DSSR-enabled G4 identification/annotation: PDB entry 2o4f
Summary information and primary citation
- PDB-id
- 2o4f
- Class
- DNA
- Method
- X-ray (1.5 Å)
- Summary
- Structure of a parallel-stranded guanine tetraplex crystallised with monovalent ions
- Reference
- Creze C, Rinaldi B, Haser R, Bouvet P, Gouet P (2007): "Structure of a d(TGGGGT) quadruplex crystallized in the presence of Li+ ions." Acta Crystallogr.,Sect.D, 63, 682-688. doi: 10.1107/S0907444907013315.
- 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.
- G4 notes
- 4 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0
Cartoon-block schematics in six views (download the tarball)
List of 4 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.277 type=bowl -- nts=4 GGGG 1:A.DG2,1:D.DG32,1:C.DG22,1:B.DG12 2 glyco-bond=---- sugar=---- groove=---- planarity=0.191 type=bowl -- nts=4 GGGG 1:A.DG3,1:D.DG33,1:C.DG23,1:B.DG13 3 glyco-bond=---- sugar=---- groove=---- planarity=0.216 type=bowl -- nts=4 GGGG 1:A.DG4,1:D.DG34,1:C.DG24,1:B.DG14 4 glyco-bond=---- sugar=---- groove=---- planarity=0.228 type=bowl -- nts=4 GGGG 1:A.DG5,1:D.DG35,1:C.DG25,1:B.DG15
List of 1 G4-helix
In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.
Helix#1, 4 G-tetrads, inter-molecular, with 1 stem
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG2,1:D.DG32,1:C.DG22,1:B.DG12 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG3,1:D.DG33,1:C.DG23,1:B.DG13 3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG4,1:D.DG34,1:C.DG24,1:B.DG14 4 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG5,1:D.DG35,1:C.DG25,1:B.DG15 step#1 pm(>>,forward) area=9.31 rise=3.39 twist=30.8 step#2 pm(>>,forward) area=11.51 rise=3.31 twist=28.7 step#3 pm(>>,forward) area=12.32 rise=3.36 twist=28.3 strand#1 DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:A.DG2,1:A.DG3,1:A.DG4,1:A.DG5 strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:D.DG32,1:D.DG33,1:D.DG34,1:D.DG35 strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:C.DG22,1:C.DG23,1:C.DG24,1:C.DG25 strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:B.DG12,1:B.DG13,1:B.DG14,1:B.DG15 |
| 3 stacking diagrams | |
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG2,1:D.DG32,1:C.DG22,1:B.DG12 |
|
2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG3,1:D.DG33,1:C.DG23,1:B.DG13 |
|
3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG4,1:D.DG34,1:C.DG24,1:B.DG14 |
List of 1 G4-stem
In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.
Stem#1, 4 G-tetrads, 0 loops, inter-molecular, UUUU, parallel, 4+0
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1 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG2,1:D.DG32,1:C.DG22,1:B.DG12 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG3,1:D.DG33,1:C.DG23,1:B.DG13 3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG4,1:D.DG34,1:C.DG24,1:B.DG14 4 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG5,1:D.DG35,1:C.DG25,1:B.DG15 step#1 pm(>>,forward) area=9.31 rise=3.39 twist=30.8 step#2 pm(>>,forward) area=11.51 rise=3.31 twist=28.7 step#3 pm(>>,forward) area=12.32 rise=3.36 twist=28.3 strand#1 U DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:A.DG2,1:A.DG3,1:A.DG4,1:A.DG5 strand#2 U DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:D.DG32,1:D.DG33,1:D.DG34,1:D.DG35 strand#3 U DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:C.DG22,1:C.DG23,1:C.DG24,1:C.DG25 strand#4 U DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:B.DG12,1:B.DG13,1:B.DG14,1:B.DG15 |