5BNA

THE PRIMARY MODE OF BINDING OF CISPLATIN TO A B-DNA DODECAMER: C-G-C-G-A-A-T-T-C-G-C-G


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Observed: 0.102 

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This is version 1.2 of the entry. See complete history


Literature

The primary mode of binding of cisplatin to a B-DNA dodecamer: C-G-C-G-A-A-T-T-C-G-C-G

Wing, R.M.Pjura, P.Drew, H.R.Dickerson, R.E.

(1984) EMBO J 3: 1201-1206

  • Primary Citation of Related Structures:  
    5BNA

  • PubMed Abstract: 
  • When cisplatin [cis- diamminodichloroplatinum (II)] is diffused into pre-grown crystals of the B-DNA double-helical dodecamer C-G-C-G-A-A-T-T-C-G-C-G, it binds preferentially to the N7 positions of guanines, with what probably is an aquo bridge between Pt and the adjacent O6 atom of the same guanine ...

    When cisplatin [cis- diamminodichloroplatinum (II)] is diffused into pre-grown crystals of the B-DNA double-helical dodecamer C-G-C-G-A-A-T-T-C-G-C-G, it binds preferentially to the N7 positions of guanines, with what probably is an aquo bridge between Pt and the adjacent O6 atom of the same guanine. The entire guanine ring moves slightly toward the platinum site, into the major groove. Only three of the eight potential cisplatin binding sites on guanines actually are occupied, and this differential reactivity can be explained in terms of the relative freedom of motion of guanines toward the major groove. This shift of guanines upon ligation may weaken the glycosyl bond and assist in the depurination that leads to mismatch SOS repair and G.C. to T.A. transversion.


    Related Citations: 
    • A Random-Walk Model for Helix Bending in B-DNA
      Dickerson, R.E., Kopka, M.L., Pjura, P.
      (1983) Proc Natl Acad Sci U S A 80: 7099
    • Helix Geometry and Hydration in A-DNA, B-DNA and Z-DNA
      Dickerson, R.E., Drew, H.R., Conner, B.N., Kopka, M.L., Pjura, P.E.
      (1983) Cold Spring Harb Symp Quant Biol 47: 13
    • Base Sequence, Helix Geometry, Hydration and Helix Stability in B-DNA
      Dickerson, R.E., Kopka, M.L., Pjura, P.
      (1985) Biological Macromolecules And Assemblies 2: 37
    • Crystal Structure Analysis of a Complete Turn of B-DNA
      Wing, R., Drew, H.R., Takano, T., Broka, C., Tanaka, S., Itakura, K., Dickerson, R.E.
      (1980) Nature 287: 755

    Organizational Affiliation

    Laboratory of Microbial Molecular Physiology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.



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

    Download Ideal Coordinates CCD File 
    C [auth A], D [auth A], E [auth B]PLATINUM TRIAMINE ION
    H9 N3 Pt
    OMAFVUDQJABSNM-PHIGXVQTAM
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.60 Å
    • R-Value Observed: 0.102 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 24.16α = 90
    b = 39.93β = 90
    c = 66.12γ = 90
    Software Package:
    Software NamePurpose
    JACK-LEVITTrefinement

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1983-11-02
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance