1D40

BASE SPECIFIC BINDING OF COPPER(II) TO Z-DNA: THE 1.3-ANGSTROMS SINGLE CRYSTAL STRUCTURE OF D(M5CGUAM5CG) IN THE PRESENCE OF CUCL2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Base-specific binding of copper(II) to Z-DNA. The 1.3-A single crystal structure of d(m5CGUAm5CG) in the presence of CuCl2.

Geierstanger, B.H.Kagawa, T.F.Chen, S.L.Quigley, G.J.Ho, P.S.

(1991) J Biol Chem 266: 20185-20191

  • DOI: 10.2210/pdb1d40/pdb
  • Primary Citation of Related Structures:  
    1D40

  • PubMed Abstract: 
  • The single crystal structure of d(m5CGUAm5CG) soaked with copper(II) chloride was solved to atomic (1.3 A) resolution to study the base specificity of copper binding to double-stranded DNA. In the present copper(II) chloride-soaked structure, four crystallographically unique copper(II) complexes were observed bound to five of the six purine bases in the hexamer duplex ...

    The single crystal structure of d(m5CGUAm5CG) soaked with copper(II) chloride was solved to atomic (1.3 A) resolution to study the base specificity of copper binding to double-stranded DNA. In the present copper(II) chloride-soaked structure, four crystallographically unique copper(II) complexes were observed bound to five of the six purine bases in the hexamer duplex. Covalent copper(II) binding occurred at N-7 of all four guanine bases and at one of the two adenine bases in the DNA duplex. Copper binding was not observed at the position (Ade4) located in an open solvent channel, whereas the second adenine site (Ade10) shared a complex with a guanine residue (Gua12) of a neighboring symmetry-related hexamer. The coordination geometries and distribution of these copper(II) complexes at the guanine bases in the crystal were comparable to the analogous sites in the isomorphous copper(II) chloride-soaked d(CGCGCG) crystal (Kagawa, T., Geierstanger, B. H., Wang, A. H.-J., and Ho, P.S. (1991) J. Biol. Chem. 266, 20175-20184). Thus, the decreased copper(II) binding affinity for Ade4 was not an artifact of crystal packing, but is intrinsic to the chemical properties of this purine base in duplex DNA. This suggests that the adenine bases in dilute solutions of Z-DNA and more generally other duplex DNA conformations are not susceptible to copper(II) modification. Thus, preferential copper(II) binding at guanine bases over adenine bases in double-stranded DNA may explain the observed specificity of copper(II)-induced oxidative DNA damage near guanine residues (Yamamoto, K., and Kawanishi, S. (1989) J. Biol. Chem. 264, 15435-15440; Sagripanti, J.-L., and Kraemer, K. H. (1989) J. Biol. Chem. 264, 1729-1734). The sharing of a single copper(II) complex by Ade10 and Gua12 of an adjacent hexamer suggests that additional and perhaps specific DNA-DNA interactions, as may be found in the densely packed environment of the nuclear matrix in the cell, may render N-7 of adenine bases prone to copper(II) modification.


    Related Citations: 
    • Stabilization of Z-DNA by Demethylation of Thymine Bases: 1.3-Angstroms Single-Crystal Structure of d(m5CGUAm5CG)
      Zhou, G., Ho, P.S.
      (1990) Biochemistry 29: 7229

    Organizational Affiliation

    Department of Biochemistry and Biophysics, Oregon State University, Corvallis 97331-6503.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*(5CM)P*(CU)GP*UP*AP*(5CM)P*(CU)G)-3')A, B6N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    CUL
    Query on CUL

    Download Ideal Coordinates CCD File 
    F [auth B]COPPER (II) CHLORIDE
    Cl2 Cu
    ORTQZVOHEJQUHG-UHFFFAOYSA-L
     Ligand Interaction
    CU
    Query on CU

    Download Ideal Coordinates CCD File 
    C [auth A], D [auth A], E [auth B]COPPER (II) ION
    Cu
    JPVYNHNXODAKFH-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.30 Å
    • R-Value Observed: 0.209 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 17.59α = 90
    b = 30.58β = 90
    c = 44.52γ = 90
    Software Package:
    Software NamePurpose
    NUCLSQrefinement

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1992-04-15
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance