109D

VARIABILITY IN DNA MINOR GROOVE WIDTH RECOGNISED BY LIGAND BINDING: THE CRYSTAL STRUCTURE OF A BIS-BENZIMIDAZOLE COMPOUND BOUND TO THE DNA DUPLEX D(CGCGAATTCGCG)2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Variability in DNA minor groove width recognised by ligand binding: the crystal structure of a bis-benzimidazole compound bound to the DNA duplex d(CGCGAATTCGCG)2.

Wood, A.A.Nunn, C.M.Czarny, A.Boykin, D.W.Neidle, S.

(1995) Nucleic Acids Res 23: 3678-3684

  • DOI: 10.1093/nar/23.18.3678
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • An analogue of the DNA-binding compound Hoechst 33258, in which the piperazine ring has been replaced by an imidazoline group, has been cocrystallized with the dodecanucleotide sequence d(CGCGAATTCGCG)2. The structure has been solved by X-ray diffrac ...

    An analogue of the DNA-binding compound Hoechst 33258, in which the piperazine ring has been replaced by an imidazoline group, has been cocrystallized with the dodecanucleotide sequence d(CGCGAATTCGCG)2. The structure has been solved by X-ray diffraction analysis and has been refined to an R-factor of 19.7% at a resolution of 2.0 A. The ligand is found to bind in the minor groove, at the central four AATT base pairs of the B-DNA double helix, with the involvement of a number of van der Waals contacts and hydrogen bonds. There are significant differences in minor groove width for the two compounds, along much of the AATT region. In particular this structure shows a narrower groove at the 3' end of the binding site consistent with the narrower cross-section of the imidazole group compared with the piperazine ring of Hoechst 33258 and therefore a smaller perturbation in groove width. The higher binding affinity to DNA shown by this analogue compared with Hoechst 33258 itself, has been rationalised in terms of these differences.


    Related Citations: 
    • Analysis of Van Der Waals and Electrostatic Contributions in the Interactions of Minor Groove Binding Benzimidazoles with DNA
      Czarny, A., Boykin, D.W., Wood, A.A., Nunn, C.M., Neidle, S., Zhao, M., Wilson, W.D.
      (1995) J Am Chem Soc 117: 4716
    • Low Temperature Crystallographic Analyses of the Binding of Hoechst 33258 to the Double Helical DNA Dodecamer C-G-C-G-A-A-T-T-C-G-C-G
      Quintana, J.R., Lipanov, A.A., Dickerson, R.E.
      (1991) Biochemistry 30: 10294

    Organizational Affiliation

    CRC Biomolecular Structure Unit, Institute of Cancer Research, Surrey, UK.



Macromolecules
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')A, B12N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IBB
Query on IBB

Download CCD File 
A
5-(2-IMIDAZOLINYL)-2-[2-(4-HYDROXYPHENYL)-5-BENZIMIDAZOLYL]BENZIMIDAZOLE
C23 H20 N6 O
SOARWAXWPUGSQA-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 24.59α = 90
b = 40.44β = 90
c = 65.76γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-05-08
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance