Detailed DSSR results for the G-quadruplex: PDB entry 2o4f
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
- 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
- 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=0.277 type=bowl nts=4 GGGG A.DG2,D.DG32,C.DG22,B.DG12 2 glyco-bond=---- sugar=---- groove=---- planarity=0.191 type=bowl nts=4 GGGG A.DG3,D.DG33,C.DG23,B.DG13 3 glyco-bond=---- sugar=---- groove=---- planarity=0.216 type=bowl nts=4 GGGG A.DG4,D.DG34,C.DG24,B.DG14 4 glyco-bond=---- sugar=---- groove=---- planarity=0.228 type=bowl nts=4 GGGG A.DG5,D.DG35,C.DG25,B.DG15 5 glyco-bond=---- sugar=3333 groove=---- planarity=0.106 type=planar nts=4 GGGG E.DG42,H.DG72,G.DG62,F.DG52 6 glyco-bond=---- sugar=---- groove=---- planarity=0.243 type=bowl nts=4 GGGG E.DG43,H.DG73,G.DG63,F.DG53 7 glyco-bond=---- sugar=---- groove=---- planarity=0.296 type=bowl nts=4 GGGG E.DG44,H.DG74,G.DG64,F.DG54 8 glyco-bond=---- sugar=---- groove=---- planarity=0.266 type=bowl nts=4 GGGG E.DG45,H.DG75,G.DG65,F.DG55
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.DG35,C.DG25,B.DG15 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG34,C.DG24,B.DG14 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,D.DG33,C.DG23,B.DG13 4* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,D.DG32,C.DG22,B.DG12 5 glyco-bond=---- sugar=3333 groove=---- Major-->WC nts=4 GGGG H.DG72,E.DG42,F.DG52,G.DG62 6 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG H.DG73,E.DG43,F.DG53,G.DG63 7 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG H.DG74,E.DG44,F.DG54,G.DG64 8 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG H.DG75,E.DG45,F.DG55,G.DG65 step#1 mp(<<,backward) area=12.32 rise=3.36 twist=28.3 step#2 mp(<<,backward) area=11.51 rise=3.31 twist=28.7 step#3 mp(<<,backward) area=9.31 rise=3.39 twist=30.8 step#4 mm(<>,outward) area=12.30 rise=3.74 twist=16.2 step#5 pm(>>,forward) area=10.09 rise=3.53 twist=30.1 step#6 pm(>>,forward) area=8.22 rise=3.50 twist=32.6 step#7 pm(>>,forward) area=12.22 rise=3.37 twist=27.2 strand#1 DNA glyco-bond=-------- sugar=----3--- nts=8 GGGGGGGG A.DG5,A.DG4,A.DG3,A.DG2,H.DG72,H.DG73,H.DG74,H.DG75 strand#2 DNA glyco-bond=-------- sugar=----3--- nts=8 GGGGGGGG D.DG35,D.DG34,D.DG33,D.DG32,E.DG42,E.DG43,E.DG44,E.DG45 strand#3 DNA glyco-bond=-------- sugar=----3--- nts=8 GGGGGGGG C.DG25,C.DG24,C.DG23,C.DG22,F.DG52,F.DG53,F.DG54,F.DG55 strand#4 DNA glyco-bond=-------- sugar=----3--- nts=8 GGGGGGGG B.DG15,B.DG14,B.DG13,B.DG12,G.DG62,G.DG63,G.DG64,G.DG65 |
| 7 stacking diagrams | |
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG35,C.DG25,B.DG15 |
 |
2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG34,C.DG24,B.DG14 |
 |
3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,D.DG33,C.DG23,B.DG13 |
 |
4* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,D.DG32,C.DG22,B.DG12 |
 |
5 glyco-bond=---- sugar=3333 groove=---- Major-->WC nts=4 GGGG H.DG72,E.DG42,F.DG52,G.DG62 |
 |
6 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG H.DG73,E.DG43,F.DG53,G.DG63 |
 |
7 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG H.DG74,E.DG44,F.DG54,G.DG64 |
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.DG32,C.DG22,B.DG12 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,D.DG33,C.DG23,B.DG13 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG34,C.DG24,B.DG14 4 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG35,C.DG25,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 A.DG2,A.DG3,A.DG4,A.DG5 strand#2 U DNA glyco-bond=---- sugar=---- nts=4 GGGG D.DG32,D.DG33,D.DG34,D.DG35 strand#3 U DNA glyco-bond=---- sugar=---- nts=4 GGGG C.DG22,C.DG23,C.DG24,C.DG25 strand#4 U DNA glyco-bond=---- sugar=---- nts=4 GGGG B.DG12,B.DG13,B.DG14,B.DG15 |
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.DG42,H.DG72,G.DG62,F.DG52 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG43,H.DG73,G.DG63,F.DG53 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG44,H.DG74,G.DG64,F.DG54 4 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG E.DG45,H.DG75,G.DG65,F.DG55 step#1 pm(>>,forward) area=10.09 rise=3.53 twist=30.1 step#2 pm(>>,forward) area=8.22 rise=3.50 twist=32.6 step#3 pm(>>,forward) area=12.22 rise=3.37 twist=27.2 strand#1 U DNA glyco-bond=---- sugar=3--- nts=4 GGGG E.DG42,E.DG43,E.DG44,E.DG45 strand#2 U DNA glyco-bond=---- sugar=3--- nts=4 GGGG H.DG72,H.DG73,H.DG74,H.DG75 strand#3 U DNA glyco-bond=---- sugar=3--- nts=4 GGGG G.DG62,G.DG63,G.DG64,G.DG65 strand#4 U DNA glyco-bond=---- sugar=3--- nts=4 GGGG F.DG52,F.DG53,F.DG54,F.DG55 |
List of 1 G4 coaxial stack
1 G4 helix#1 contains 2 G4 stems: [#1,#2] [5'/5']