311d
From Proteopedia
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|PDB= 311d |SIZE=350|CAPTION= <scene name='initialview01'>311d</scene>, resolution 2.200Å | |PDB= 311d |SIZE=350|CAPTION= <scene name='initialview01'>311d</scene>, resolution 2.200Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=HT2:5-AMIDINO-2-[2-(4-AMIDINOPHENYL)-5-BENZIMIDAZOLYL]BENZIMIDAZOLE'>HT2</scene> | + | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=HT2:5-AMIDINO-2-[2-(4-AMIDINOPHENYL)-5-BENZIMIDAZOLYL]BENZIMIDAZOLE'>HT2</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=311d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=311d OCA], [http://www.ebi.ac.uk/pdbsum/311d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=311d RCSB]</span> | ||
}} | }} | ||
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[[Category: Czarny, A.]] | [[Category: Czarny, A.]] | ||
[[Category: Neidle, S.]] | [[Category: Neidle, S.]] | ||
| - | [[Category: HT2]] | ||
[[Category: b-dna]] | [[Category: b-dna]] | ||
[[Category: complexed with drug]] | [[Category: complexed with drug]] | ||
[[Category: double helix]] | [[Category: double helix]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:21:12 2008'' |
Revision as of 02:21, 31 March 2008
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| , resolution 2.200Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
THE ROLE OF HYDROGEN BONDING IN MINOR-GROOVE DRUG-DNA RECOGNITION. STRUCTURE OF A BIS-AMIDINIUM DERIVATIVE OF HOECHST 33258 COMPLEXED TO THE DODECANUCLEOTIDE D(CGCGAATTCGCG)2
Overview
The crystal structure is reported of a complex between the dodecanucleotide sequence d(CGCGAATTCGCG)2and an analogue of the DNA binding drug Hoechst 33258, in which the piperazine ring has been replaced by an amidinium group and the phenol ring by a phenylamidinium group. The structure has been refined to an R factor of 19.5% at 2.2 A resolution. The drug is held in the minor groove by five strong hydrogen bonds, together with bridging water molecules at both ends. There are few other contacts with the floor of the groove, indicating a lack of isohelicity with the groove and suggesting (i) that the observed high DNA affinity of this drug is primarily due to the array of hydrogen bonds and (ii) that these more than compensate for its poor isohelicity.
About this Structure
311D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Structure of a bis-amidinium derivative of hoechst 33258 complexed to dodecanucleotide d(CGCGAATTCGCG)2: the role of hydrogen bonding in minor groove drug-DNA recognition., Clark GR, Boykin DW, Czarny A, Neidle S, Nucleic Acids Res. 1997 Apr 15;25(8):1510-5. PMID:9162901
Page seeded by OCA on Mon Mar 31 05:21:12 2008
