4FS5

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.211 

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:  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 ...

    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

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Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')A,B6N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.211 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 18.593α = 90.00
b = 18.593β = 90.00
c = 72.700γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
BSSdata collection
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

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