261d
From Proteopedia
|
CRYSTAL STRUCTURE OF THE DNA DECAMER D(CGCAATTGCG) COMPLEXED WITH THE MINOR GROOVE BINDING DRUG NETROPSIN
Overview
The crystal structure of netropsin bound to the decamer d(CGCAATTGCG) has been determined at 2.4 A resolution. This is the first example of a crystal structure of netropsin bound to decamer DNA. The central eight bases of each DNA single-strand base pair with a self-complementary strand to form an octamer B-DNA duplex. These duplexes lie end to end within the unit cell. The terminal 5'-C and G-3' bases are unpaired and interact with the neighboring duplexes via interactions within both the major and minor groove to form base triplet interactions of the type C(+)-G x C and G*(G x C), respectively. The triplet interaction of the type C(+)-G x C is known to exist within triplex DNA with the C+ base oriented parallel with the Watson-Crick guanine base to which it hydrogen bonds. The netropsin molecule lies within the minor groove of the octamer duplex and assumes a class I type position, with bifurcated hydrogen-bonding interactions from the amide groups of the netropsin to the A x T base pairs of the minor groove. The netropsin molecule fits within a five base pair long minor groove site by bending of the flexible amidinium group at one end of the drug.
About this Structure
261D is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
Reference
Crystal structure of the DNA decamer d(CGCAATTGCG) complexed with the minor groove binding drug netropsin., Nunn CM, Garman E, Neidle S, Biochemistry. 1997 Apr 22;36(16):4792-9. PMID:9125500
Page seeded by OCA on Thu Feb 21 16:21:55 2008
