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Nunn, Christine M., Jenkins, Terence C. and Neidle, Stephen (1994) Crystal Structure of gamma-Oxapentamidine complexed with d(CGCGAATTCGCG)2. the effects of drug structural change on DNA minor-groove recognition. European Journal of Biochemistry, 226 (3). pp. 953-961. ISSN 0014-2956
The crystal structure of the complex of y-oxapentamidine and the DNA dodecamer d(CGCGAATTCGCG), has been determined to a resolution of 0.22 nm and an R factor of 18.9%. The y-oxapentamidine ligand interacts with the dodecamer by classic minor groove binding via interactions within the A+T-rich region of the minor groove. A chain of solvent molecules lies along the mouth of the minor groove on the outside of the bound ligand. The structural details of the complex are discussed and compared with the closely analogous complex with pentamidine bound to the same dodecamer [Edwards, K. J., Jenkins, T. C. & Neidle, S. (1992) Biochemistry 31, 7104-71091. The amidinium groups of the ligand do not hydrogen bond to bases, but are in close contact with 04' sugar ring atoms. This in part explains the reduced DNA binding affinity of this ligand compared to pentamidine.
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