1XAM

Cobalt hexammine induced tautameric shift in Z-DNA: structure of d(CGCGCA).d(TGCGCG) in two crystal forms.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.346 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.279 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Cobalt hexammine induced tautomeric shift in Z-DNA: the structure of d(CGCGCA)*d(TGCGCG) in two crystal forms.

Thiyagarajan, S.Rajan, S.S.Gautham, N.

(2004) Nucleic Acids Res 32: 5945-5953

  • DOI: 10.1093/nar/gkh919
  • Primary Citation of Related Structures:  
    1XA2, 1XAM

  • PubMed Abstract: 
  • We report here the crystal structure of the DNA hexamer duplex d(CGCGCA)*d(TGCGCG) at 1.71 A resolution. The crystals, in orthorhombic space group, were grown in the presence of cobalt hexammine, a known inducer of the left-handed Z form of DNA. The ...

    We report here the crystal structure of the DNA hexamer duplex d(CGCGCA)*d(TGCGCG) at 1.71 A resolution. The crystals, in orthorhombic space group, were grown in the presence of cobalt hexammine, a known inducer of the left-handed Z form of DNA. The interaction of this ion with the DNA helix results in a change of the adenine base from the common amino tautomeric form to the imino tautomer. Consequently the A:T base pair is disrupted from the normal Watson-Crick base pairing to a 'wobble' like base pairing. This change is accommodated easily within the helix, and the helical parameters are those expected for Z-DNA. When the cobalt hexammine concentration is decreased slightly in the crystallization conditions, the duplex crystallizes in a different, hexagonal space group, with two hexamer duplexes in the asymmetric unit. One of these is situated on a crystallographic 6-fold screw axis, leading to disorder. The tautomeric shift is not observed in this space group. We show that the change in inter-helix interactions that lead to the two different space groups probably arise from the small decrease in ion concentration, and consequently disordered positions for the ion.


    Related Citations: 
    • Structure of d(TGCGCG). d(CGCGCA) in two crystal forms: effects of sequence and crystal packing in Z-DNA
      Thiyagarajan, S., Rajan, S.S., Gautham, N.
      (2005) Acta Crystallogr D Biol Crystallogr 61: 1125

    Organizational Affiliation

    Department of Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    CGCGCAA6N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      TGCGCGB6N/A
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
        MoleculeChainsLengthOrganismImage
        TGD, E2N/A
        Small Molecules
        Ligands 1 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        NCO
        Query on NCO

        Download CCD File 
        E
        COBALT HEXAMMINE(III)
        Co H18 N6
        DYLMFCCYOUSRTK-FGTKAUEHAT
         Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 1.86 Å
        • R-Value Free: 0.346 
        • R-Value Work: 0.273 
        • R-Value Observed: 0.279 
        • Space Group: P 65
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 35.588α = 90
        b = 35.588β = 90
        c = 44.518γ = 120
        Software Package:
        Software NamePurpose
        REFMACrefinement
        XDSdata reduction
        AUTOMARdata reduction
        AMoREphasing

        Structure Validation

        View Full Validation Report



        Entry History 

        Deposition Data

        Revision History 

        • Version 1.0: 2004-11-16
          Type: Initial release
        • Version 1.1: 2008-04-30
          Changes: Version format compliance
        • Version 1.2: 2011-07-13
          Changes: Version format compliance
        • Version 1.3: 2017-10-11
          Changes: Refinement description