264D: Three-dimensional Crystal Structure Of The A-tract Dna Dodecamer D(cgcaaatttgcg) Complexed With The Minor-groove-binding Drug Hoechst 33258

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.
PDB ID: 264DDownload
MMDB ID: 52403
PDB Deposition Date: 1994/9/22
Updated in MMDB: 2016/12
Experimental Method:
x-ray diffraction
Resolution: 2.44  Å
Biological Unit for 264D: dimeric; determined by author
Molecular Components in 264D
Label Count Molecule
Nucleotide(1 molecule)
DNA (5'-d(*cp*gp*cp*ap*ap*ap*tp*tp*tp*gp*cp*g)-3')
Molecule annotation
Chemical (1 molecule)
* Click molecule labels to explore molecular sequence information.

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