1D32

DRUG-INDUCED DNA REPAIR: X-RAY STRUCTURE OF A DNA-DITERCALINIUM COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Drug-induced DNA repair: X-ray structure of a DNA-ditercalinium complex.

Gao, Q.Williams, L.D.Egli, M.Rabinovich, D.Chen, S.L.Quigley, G.J.Rich, A.

(1991) Proc Natl Acad Sci U S A 88: 2422-2426

  • DOI: 10.1073/pnas.88.6.2422
  • Primary Citation of Related Structures:  
    1D32

  • PubMed Abstract: 
  • Ditercalinium is a synthetic anticancer drug that binds to DNA by bis-intercalation and activates DNA repair processes. In prokaryotes, noncovalent DNA-ditercalinium complexes are incorrectly recognized by the uvrABC repair system as covalent lesions on DNA ...

    Ditercalinium is a synthetic anticancer drug that binds to DNA by bis-intercalation and activates DNA repair processes. In prokaryotes, noncovalent DNA-ditercalinium complexes are incorrectly recognized by the uvrABC repair system as covalent lesions on DNA. In eukaryotes, mitochondrial DNA is degraded by excess and futile DNA repair. Using x-ray crystallography, we have determined, to 1.7 A resolution, the three-dimensional structure of a complex of ditercalinium bound to the double-stranded DNA fragment [d(CGCG)]2. The DNA in the complex with ditercalinium is kinked (by 15 degrees) and severely unwound (by 36 degrees) with exceptionally wide major and minor grooves. Recognition of the DNA-ditercalinium complex by uvrABC in prokaryotes, and by mitochondrial DNA repair systems in eukaryotes, might be related to drug-induced distortion of the DNA helix.


    Related Citations: 
    • DNA-Ditercalinium Interactions: Implications for Recognition of Damaged DNA
      Williams, L.D., Gao, Q.
      (1992) Biochemistry 31: 4315

    Organizational Affiliation

    Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*GP*CP*G)-3')A, B4N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    DIT (Subject of Investigation/LOI)
    Query on DIT

    Download Ideal Coordinates CCD File 
    C [auth A]DITERCALINIUM
    C46 H50 N6 O2
    NHUWXMNVGMRODJ-UHFFFAOYSA-P
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.70 Å
    • R-Value Observed: 0.225 
    • Space Group: P 41 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 26.88α = 90
    b = 26.88β = 90
    c = 82.6γ = 90
    Software Package:
    Software NamePurpose
    NUCLSQrefinement

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1992-04-15
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance