261D: CRYSTAL STRUCTURE OF THE DNA DECAMER D(CGCAATTGCG) COMPLEXED WITH THE MINOR GROOVE BINDING DRUG NETROPSIN

Citation:
Abstract
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.
PDB ID: 261DDownload
MMDB ID: 52401
PDB Deposition Date: 1996/11/8
Updated in MMDB: 2007/10
Experimental Method:
x-ray diffraction
Resolution: 2.4  Å
Biological Unit for 261D: dimeric; determined by author
Molecular Components in 261D
Label Count Molecule
Nucleotide(1 molecule)
2
DNA (5'-d(*cp*gp*cp*ap*ap*tp*tp*gp*cp*g)-3')
Molecule annotation
Chemical (1 molecule)
1
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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