264D

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 

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This is version 1.4 of the entry. See complete history


Literature

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.

(1994) Eur J Biochem 222: 721-726

  • DOI: https://doi.org/10.1111/j.1432-1033.1994.tb18917.x
  • Primary Citation of Related Structures:  
    264D

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    Departament de Biologia Molecular i Cel-lular, Centre d'Investigació i Desenvolupament-C.S.I.C., Barcelona, Spain.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3')
A, B
12N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HT
Query on HT

Download Ideal Coordinates CCD File 
C [auth B]2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE
C25 H24 N6 O
INAAIJLSXJJHOZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 25.5α = 90
b = 41.4β = 90
c = 65.3γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-03-31
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2016-12-14
    Changes: Database references
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations