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

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.
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 [summary · tetrads · helices · stems · costacks · homepage]

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

 1 glyco-bond=---- groove=---- planarity=0.277 type=bowl   nts=4 GGGG A.DG2,D.DG32,C.DG22,B.DG12
 2 glyco-bond=---- groove=---- planarity=0.191 type=bowl   nts=4 GGGG A.DG3,D.DG33,C.DG23,B.DG13
 3 glyco-bond=---- groove=---- planarity=0.216 type=bowl   nts=4 GGGG A.DG4,D.DG34,C.DG24,B.DG14
 4 glyco-bond=---- groove=---- planarity=0.228 type=bowl   nts=4 GGGG A.DG5,D.DG35,C.DG25,B.DG15
 5 glyco-bond=---- groove=---- planarity=0.106 type=planar nts=4 GGGG E.DG42,H.DG72,G.DG62,F.DG52
 6 glyco-bond=---- groove=---- planarity=0.243 type=bowl   nts=4 GGGG E.DG43,H.DG73,G.DG63,F.DG53
 7 glyco-bond=---- groove=---- planarity=0.296 type=bowl   nts=4 GGGG E.DG44,H.DG74,G.DG64,F.DG54
 8 glyco-bond=---- groove=---- planarity=0.266 type=bowl   nts=4 GGGG E.DG45,H.DG75,G.DG65,F.DG55

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.DG35,C.DG25,B.DG15
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG34,C.DG24,B.DG14
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,D.DG33,C.DG23,B.DG13
 4* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,D.DG32,C.DG22,B.DG12
 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG H.DG72,E.DG42,F.DG52,G.DG62
 6  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG H.DG73,E.DG43,F.DG53,G.DG63
 7  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG H.DG74,E.DG44,F.DG54,G.DG64
 8  glyco-bond=---- 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=-------- nts=8 GGGGGGGG A.DG5,A.DG4,A.DG3,A.DG2,H.DG72,H.DG73,H.DG74,H.DG75
  strand#2 DNA glyco-bond=-------- nts=8 GGGGGGGG D.DG35,D.DG34,D.DG33,D.DG32,E.DG42,E.DG43,E.DG44,E.DG45
  strand#3 DNA glyco-bond=-------- nts=8 GGGGGGGG C.DG25,C.DG24,C.DG23,C.DG22,F.DG52,F.DG53,F.DG54,F.DG55
  strand#4 DNA glyco-bond=-------- nts=8 GGGGGGGG B.DG15,B.DG14,B.DG13,B.DG12,G.DG62,G.DG63,G.DG64,G.DG65

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7 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,D.DG35,C.DG25,B.DG15
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG34,C.DG24,B.DG14
step#1 mp(<<,backward) area=12.32 rise=3.36 twist=28.3

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG34,C.DG24,B.DG14
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,D.DG33,C.DG23,B.DG13
step#2 mp(<<,backward) area=11.51 rise=3.31 twist=28.7

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 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,D.DG33,C.DG23,B.DG13
4* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,D.DG32,C.DG22,B.DG12
step#3 mp(<<,backward) area=9.31 rise=3.39 twist=30.8

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 4* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,D.DG32,C.DG22,B.DG12
5 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG H.DG72,E.DG42,F.DG52,G.DG62
step#4 mm(<>,outward) area=12.30 rise=3.74 twist=16.2

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 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG H.DG72,E.DG42,F.DG52,G.DG62
6 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG H.DG73,E.DG43,F.DG53,G.DG63
step#5 pm(>>,forward) area=10.09 rise=3.53 twist=30.1

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 6  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG H.DG73,E.DG43,F.DG53,G.DG63
7 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG H.DG74,E.DG44,F.DG54,G.DG64
step#6 pm(>>,forward) area=8.22 rise=3.50 twist=32.6

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 7  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG H.DG74,E.DG44,F.DG54,G.DG64
8 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG H.DG75,E.DG45,F.DG55,G.DG65
step#7 pm(>>,forward) area=12.22 rise=3.37 twist=27.2

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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.DG32,C.DG22,B.DG12
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,D.DG33,C.DG23,B.DG13
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,D.DG34,C.DG24,B.DG14
 4  glyco-bond=---- 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=---- nts=4 GGGG A.DG2,A.DG3,A.DG4,A.DG5
  strand#2  U DNA glyco-bond=---- nts=4 GGGG D.DG32,D.DG33,D.DG34,D.DG35
  strand#3  U DNA glyco-bond=---- nts=4 GGGG C.DG22,C.DG23,C.DG24,C.DG25
  strand#4  U DNA glyco-bond=---- nts=4 GGGG B.DG12,B.DG13,B.DG14,B.DG15

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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.DG42,H.DG72,G.DG62,F.DG52
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.DG43,H.DG73,G.DG63,F.DG53
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG E.DG44,H.DG74,G.DG64,F.DG54
 4  glyco-bond=---- 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=---- nts=4 GGGG E.DG42,E.DG43,E.DG44,E.DG45
  strand#2  U DNA glyco-bond=---- nts=4 GGGG H.DG72,H.DG73,H.DG74,H.DG75
  strand#3  U DNA glyco-bond=---- nts=4 GGGG G.DG62,G.DG63,G.DG64,G.DG65
  strand#4  U DNA glyco-bond=---- nts=4 GGGG F.DG52,F.DG53,F.DG54,F.DG55

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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)