ISDA: 121D

Deposition Date 1993-04-14

Release Date 1994-01-15

Last Version Date 2024-02-07

Entry Detail

PDB ID:

121D

Keywords:

DNA

Title:

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

Biological Source:

Source Organism:

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.20 Å

R-Value Work:

0.19

R-Value Observed:

0.19

Space Group:

P 21 21 21

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Macromolecular Entities

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3')
Chain IDs:A, B
Chain Length:12
Number of Molecules:2
Biological Source:

Ligand Molecules

Primary Citation

Molecular structure of the A-tract DNA dodecamer d(CGCAAATTTGCG) complexed with the minor groove binding drug netropsin.

Tabernero, L, Verdaguer, N, Coll, M, Fita, I, van der Marel, G.A, van Boom, J.H, Rich, A, Aymami, J.Show

Biochemistry 32 8403 8410 (1993)

PMID: 8395202 DOI: 10.1021/bi00084a004

Abstact

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.

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