1F69

CRYSTAL STRUCTURE OF THE B-DNA HEXAMER GGCGCC WITH COBALT HEXAMINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The extended and eccentric E-DNA structure induced by cytosine methylation or bromination.

Vargason, J.M.Eichman, B.F.Ho, P.S.

(2000) Nat Struct Biol 7: 758-761

  • DOI: 10.1038/78985
  • Primary Citation of Related Structures:  
    1F69, 1F6E, 1F6C, 1F6J, 1F6I

  • PubMed Abstract: 
  • Cytosine methylation or bromination of the DNA sequence d(GGCGCC)2 is shown here to induce a novel extended and eccentric double helix, which we call E-DNA. Like B-DNA, E-DNA has a long helical rise and bases perpendicular to the helix axis. However, ...

    Cytosine methylation or bromination of the DNA sequence d(GGCGCC)2 is shown here to induce a novel extended and eccentric double helix, which we call E-DNA. Like B-DNA, E-DNA has a long helical rise and bases perpendicular to the helix axis. However, the 3'-endo sugar conformation gives the characteristic deep major groove and shallow minor groove of A-DNA. Also, if allowed to crystallize for a period of time longer than that yielding E-DNA, the methylated sequence forms standard A-DNA, suggesting that E-DNA is a kinetically trapped intermediate in the transition to A-DNA. Thus, the structures presented here chart a crystallographic pathway from B-DNA to A-DNA through the E-DNA intermediate in a single sequence. The E-DNA surface is highly accessible to solvent, with waters in the major groove sitting on exposed faces of the stacked nucleotides. We suggest that the geometry of the waters and the stacked base pairs would promote the spontaneous deamination of 5-methylcytosine in the transition mutation of dm5C-dG to dT-dA base pairs.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, ALS 2011, Oregon State University, Corvallis, Oregon 97331-7305, USA.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*GP*CP*GP*CP*C)-3')A, B6N/A
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    NCO
    Query on NCO

    Download CCD File 
    A
    COBALT HEXAMMINE(III)
    Co H18 N6
    DYLMFCCYOUSRTK-FGTKAUEHAT
     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: 2.60 Å
    • R-Value Free: 0.279 
    • R-Value Work: 0.205 
    • R-Value Observed: 0.213 
    • Space Group: P 41 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 42.59α = 90
    b = 42.59β = 90
    c = 63.3γ = 90
    Software Package:
    Software NamePurpose
    X-PLORmodel building
    X-PLORrefinement
    d*TREKdata reduction
    d*TREKdata scaling
    X-PLORphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2000-08-28
      Type: Initial release
    • Version 1.1: 2008-04-27
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance