DSSR-enabled G4 identification/annotation: PDB entry 2gw0
Summary information and primary citation
- PDB-id
- 2gw0
- Class
- DNA
- Method
- X-ray (1.55 Å)
- Summary
- A d(tggggt)- sodium and calcium complex.
- Reference
- Lee MP, Parkinson GN, Hazel P, Neidle S (2007): "Observation of the coexistence of sodium and calcium ions in a DNA G-quadruplex ion channel." J.Am.Chem.Soc., 129, 10106-10107. doi: 10.1021/ja0740869.
- Abstract
- 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=0.248 type=bowl -- nts=4 GGGG 1:A.DG2,1:D.DG20,1:C.DG14,1:B.DG8 2 glyco-bond=---- sugar=---- groove=---- planarity=0.216 type=bowl -- nts=4 GGGG 1:A.DG3,1:D.DG21,1:C.DG15,1:B.DG9 3 glyco-bond=---- sugar=---- groove=---- planarity=0.216 type=bowl -- nts=4 GGGG 1:A.DG4,1:D.DG22,1:C.DG16,1:B.DG10 4 glyco-bond=---- sugar=---- groove=---- planarity=0.322 type=bowl -- nts=4 GGGG 1:A.DG5,1:D.DG23,1:C.DG17,1:B.DG11
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
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1 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG2,1:D.DG20,1:C.DG14,1:B.DG8 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG3,1:D.DG21,1:C.DG15,1:B.DG9 3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG4,1:D.DG22,1:C.DG16,1:B.DG10 4 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG5,1:D.DG23,1:C.DG17,1:B.DG11 step#1 pm(>>,forward) area=8.38 rise=3.32 twist=31.9 step#2 pm(>>,forward) area=10.76 rise=3.30 twist=28.6 step#3 pm(>>,forward) area=11.87 rise=3.40 twist=26.9 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.DG20,1:D.DG21,1:D.DG22,1:D.DG23 strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:C.DG14,1:C.DG15,1:C.DG16,1:C.DG17 strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:B.DG8,1:B.DG9,1:B.DG10,1:B.DG11 |
| 3 stacking diagrams | |
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG2,1:D.DG20,1:C.DG14,1:B.DG8 |
|
2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG3,1:D.DG21,1:C.DG15,1:B.DG9 |
|
3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG4,1:D.DG22,1:C.DG16,1:B.DG10 |
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.DG20,1:C.DG14,1:B.DG8 2 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG3,1:D.DG21,1:C.DG15,1:B.DG9 3 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG4,1:D.DG22,1:C.DG16,1:B.DG10 4 glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG 1:A.DG5,1:D.DG23,1:C.DG17,1:B.DG11 step#1 pm(>>,forward) area=8.38 rise=3.32 twist=31.9 step#2 pm(>>,forward) area=10.76 rise=3.30 twist=28.6 step#3 pm(>>,forward) area=11.87 rise=3.40 twist=26.9 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.DG20,1:D.DG21,1:D.DG22,1:D.DG23 strand#3 U DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:C.DG14,1:C.DG15,1:C.DG16,1:C.DG17 strand#4 U DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:B.DG8,1:B.DG9,1:B.DG10,1:B.DG11 |