ISDA

Deposition Date 1994-09-22

Release Date 1995-03-31

Last Version Date 2024-02-14

Entry Detail

PDB ID:

264D

Keywords:

DNA

Title:

THREE-DIMENSIONAL CRYSTAL STRUCTURE OF THE A-TRACT DNA DODECAMER D(CGCAAATTTGCG) COMPLEXED WITH THE MINOR-GROOVE-BINDING DRUG HOECHST 33258

Biological Source:

Source Organism:

(Taxon ID: ) (Taxon ID: )

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.44 Å

R-Value Work:

0.20

R-Value Observed:

0.20

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

Three-dimensional crystal structure of the A-tract DNA dodecamer d(CGCAAATTTGCG) complexed with the minor-groove-binding drug Hoechst 33258.

Vega, M.C, Garcia Saez, I, Aymami, J, Eritja, R, Van der Marel, G.A, Van Boom, J.H, Rich, A, Coll, M, Carrondo, M.A, Coll, M, Aymami, J, Wang, A.H, van der Marel, G.A, van Boom, J.H, Rich, A, Coll, M, Frederick, C.A, Wang, A.H.-J, Rich, A.Show

Eur.J.Biochem. 222 721 726 (1994)

PMID: 7517864 DOI: 10.1111/j.1432-1033.1994.tb18917.x

Abstact

The molecular structure of the DNA A-tract dodecamer d(CGCAAATTTGCG) complexed with the drug Hoechst 33258 has been determined by X-ray diffraction analysis. The Hoechst molecule binds in the DNA minor groove covering the sequence AATTT of the central A-tract, with the piperazine group close to one of the GC regions. The drug molecule makes two three-centered hydrogen bonds from the nitrogen atoms of the benzimidazole rings to the N3 and O2 atoms of the DNA bases. Although a high propeller twist is observed in the A-tract, only one unsymmetrical three-centered hydrogen bond is present in the DNA major groove. The structure is compared with other minor-groove-binding drug complexes and the influence of these drugs on DNA A-tracts is discussed.

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Primary Citation of related structures