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PDBsum entry 2o4f

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dna_rna metals links
DNA PDB id
2o4f
Jmol
Contents
DNA/RNA
Metals
_NA ×7
_LI
Waters ×228
PDB id:
2o4f
Name: DNA
Title: Structure of a parallel-stranded guanine tetraplex crystallised with monovalent ions
Structure: 5'-d( Tp Gp Gp Gp Gp T)-3'. Chain: a, b, c, d, e, f, g, h. Engineered: yes
Source: Synthetic: yes
Resolution:
1.50Å     R-factor:   0.204     R-free:   0.257
Authors: C.Creze,B.Rinaldi,R.Haser,P.Bouvet,P.Gouet
Key ref:
C.Creze et al. (2007). Structure of a d(TGGGGT) quadruplex crystallized in the presence of Li+ ions. Acta Crystallogr D Biol Crystallogr, 63, 682-688. PubMed id: 17505106 DOI: 10.1107/S0907444907013315
Date:
04-Dec-06     Release date:   22-May-07    
 Headers
 References

 

 
DOI no: 10.1107/S0907444907013315 Acta Crystallogr D Biol Crystallogr 63:682-688 (2007)
PubMed id: 17505106  
 
 
Structure of a d(TGGGGT) quadruplex crystallized in the presence of Li+ ions.
C.Creze, B.Rinaldi, R.Haser, P.Bouvet, P.Gouet.
 
  ABSTRACT  
 
A parallel 5'-d(TGGGGT)-3' quadruplex was formed in Na(+) solution and crystallized using lithium sulfate as the main precipitating agent. The X-ray structure was determined to 1.5 A resolution in space group P2(1) by molecular replacement. The asymmetric unit consists of a characteristic motif of two quadruplexes stacked at their 5' ends. All nucleotides are clearly defined in the density and could be positioned. A single bound Li(+) ion is observed at the surface of the column formed by the two joined molecules. Thus, this small alkali metal ion appears to be unsuitable as a replacement for the Na(+) ion in the central channel of G-quartets, unlike K(+) or Tl(+) ions. A well conserved constellation of water molecules is observed in the grooves of the dimeric structure.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 Representative electron-density view of a guanine tetrad. The 2F[o] - F[c] map is contoured at 1 . The Na^+ ion is rendered as a violet ball. This ion is coordinated to the O6 atoms of the guanines.
Figure 3.
Figure 3 Schematic view of two adjacent quadruplexes showing the separation of the guanine tetrads and of Na^+ ions. The upper quadruplex is made up of strands A, B, C and D. The lower quadruplex contains strands E, F, G and H and the guanine tetrads at the 5' extremity that break the dyad symmetry. Guanines are rendered as green rectangles, thymines as blue rectangles and thymines of the adjacent quadruplex as striped blue rectangles. Na^+ ions are pictured as violet balls. The two capping water molecules are shown as red balls. Distances are in Å.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2007, 63, 682-688) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18156672 P.R.Strickland, and B.McMahon (2008).
Crystallographic publishing in the electronic age.
  Acta Crystallogr A, 64, 38-51.  
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