1DN8

STRUCTURE OF A Z-DNA WITH TWO DIFFERENT BACKBONE CHAIN CONFORMATIONS. STABILIZATION OF THE DECADEOXYOLIGONUCLEOTIDE D(CGTACGTACG) BY (CO(NH3)6)3+ BINDING TO THE GUANINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Observed: 0.250 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of a Z-DNA with two different backbone chain conformations. Stabilization of the decadeoxyoligonucleotide d(CGTACGTACG) by [Co(NH3)6]3+ binding to the guanine.

Brennan, R.G.Westhof, E.Sundaralingam, M.

(1986) J Biomol Struct Dyn 3: 649-665

  • DOI: 10.1080/07391102.1986.10508453
  • Primary Citation of Related Structures:  
    1DN8

  • PubMed Abstract: 
  • The complex between cobalt hexammine and decadeoxyoligomer d(CGTACGTACG) crystallizes into the space group P65 with unit cell constants a = b = 17.93A, and c = 43.41A. The molecules have the helix axis coincident with the crystal c-axis. The decamers ...

    The complex between cobalt hexammine and decadeoxyoligomer d(CGTACGTACG) crystallizes into the space group P65 with unit cell constants a = b = 17.93A, and c = 43.41A. The molecules have the helix axis coincident with the crystal c-axis. The decamers stack on top of each other and form a quasi-continuous helix. The structure is disordered. The asymmetric unit is a dimer (pPyr-pPur)2 with each base pair 60% of the time a C-G and 40% of the time a T-A. Restrainted least-squares refinement led to an R-factor of 25.5% for 506 observed reflections above the two-sigma level. The structure was found to have one strand in the ZI-conformation and the other in the ZII-conformation. The cobalt hexammine binds to two ZII-chains of symmetrically related molecules. On one ZII chain, two ammonia molecules of the cobalt hexammine bind to the N7 nitrogen and 06 oxygen atoms of the guanine bases and a third ammonia to the phosphate anionic oxygen atom of the preceding pyrimidine base, resulting in an "external" binding mode. On the other ZII chain, one ammonia molecule of the cobalt hexammine binds only to the anionic oxygens of the phosphate group of the guanine bases, leading to an "internal" binding mode. Thus, the basis of the stabilization of Z-DNA by [Co(NH3)6]3+ is its binding to only guanine nucleotides. It is surmised that statistical disordering of deoxyoligonucleotide structures which take a Z conformation, depends on the length of the oligomer. That is to say, octamers and decamers (which cannot use an integral number of molecules for a 12 base pair repeat) form disordered structures whereas tetramers and hexamers form well ordered structures.


    Related Citations: 
    • Crystallization and Preliminary Crystallographic Studies of the Decadeoxyoligonucleotide d(CpGpTpApCpGpTpApCpG)
      Brennan, R.G., Sundaralingam, M.
      (1985) J Mol Biol 181: 561

    Organizational Affiliation

    Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin, Madison 53706.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*P*CP*GP*TP*AP*CP*GP*TP*AP*CP*G)-3')A, B2N/A
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    NCO
    Query on NCO

    Download CCD File 
    B
    COBALT HEXAMMINE(III)
    Co H18 N6
    DYLMFCCYOUSRTK-FGTKAUEHAT
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.50 Å
    • R-Value Observed: 0.250 
    • Space Group: P 65
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 17.93α = 90
    b = 17.93β = 90
    c = 43.41γ = 120
    Software Package:
    Software NamePurpose
    NUCLSQrefinement

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 1988-04-16
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2018-04-18
      Changes: Data collection