4HIF

Ultrahigh-resolution crystal structure of Z-DNA in complex with Zn2+ ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.85 Å
  • R-Value Free: 0.113 

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Literature

Ultrahigh-resolution crystal structures of Z-DNA in complex with Mn(2+) and Zn(2+) ions.

Drozdzal, P.Gilski, M.Kierzek, R.Lomozik, L.Jaskolski, M.

(2013) Acta Crystallogr.,Sect.D 69: 1180-1190

  • DOI: 10.1107/S0907444913007798
  • Primary Citation of Related Structures:  4HIG
  • Also Cited By: 4R15, 5EBI, 5JZQ

  • PubMed Abstract: 
  • X-ray crystal structures of the spermine(4+) form of the Z-DNA duplex with the self-complementary d(CG)3 sequence in complexes with Mn(2+) and Zn(2+) cations have been determined at the ultrahigh resolutions of 0.75 and 0.85 Å, respectively. Stereoch ...

    X-ray crystal structures of the spermine(4+) form of the Z-DNA duplex with the self-complementary d(CG)3 sequence in complexes with Mn(2+) and Zn(2+) cations have been determined at the ultrahigh resolutions of 0.75 and 0.85 Å, respectively. Stereochemical restraints were only used for the sperminium cation (in both structures) and for nucleotides with dual conformation in the Zn(2+) complex. The Mn(2+) and Zn(2+) cations at the major site, designated M(2+)(1), bind at the N7 position of G6 by direct coordination. The coordination geometry of this site was octahedral, with complete hydration shells. An additional Zn(2+)(2) cation was bis-coordinated in a tetrahedral fashion by the N7 atoms of G10 and G12 from a symmetry-related molecule. The coordination distances of Zn(2+)(1) and Zn(2+)(2) to the O6 atom of the guanine residues were 3.613 (6) and 3.258 (5) Å, respectively. Moreover, a chloride ion was also identified in the coordination sphere of Zn(2+)(2). Alternate conformations were observed in the Z-DNA-Zn(2+) structure not only at internucleotide linkages but also at the terminal C3'-OH group of G12. The conformation of the sperminium chain in the Z-DNA-Mn(2+) complex is similar to the spermine(4+) conformation in analogous Z-DNA-Mg(2+) structures. In the Z-DNA-Zn(2+) complex the sperminium cation is disordered and partially invisible in electron-density maps. In the Z-DNA-Zn(2+) complex the sperminium cation only interacts with the phosphate groups of the Z-DNA molecules, while in the Z-DNA-Mn(2+) structure it forms hydrogen bonds to both the phosphate groups and DNA bases.


    Related Citations: 
    • High regularity of Z-DNA revealed by ultra high-resolution crystal structure at 0.55 A
      Brzezinski, K.,Brzuszkiewicz, A.,Dauter, M.,Kubicki, M.,Jaskolski, M.,Dauter, Z.
      (2011) Nucleic Acids Res. 39: 6238
    • Anomalous signal of phosphorus used for phasing DNA oligomer: importance of data redundancy
      Dauter, Z.,Adamiak, D.A.
      (2001) Acta Crystallogr.,Sect.D 57: 990


    Organizational Affiliation

    Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')A,B6synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
SPK
Query on SPK

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B
SPERMINE (FULLY PROTONATED FORM)
C10 H30 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-R
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.85 Å
  • R-Value Free: 0.113 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 17.791α = 90.00
b = 30.907β = 90.00
c = 44.196γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
MAR345dtbdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-05
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Advisory, Data collection