1XA2

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

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 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 ...

    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
    5'-D(*CP*GP*CP*GP*CP*A)-3'A6N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*TP*GP*CP*GP*CP*G)-3'B6N/A
      Protein Feature View
      Expand
      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      NCO
      Query on NCO

      Download Ideal Coordinates CCD File 
      C [auth A]COBALT HEXAMMINE(III)
      Co H18 N6
      DYLMFCCYOUSRTK-FGTKAUEHAT
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.71 Å
      • R-Value Free: 0.240 
      • R-Value Work: 0.208 
      • R-Value Observed: 0.210 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 17.976α = 90
      b = 30.926β = 90
      c = 44.625γ = 90
      Software Package:
      Software NamePurpose
      REFMACrefinement
      MAR345data collection
      AUTOMARdata reduction
      AMoREphasing

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • 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