Detailed DSSR results for the G-quadruplex: PDB entry 2gw0
Created and maintained by Xiang-Jun Lu <xiangjun@x3dna.org>
Citation: Please cite the NAR'20 DSSR-PyMOL schematics paper and/or the NAR'15 DSSR method paper.
Summary information
- 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
- 8 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, parallel(4+0), UUUU, coaxial interfaces: 5'/5'
Base-block schematics in six views
List of 8 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.248 type=bowl nts=4 GGGG A.DG2,D.DG20,C.DG14,B.DG8 2 glyco-bond=---- sugar=---- groove=---- planarity=0.216 type=bowl nts=4 GGGG A.DG3,D.DG21,C.DG15,B.DG9 3 glyco-bond=---- sugar=---- groove=---- planarity=0.216 type=bowl nts=4 GGGG A.DG4,D.DG22,C.DG16,B.DG10 4 glyco-bond=---- sugar=---- groove=---- planarity=0.322 type=bowl nts=4 GGGG A.DG5,D.DG23,C.DG17,B.DG11 5 glyco-bond=---- sugar=3333 groove=---- planarity=0.108 type=planar nts=4 GGGG E.DG26,H.DG44,G.DG38,F.DG32 6 glyco-bond=---- sugar=---- groove=---- planarity=0.205 type=bowl nts=4 GGGG E.DG27,H.DG45,G.DG39,F.DG33 7 glyco-bond=---- sugar=---- groove=---- planarity=0.241 type=bowl nts=4 GGGG E.DG28,H.DG46,G.DG40,F.DG34 8 glyco-bond=---- sugar=---- groove=---- planarity=0.245 type=bowl nts=4 GGGG E.DG29,H.DG47,G.DG41,F.DG35
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, 8 G-tetrad layers, inter-molecular, with 2 stems
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG23,C.DG17,B.DG11 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG22,C.DG16,B.DG10 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,D.DG21,C.DG15,B.DG9 4* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,D.DG20,C.DG14,B.DG8 5 glyco-bond=---- sugar=3333 groove=---- Major-->WC nts=4 GGGG E.DG26,F.DG32,G.DG38,H.DG44 6 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG E.DG27,F.DG33,G.DG39,H.DG45 7 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG E.DG28,F.DG34,G.DG40,H.DG46 8 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG E.DG29,F.DG35,G.DG41,H.DG47 step#1 mp(<<,backward) area=11.87 rise=3.40 twist=26.9 step#2 mp(<<,backward) area=10.76 rise=3.30 twist=28.6 step#3 mp(<<,backward) area=8.38 rise=3.32 twist=31.9 step#4 mm(<>,outward) area=14.74 rise=3.53 twist=16.0 step#5 pm(>>,forward) area=7.23 rise=3.48 twist=34.5 step#6 pm(>>,forward) area=11.46 rise=3.32 twist=28.6 step#7 pm(>>,forward) area=10.73 rise=3.34 twist=28.6 strand#1 DNA glyco-bond=-------- sugar=----3--- nts=8 GGGGGGGG A.DG5,A.DG4,A.DG3,A.DG2,E.DG26,E.DG27,E.DG28,E.DG29 strand#2 DNA glyco-bond=-------- sugar=----3--- nts=8 GGGGGGGG D.DG23,D.DG22,D.DG21,D.DG20,F.DG32,F.DG33,F.DG34,F.DG35 strand#3 DNA glyco-bond=-------- sugar=----3--- nts=8 GGGGGGGG C.DG17,C.DG16,C.DG15,C.DG14,G.DG38,G.DG39,G.DG40,G.DG41 strand#4 DNA glyco-bond=-------- sugar=----3--- nts=8 GGGGGGGG B.DG11,B.DG10,B.DG9,B.DG8,H.DG44,H.DG45,H.DG46,H.DG47 |
| 7 stacking diagrams | |
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG23,C.DG17,B.DG11 |
 |
2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG22,C.DG16,B.DG10 |
 |
3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,D.DG21,C.DG15,B.DG9 |
 |
4* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,D.DG20,C.DG14,B.DG8 |
 |
5 glyco-bond=---- sugar=3333 groove=---- Major-->WC nts=4 GGGG E.DG26,F.DG32,G.DG38,H.DG44 |
 |
6 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG E.DG27,F.DG33,G.DG39,H.DG45 |
 |
7 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG E.DG28,F.DG34,G.DG40,H.DG46 |
List of 2 G4-stems
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-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,D.DG20,C.DG14,B.DG8 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,D.DG21,C.DG15,B.DG9 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG22,C.DG16,B.DG10 4 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG23,C.DG17,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 A.DG2,A.DG3,A.DG4,A.DG5 strand#2 U DNA glyco-bond=---- sugar=---- nts=4 GGGG D.DG20,D.DG21,D.DG22,D.DG23 strand#3 U DNA glyco-bond=---- sugar=---- nts=4 GGGG C.DG14,C.DG15,C.DG16,C.DG17 strand#4 U DNA glyco-bond=---- sugar=---- nts=4 GGGG B.DG8,B.DG9,B.DG10,B.DG11 |
Stem#2, 4 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)
 |
1 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 GGGG E.DG26,H.DG44,G.DG38,F.DG32 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG27,H.DG45,G.DG39,F.DG33 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG28,H.DG46,G.DG40,F.DG34 4 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG29,H.DG47,G.DG41,F.DG35 step#1 pm(>>,forward) area=7.23 rise=3.48 twist=34.5 step#2 pm(>>,forward) area=11.46 rise=3.32 twist=28.6 step#3 pm(>>,forward) area=10.73 rise=3.34 twist=28.6 strand#1 U DNA glyco-bond=---- sugar=3--- nts=4 GGGG E.DG26,E.DG27,E.DG28,E.DG29 strand#2 U DNA glyco-bond=---- sugar=3--- nts=4 GGGG H.DG44,H.DG45,H.DG46,H.DG47 strand#3 U DNA glyco-bond=---- sugar=3--- nts=4 GGGG G.DG38,G.DG39,G.DG40,G.DG41 strand#4 U DNA glyco-bond=---- sugar=3--- nts=4 GGGG F.DG32,F.DG33,F.DG34,F.DG35 |
List of 1 G4 coaxial stack
1 G4 helix#1 contains 2 G4 stems: [#1,#2] [5'/5']