1DCG

THE MOLECULAR STRUCTURE OF THE LEFT-HANDED Z-DNA DOUBLE HELIX AT 1.0 ANGSTROM ATOMIC RESOLUTION. GEOMETRY, CONFORMATION, AND IONIC INTERACTIONS OF D(CGCGCG)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The molecular structure of the left-handed Z-DNA double helix at 1.0-A atomic resolution. Geometry, conformation, and ionic interactions of d(CGCGCG).

Gessner, R.V.Frederick, C.A.Quigley, G.J.Rich, A.Wang, A.H.

(1989) J Biol Chem 264: 7921-7935

  • DOI: 10.2210/pdb1dcg/pdb
  • Primary Citation of Related Structures:  
    1DCG

  • PubMed Abstract: 
  • The structure of d(CGCGCG) crystallized in the presence of magnesium and sodium ions alone is compared to that of the spermine form of the molecule. The very high resolution nature of these structure determinations allows the first true examination of an oligonucleotide structure in fine detail ...

    The structure of d(CGCGCG) crystallized in the presence of magnesium and sodium ions alone is compared to that of the spermine form of the molecule. The very high resolution nature of these structure determinations allows the first true examination of an oligonucleotide structure in fine detail. The values of bond distances and angles are compared to those derived from small molecule crystal structures. In addition, the interactions of cations and polyamines with the Z-DNA helix are analyzed. In particular, multiple cationic charges appear to offer enhanced stabilization for the Z-DNA conformation. The location of spermine molecules along the edge of the deep groove and also spanning the entrance to the groove emphasizes the importance of polyamines for stabilizing this left-handed structure. On averaging, we obtained very similar structural parameters for the two different structures with standard deviations generally smaller than the deviations of the crystallographic model from ideal values. This indicates a high degree of accuracy of the two structures, which have been refined using different data and different refinement methods. The derived bond lengths and angles may thus be more representative of this polymeric DNA structure than those derived from mono- and dinucleotide structures at a similar accuracy.


    Related Citations: 
    • Molecular Structure of a Left-Handed Double Helical DNA Fragment at Atomic Resolution
      Wang, A.H.-J., Quigley, G.J., Kolpak, F.J., Crawford, J.L., Van Boom, J.H., Van Der Marel, G.A., Rich, A.
      (1979) Nature 282: 680

    Organizational Affiliation

    Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')A, B6N/A
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.00 Å
    • R-Value Observed: 0.175 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 18.01α = 90
    b = 31.03β = 90
    c = 44.8γ = 90
    Software Package:
    Software NamePurpose
    NUCLSQrefinement

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1989-01-09
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance