Cm. Nunn et al., 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), 1994, pp. 953-961
The crystal structure of the complex of gamma-oxapentamidine and the D
NA dodecamer d(CGCGAATTCGCG), has been determined to a resolution of 0
.22 nm and an R factor of 18.9%. The gamma-oxapentamidine ligand inter
acts with the dodecamer by classic minor groove binding via interactio
ns 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 t
he bound ligand. The structural details of the complex are discussed a
nd compared with the closely analogous complex with pentamidine bound
to the same dodecamer [Edwards, K. J., Jenkins, T. C. and Neidle, S. (
1992) Biochemistry 31, 7104-7109]. The amidinium groups of the ligand
do not hydrogen bond to bases, but are in close contact with O4' sugar
ring atoms. This in part explains the reduced DNA binding affinity of
this ligand compared to pentamidine.