263d

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spinqualitylabelsall models PDB ID 263d Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image
, resolution 2.200Å
Ligands:
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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