Summary information [schematics · tetrads · helices · stems · costacks · homepage]

PDB-id
2gw0
Class
DNA
Method
X-ray (1.55 Å)
Summary
A d(tggggt)- sodium and calcium complex
Reference
Lee, M.P., Parkinson, G.N., 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.
Abstract
The crystal structure of a DNA quadruplex, d(TGGGGT), crystallized in the presence of calcium and sodium ions, shows the presence of both ions in the central channel of the structure. This was verified by anomalous dispersion maps, which unequivocally showed the presence of calcium ions.
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 [summary · tetrads · helices · stems · costacks · homepage]

PyMOL session file PDB file View in 3Dmol.js

List of 8 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.248 type=bowl   nts=4 GGGG A.DG2,D.DG20,C.DG14,B.DG8
 2 glyco-bond=---- groove=---- planarity=0.216 type=bowl   nts=4 GGGG A.DG3,D.DG21,C.DG15,B.DG9
 3 glyco-bond=---- groove=---- planarity=0.216 type=bowl   nts=4 GGGG A.DG4,D.DG22,C.DG16,B.DG10
 4 glyco-bond=---- groove=---- planarity=0.322 type=bowl   nts=4 GGGG A.DG5,D.DG23,C.DG17,B.DG11
 5 glyco-bond=---- groove=---- planarity=0.108 type=planar nts=4 GGGG E.DG26,H.DG44,G.DG38,F.DG32
 6 glyco-bond=---- groove=---- planarity=0.205 type=bowl   nts=4 GGGG E.DG27,H.DG45,G.DG39,F.DG33
 7 glyco-bond=---- groove=---- planarity=0.241 type=bowl   nts=4 GGGG E.DG28,H.DG46,G.DG40,F.DG34
 8 glyco-bond=---- groove=---- planarity=0.245 type=bowl   nts=4 GGGG E.DG29,H.DG47,G.DG41,F.DG35

List of 1 G4-helix [summary · schematics · tetrads · stems · costacks · homepage]

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=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG23,C.DG17,B.DG11
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG22,C.DG16,B.DG10
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,D.DG21,C.DG15,B.DG9
 4* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,D.DG20,C.DG14,B.DG8
 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG E.DG26,F.DG32,G.DG38,H.DG44
 6  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG E.DG27,F.DG33,G.DG39,H.DG45
 7  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG E.DG28,F.DG34,G.DG40,H.DG46
 8  glyco-bond=---- 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=-------- nts=8 GGGGGGGG A.DG5,A.DG4,A.DG3,A.DG2,E.DG26,E.DG27,E.DG28,E.DG29
  strand#2 DNA glyco-bond=-------- nts=8 GGGGGGGG D.DG23,D.DG22,D.DG21,D.DG20,F.DG32,F.DG33,F.DG34,F.DG35
  strand#3 DNA glyco-bond=-------- nts=8 GGGGGGGG C.DG17,C.DG16,C.DG15,C.DG14,G.DG38,G.DG39,G.DG40,G.DG41
  strand#4 DNA glyco-bond=-------- nts=8 GGGGGGGG B.DG11,B.DG10,B.DG9,B.DG8,H.DG44,H.DG45,H.DG46,H.DG47

Download PDB file
Interactive view in 3Dmol.js

7 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG23,C.DG17,B.DG11
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG22,C.DG16,B.DG10
step#1 mp(<<,backward) area=11.87 rise=3.40 twist=26.9

Download PDB file
Interactive view in 3Dmol.js

 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG22,C.DG16,B.DG10
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,D.DG21,C.DG15,B.DG9
step#2 mp(<<,backward) area=10.76 rise=3.30 twist=28.6

Download PDB file
Interactive view in 3Dmol.js

 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,D.DG21,C.DG15,B.DG9
4* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,D.DG20,C.DG14,B.DG8
step#3 mp(<<,backward) area=8.38 rise=3.32 twist=31.9

Download PDB file
Interactive view in 3Dmol.js

 4* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,D.DG20,C.DG14,B.DG8
5 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG E.DG26,F.DG32,G.DG38,H.DG44
step#4 mm(<>,outward) area=14.74 rise=3.53 twist=16.0

Download PDB file
Interactive view in 3Dmol.js

 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG E.DG26,F.DG32,G.DG38,H.DG44
6 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG E.DG27,F.DG33,G.DG39,H.DG45
step#5 pm(>>,forward) area=7.23 rise=3.48 twist=34.5

Download PDB file
Interactive view in 3Dmol.js

 6  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG E.DG27,F.DG33,G.DG39,H.DG45
7 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG E.DG28,F.DG34,G.DG40,H.DG46
step#6 pm(>>,forward) area=11.46 rise=3.32 twist=28.6

Download PDB file
Interactive view in 3Dmol.js

 7  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG E.DG28,F.DG34,G.DG40,H.DG46
8 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG E.DG29,F.DG35,G.DG41,H.DG47
step#7 pm(>>,forward) area=10.73 rise=3.34 twist=28.6

Download PDB file
Interactive view in 3Dmol.js

List of 2 G4-stems [summary · schematics · tetrads · helices · costacks · homepage]

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=---- groove=---- WC-->Major nts=4 GGGG A.DG2,D.DG20,C.DG14,B.DG8
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,D.DG21,C.DG15,B.DG9
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG22,C.DG16,B.DG10
 4  glyco-bond=---- 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=---- nts=4 GGGG A.DG2,A.DG3,A.DG4,A.DG5
  strand#2  U DNA glyco-bond=---- nts=4 GGGG D.DG20,D.DG21,D.DG22,D.DG23
  strand#3  U DNA glyco-bond=---- nts=4 GGGG C.DG14,C.DG15,C.DG16,C.DG17
  strand#4  U DNA glyco-bond=---- nts=4 GGGG B.DG8,B.DG9,B.DG10,B.DG11

Download PDB file
Interactive view in 3Dmol.js

Stem#2, 4 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.DG26,H.DG44,G.DG38,F.DG32
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.DG27,H.DG45,G.DG39,F.DG33
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.DG28,H.DG46,G.DG40,F.DG34
 4  glyco-bond=---- 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=---- nts=4 GGGG E.DG26,E.DG27,E.DG28,E.DG29
  strand#2  U DNA glyco-bond=---- nts=4 GGGG H.DG44,H.DG45,H.DG46,H.DG47
  strand#3  U DNA glyco-bond=---- nts=4 GGGG G.DG38,G.DG39,G.DG40,G.DG41
  strand#4  U DNA glyco-bond=---- nts=4 GGGG F.DG32,F.DG33,F.DG34,F.DG35

Download PDB file
Interactive view in 3Dmol.js

List of 1 G4 coaxial stack [summary · schematics · tetrads · helices · stems · homepage]

 1 G4 helix#1 contains 2 G4 stems: [#1,#2]  [5'/5']

List of 0 non-stem G4-loops (including the two closing Gs)