261D

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

Summary for 261D

• Entry DOI: 10.2210/pdb261d/pdb
• Descriptor: DNA (5'-D(*CP*GP*CP*AP*AP*TP*TP*GP*CP*G)-3'), NETROPSIN (3 entities in total)
• Functional Keywords: b-dna, double helix, flipped-out bases, intermolecular base triplet, continuous helix, complexed with drug, dna
• Total number of polymer chains: 2
• Total formula weight: 6520.47

Authors

Nunn, C.M.,Garman, E.,Neidle, S. (deposition date: 1996-11-08, release date: 1997-04-22, Last modification date: 2024-02-14)

Primary citation

Nunn, C.M.,Garman, E.,Neidle, S.
Crystal structure of the DNA decamer d(CGCAATTGCG) complexed with the minor groove binding drug netropsin.
Biochemistry, 36:4792-4799, 1997

PubMed 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.

PubMed: 9125500
DOI: 10.1021/bi9628228

Experimental method

X-RAY DIFFRACTION (2.4 Å)