1P26

Crystal structure of zinc(II)-d(GGCGCC)2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cobalt(II), nickel(II) and zinc(II) do not bind to intra-helical N(7) guanine positions in the B-form crystal structure of d(GGCGCC)

Labiuk, S.L.Delbaere, L.T.Lee, J.S.

(2003) J.Biol.Inorg.Chem. 8: 715-720

  • DOI: 10.1007/s00775-003-0473-4
  • Primary Citation of Related Structures:  1P24, 1P25

  • PubMed Abstract: 
  • Three novel X-ray crystal structures for the DNA hexamer d(GGCGCC) in the B-form complexed to divalent cobalt, nickel and zinc ions have been determined to a resolution of 2.9-3.0 A. The structures were isomorphous and had five DNA strands and five m ...

    Three novel X-ray crystal structures for the DNA hexamer d(GGCGCC) in the B-form complexed to divalent cobalt, nickel and zinc ions have been determined to a resolution of 2.9-3.0 A. The structures were isomorphous and had five DNA strands and five metal cations per asymmetric unit. In all three cases, divalent metal cations were coordinated only to the terminal guanine residue at the N(7) position, with no metal ions binding to non-terminal guanine positions. Water molecules bound to the metal cations interacted with neighboring guanine residues 3' to the ones to which the cations were coordinated, affecting the propeller twist. Even though DNA occupied only about 35% of the unit cell volume, it is interesting that the few interactions involving the metal cations were sufficient to stabilize the crystal lattice. As well as lending support to the proposal that these metals do not coordinate to B-DNA in a stable manner, the results presented here also extend the crystallographic evidence for this phenomenon to the GGC and CGC sequences for all three metal cations.


    Organizational Affiliation

    Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, S7N 5E5, Saskatoon, SK, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*GP*CP*GP*CP*C)-3'A,B,C,D,E6N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.210 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 68.800α = 90.00
b = 68.800β = 90.00
c = 55.280γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-12-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance