131D

THE LOW-TEMPERATURE CRYSTAL STRUCTURE OF THE PURE-SPERMINE FORM OF Z-DNA REVEALS BINDING OF A SPERMINE MOLECULE IN THE MINOR GROOVE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Observed: 0.180 

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This is version 1.2 of the entry. See complete history


Literature

The low-temperature crystal structure of the pure-spermine form of Z-DNA reveals binding of a spermine molecule in the minor groove.

Bancroft, D.Williams, L.D.Rich, A.Egli, M.

(1994) Biochemistry 33: 1073-1086

  • DOI: 10.1021/bi00171a005
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The X-ray crystal structure of the pure-spermine form of the left-handed Z-DNA duplex [d(CGCGCG)]2 has been determined at a temperature of -110 degrees C. Whereas the previously described room temperature structure of the pure-spermine form showed on ...

    The X-ray crystal structure of the pure-spermine form of the left-handed Z-DNA duplex [d(CGCGCG)]2 has been determined at a temperature of -110 degrees C. Whereas the previously described room temperature structure of the pure-spermine form showed only the presence of a single "interhelix" spermine molecule, mediating contacts between neighboring duplexes (Egli et al., 1991), a second "intrahelix" spermine molecule as well as two hydrated sodium ions were found in the structure determined at low temperature. This second spermine molecule binds primarily within the minor groove of two hexamer duplexes that are stacked in an end-to-end fashion in the crystal lattice. Thus, the intrahelix spermine molecule interacts with a single infinite helix. The spine of hydration observed in other structures of Z-DNA hexamers is partially replaced and partially displaced by the intrahelix spermine molecule. In Z-DNA, phosphate groups are relatively closely spaced across the minor groove compared to the right-handed double-helical conformation of B-DNA. The intrahelix spermine molecule decreases cross-groove electrostatic repulsion within the Z-DNA helix, thereby increasing its relative stability. This structure may therefore provide an explanation for the role of spermine as a very effective inducer of the conformational B-DNA to Z-DNA transition with alternating dG-dC sequences in solution.


    Related Citations: 
    • Structure of the Pure-Spermine Form of Z-DNA (Magnesium Free) at 1 Angstrom Resolution
      Egli, M., Williams, L.D., Gao, Q., Rich, A.
      (1991) Biochemistry 30: 11388

    Organizational Affiliation

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



Macromolecules
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')A, B6N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPM
Query on SPM

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A, B
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 18.265α = 90
b = 30.69β = 90
c = 42.46γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement
MODIFIEDrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-15
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance