121D

MOLECULAR STRUCTURE OF THE A-TRACT DNA DODECAMER D(CGCAAATTTGCG) COMPLEXED WITH THE MINOR GROOVE BINDING DRUG NETROPSIN

Summary for 121D

• Entry DOI: 10.2210/pdb121d/pdb
• Descriptor: DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3'), NETROPSIN (3 entities in total)
• Functional Keywords: b-dna, double helix, complexed with drug, dna
• Total number of polymer chains: 2
• Total formula weight: 7755.27

Authors

Tabernero, L.,Verdaguer, N.,Coll, M.,Fita, I.,Van Der Marel, G.A.,Van Boom, J.H.,Rich, A.,Aymami, J. (deposition date: 1993-04-14, release date: 1994-01-15, Last modification date: 2024-02-07)

Primary citation

Tabernero, L.,Verdaguer, N.,Coll, M.,Fita, I.,van der Marel, G.A.,van Boom, J.H.,Rich, A.,Aymami, J.
Molecular structure of the A-tract DNA dodecamer d(CGCAAATTTGCG) complexed with the minor groove binding drug netropsin.
Biochemistry, 32:8403-8410, 1993

PubMed Abstract: The molecular structure of the complex between the minor groove binding drug netropsin and the dodecamer d(CGCAAATTTGCG) has been solved and refined by X-ray diffraction analysis to an R-factor of 19.8% and 2.2-A resolution. The drug lies in the narrow minor groove of the B-DNA fragment, covering five of the six A.T base pairs (from A5.T20 to T9.A16). The long six A.T base pair tract allows the drug to bind in a position that optimizes its contacts with the DNA, establishing hydrogen bonds with O2 of thymines and N3 of adenines. The DNA molecule shows a high propeller twist only at the A6.T19 step of the A-tract. Two three-centered hydrogen bonds are observed in the major groove at half of the A-tract.

PubMed: 8395202
DOI: 10.1021/bi00084a004

Experimental method

X-RAY DIFFRACTION (2.2 Å)