4FS5

Crystal structure of the Z-DNA hexamer CGCGCG at 500 mM MgCl2

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 2012-06-26 Released: 2013-05-15 
  • Deposition Author(s): Chatake, T., Sunami, T.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Direct interactions between Z-DNA and alkaline earth cations, discovered in the presence of high concentrations of MgCl2 and CaCl2

Chatake, T.Sunami, T.

(2013) J Inorg Biochem 124: 15-25

  • DOI: 10.1016/j.jinorgbio.2013.03.004
  • Primary Citation of Related Structures:  
    4FS5, 4FS6

  • PubMed Abstract: 
  • In this study, crystals of Z-DNA hexamer d(CGCGCG) complexed with MgCl2 and CaCl2 were obtained in the presence of high concentrations of alkaline earth salts (500mM) using a temperature control technique, and their crystal structures were determined at 1 ...

    In this study, crystals of Z-DNA hexamer d(CGCGCG) complexed with MgCl2 and CaCl2 were obtained in the presence of high concentrations of alkaline earth salts (500mM) using a temperature control technique, and their crystal structures were determined at 1.3Å resolution. Mg(2+) and Ca(2+) cations in these structures tend to interact directly with phosphate groups of Z-DNA duplexes; however, they tend to form water-mediated interactions with Z-DNA in the presence of lower concentrations of alkaline earth salts. In these crystals, a DNA duplex was laid along its c-axis and interacted with its 6 neighboring DNA duplexes through coordination bonds of PO…(Mg(2+) or Ca(2+))…OP. A symmetrical hexagonal Z-DNA duplex assembly model may explain DNA condensation caused by alkaline earth salts. These structures offer insights into the functions of alkaline earth cations essential to the structures and assembly of Z-DNA duplexes.


    Organizational Affiliation

    Research Reactor Institute, Kyoto University, Asashironishi 2, Kumatori, Osaka, 590-0494, Japan. chatake@rri.kyoto-u.ac.jp



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')A, B6N/A
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.30 Å
    • R-Value Free: 0.264 
    • R-Value Work: 0.211 
    • R-Value Observed: 0.213 
    • Space Group: P 32
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 18.593α = 90
    b = 18.593β = 90
    c = 72.7γ = 120
    Software Package:
    Software NamePurpose
    BSSdata collection
    AMoREphasing
    PHENIXrefinement
    MOSFLMdata reduction
    SCALAdata scaling

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2013-05-15
      Type: Initial release