal a mechanism for inducing pyrimidine transition mutations
Nucleic Acids Res., 41, 2013
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457D
 | | MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGMO6AATTCGCG): N6-METHOXYADENOSINE/ THYMIDINE BASE-PAIRS IN B-DNA | | Descriptor: | DNA (5'-D(*CP*GP*CP*GP*(A47)P*AP*TP*TP*CP*GP*CP*G)-3'), MAGNESIUM ION | | Authors: | Chatake, T, Ono, A, Ueno, Y, Matsuda, A, Takenaka, A. | | Deposit date: | 1999-03-06 | | Release date: | 2000-01-01 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Crystallographic studies on damaged DNAs. II. N(6)-methoxyadenine can present two alternate faces for Watson-Crick base-pairing, leading to pyrimidine transition mutagenesis.
J.Mol.Biol., 294, 1999
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4G1R
 | | Crystal structure of anti-HIV actinohivin in complex with alphs-1,2-mannobiose (Form II) | | Descriptor: | Actinohivin, alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose | | Authors: | Hoque, M.M, Suzuki, K, Tsunoda, M, Jiang, J, Zhang, F, Takahashi, A, Naomi, O, Zhang, X, Sekiguchi, T, Tanaka, H, Omura, S, Takenaka, A. | | Deposit date: | 2012-07-11 | | Release date: | 2013-07-17 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.57 Å) | | Cite: | Matured structure of anti-HIV lectin actinohivin in complex with alpha-1,2-mannobiose
To be Published
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4DEN
 | | Structural insightsinto potent, specific anti-HIV property of actinohivin; Crystal structure of actinohivin in complex with alpha(1-2) mannobiose moiety of high-mannose type glycan of gp120 | | Descriptor: | Actinohivin, POTASSIUM ION, alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose | | Authors: | Hoque, M.M, Suzuki, K, Tsunoda, M, Jiang, J, Zhang, F, Takahashi, A, Naomi, O, Zhang, X, Sekiguchi, T, Tanaka, H, Omura, S, Takenaka, A. | | Deposit date: | 2012-01-20 | | Release date: | 2012-11-28 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Structural insights into the specific anti-HIV property of actinohivin: structure of its complex with the alpha(1–2)mannobiose moiety of gp120
Acta Crystallogr.,Sect.D, 68, 2012
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1EDR
 | | MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGMO6AATTCGCG) AT 1.6 ANGSTROM | | Descriptor: | 5'-D(*CP*GP*CP*GP*(A47)AP*AP*TP*TP*CP*GP*CP*G)-3', MAGNESIUM ION, SPERMINE | | Authors: | Chatake, T, Hikima, T, Ono, A, Ueno, Y, Matsuda, A, Takenaka, A. | | Deposit date: | 2000-01-28 | | Release date: | 2000-02-16 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Crystallographic studies on damaged DNAs. II. N(6)-methoxyadenine can present two alternate faces for Watson-Crick base-pairing, leading to pyrimidine transition mutagenesis.
J.Mol.Biol., 294, 1999
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4END
 | | Crystal structure of anti-HIV actinohivin in complex with alpha-1,2-mannobiose (P 2 21 21 form) | | Descriptor: | ACETONITRILE, Actinohivin, alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose | | Authors: | Hoque, M.M, Suzuki, K, Tsunoda, M, Jiang, J, Zhang, F, Takahashi, A, Naomi, O, Zhang, X, Sekiguchi, T, Tanaka, H, Omura, S, Takenaka, A. | | Deposit date: | 2012-04-13 | | Release date: | 2013-07-17 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Matured structure of anti-HIV lectin actinohivin in complex with 1,2-mannobiose
To be Published
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4O5Y
 | | O6-carboxymethylguanine in DNA forms a sequence context dependent wobble base pair structure with thymine | | Descriptor: | BARIUM ION, DNA (5'-D(*CP*GP*CP*(C6G)P*AP*AP*TP*TP*TP*GP*CP*G)-3'), POTASSIUM ION | | Authors: | Zhang, F, Tsunoda, M, Suzuki, K, Kikuchi, Y, Wilkinson, O, Millington, C.L, Margison, G.P, Williams, D.M, Takenaka, A. | | Deposit date: | 2013-12-20 | | Release date: | 2014-07-02 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | O(6)-Carboxymethylguanine in DNA forms a sequence context-dependent wobble base-pair structure with thymine
Acta Crystallogr.,Sect.D, 70, 2014
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1G8N
 | | MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGAATF5UCGCG):5-FORMYLURIDINE/ ADENOSINE BASE-PAIRS IN B-DNA | | Descriptor: | 5'-D(*CP*GP*CP*GP*AP*AP*TP*(UFR)P*CP*GP*CP*G)-3', MAGNESIUM ION | | Authors: | Tsunoda, M, Karino, N, Ueno, Y, Matsuda, A, Takenaka, A. | | Deposit date: | 2000-11-20 | | Release date: | 2001-02-05 | | Last modified: | 2023-08-09 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | Crystallization and preliminary X-ray analysis of a DNA dodecamer containing 2'-deoxy-5-formyluridine; what is the role of magnesium cation in crystallization of Dickerson-type DNA dodecamers?
Acta Crystallogr.,Sect.D, 57, 2001
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4O5X
 | | O6-carboxymethylguanine in DNA forms a sequence context dependent wobble base pair structure with thymine. | | Descriptor: | 2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE, DNA (5'-D(*CP*GP*CP*(C6G)P*AP*AP*TP*TP*TP*GP*CP*G)-3'), MAGNESIUM ION | | Authors: | Zhang, F, Tsunoda, M, Suzuki, K, Kikuchi, Y, Wilkinson, O, Millington, C.L, Margison, G.P, Williams, D.M, Takenaka, A. | | Deposit date: | 2013-12-20 | | Release date: | 2014-07-02 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | O(6)-Carboxymethylguanine in DNA forms a sequence context-dependent wobble base-pair structure with thymine
Acta Crystallogr.,Sect.D, 70, 2014
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4O5W
 | | O6-carboxymethylguanine in DNA forms a sequence context dependent wobble base pair structure with thymine | | Descriptor: | 2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE, DNA (5'-D(*CP*GP*CP*(C6G)P*AP*AP*TP*TP*TP*GP*CP*G)-3'), MAGNESIUM ION, ... | | Authors: | Zhang, F, Tsunoda, M, Suzuki, K, Kikuchi, Y, Wilkinson, O, Millington, C.L, Margison, G.P, Williams, D.M, Takenaka, A. | | Deposit date: | 2013-12-20 | | Release date: | 2014-07-02 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | O(6)-Carboxymethylguanine in DNA forms a sequence context-dependent wobble base-pair structure with thymine
Acta Crystallogr.,Sect.D, 70, 2014
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4O5Z
 | | O6-carboxymethylguanine in DNA forms a sequence context dependent wobble base pair structure with thymine | | Descriptor: | BARIUM ION, DNA (5'-D(*CP*GP*CP*(C6G)P*AP*AP*TP*TP*TP*GP*CP*G)-3'), SODIUM ION | | Authors: | Zhang, F, Tsunoda, M, Suzuki, K, Kikuchi, Y, Wilkinson, O, Millington, C.L, Margison, G.P, Williams, D.M, Takenaka, A. | | Deposit date: | 2013-12-20 | | Release date: | 2014-07-02 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | O(6)-Carboxymethylguanine in DNA forms a sequence context-dependent wobble base-pair structure with thymine
Acta Crystallogr.,Sect.D, 70, 2014
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1G75
 | | MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGAATF5UCGCG): 5-FORMYLURIDINE/ ADENOSINE BASE-PAIRS IN B-DNA | | Descriptor: | 5'-D(*CP*GP*CP*GP*AP*AP*TP*(UFR)P*CP*GP*CP*G)-3', MAGNESIUM ION, POTASSIUM ION | | Authors: | Tsunoda, M, Karino, N, Ueno, Y, Matsuda, A, Takenaka, A. | | Deposit date: | 2000-11-09 | | Release date: | 2001-02-05 | | Last modified: | 2023-08-09 | | Method: | X-RAY DIFFRACTION (1.57 Å) | | Cite: | Crystallization and preliminary X-ray analysis of a DNA dodecamer containing 2'-deoxy-5-formyluridine; what is the role of magnesium cation in crystallization of Dickerson-type DNA dodecamers?
Acta Crystallogr.,Sect.D, 57, 2001
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