362D

THE STRUCTURE OF D(TGCGCA)2 AND A COMPARISON TO OTHER Z-DNA HEXAMERS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.173 
  • R-Value Observed: 0.117 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of d(TGCGCA)2 and a comparison to other DNA hexamers.

Harper, A.Brannigan, J.A.Buck, M.Hewitt, L.Lewis, R.J.Moore, M.H.Schneider, B.

(1998) Acta Crystallogr D Biol Crystallogr 54: 1273-1284

  • DOI: 10.1107/s0907444998002807
  • Primary Citation of Related Structures:  
    362D

  • PubMed Abstract: 
  • The X-ray crystal structure of d(TGCGCA)2 has been determined at 120 K to a resolution of 1.3 A. Hexamer duplexes, in the Z-DNA conformation, pack in an arrangement similar to the 'pure spermine form' [Egli et al. (1991). Biochemistry, 30, 11388-11402] but with significantly different cell dimensions ...

    The X-ray crystal structure of d(TGCGCA)2 has been determined at 120 K to a resolution of 1.3 A. Hexamer duplexes, in the Z-DNA conformation, pack in an arrangement similar to the 'pure spermine form' [Egli et al. (1991). Biochemistry, 30, 11388-11402] but with significantly different cell dimensions. The phosphate backbone exists in two equally populated discrete conformations at one nucleotide step, around phosphate 11. The structure contains two ordered cobalt hexammine molecules which have roles in stabilization of both the Z-DNA conformation of the duplex and in crystal packing. A comparison of d(TGCGCA)2 with other Z-DNA hexamer structures available in the Nucleic Acid Database illustrates the elusive nature of crystal packing. A review of the interactions with the metal cations Na+, Mg2+ and Co3+ reveals a relatively small proportion of phosphate binding and that close contacts between metal ions are common. A prediction of the water structure is compared with the observed pattern in the reported structure.


    Organizational Affiliation

    Department of Chemistry, University of York, Heslington, York YO1 5DD, England.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*GP*CP*GP*CP*A)-3')A, 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], D [auth A]COBALT HEXAMMINE(III)
    Co H18 N6
    DYLMFCCYOUSRTK-FGTKAUEHAT
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.30 Å
    • R-Value Free: 0.173 
    • R-Value Observed: 0.117 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 21.162α = 90
    b = 28.67β = 90
    c = 44.335γ = 90
    Software Package:
    Software NamePurpose
    AMoREphasing
    SHELXL-96refinement
    DENZOdata reduction
    SCALEPACKdata scaling

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1997-11-20
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance