263d: Difference between revisions
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|PDB= 263d |SIZE=350|CAPTION= <scene name='initialview01'>263d</scene>, resolution 2.200Å | |PDB= 263d |SIZE=350|CAPTION= <scene name='initialview01'>263d</scene>, resolution 2.200Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=TBZ:2 | |LIGAND= <scene name='pdbligand=TBZ:2''-(4-METHOXYPHENYL)-5-(3-AMINO-1-PYRROLIDINYL)-2,5',2',5''-TRI-BENZIMIDAZOLE'>TBZ</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
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[[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 Sun Mar 23 14:33:27 2008'' | ||
Revision as of 12:33, 23 March 2008
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| 263d, resolution 2.200Å | |||||||||||||
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| Ligands: | TBZ | ||||||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
ISOHELICITY AND PHASING IN DRUG-DNA SEQUENCE RECOGNITION: CRYSTAL STRUCTURE OF A TRIS(BENZIMIDAZOLE)-OLIGONUCLEOTIDE COMPLEX
Overview
The crystal structure is reported of a tris(benzimidazole) analogue of the minor-groove drug Hoechst 33258 bound to the sequence d(CGCAAATTTGCG)2. The structure has been refined to an R factor of 17.4% at a resolution of 2.2 A. The ligand covers approximately 7 1/2 base pairs, including the 5'-AAATTT central sequence. This has an exceptionally narrow minor-groove width, together with high propeller twists for individual base pairs. The ligand has a highly twisted structure, with an overall twist of 50 degrees between aromatic rings. All three benzimidazole subunits are in register with the DNA, and there is a symmetric group of six hydrogen bonds between ligand and A.T base-pair edges. By contrast, the ligand does not show an optimal isohelical fit to the DNA. The correct phasing of drug and DNA base pairs is ensured by a number of changes to the DNA such that the central 5'-AAATTT region is slightly unwound relative to the structures of other noncovalent minor-groove drug complexes.
About this Structure
263D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Isohelicity and phasing in drug--DNA sequence recognition: crystal structure of a tris(benzimidazole)--oligonucleotide complex., Clark GR, Gray EJ, Neidle S, Li YH, Leupin W, Biochemistry. 1996 Oct 29;35(43):13745-52. PMID:8901516
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