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

PDB-id
6ims
Class
DNA
Method
NMR
Summary
NMR structure of an alternating antiparallel tetrameric G-quadruplex assembled by the single-repeat of human telomeric DNA d(gggtta)
Reference
Jing, H.T., Fu, W.Q., Wan, C.J., Zhang, N.: "Antiparallel tetrameric G-quadruplex with alternating strand orientations assembled by single-repeat of human telomeric DNA d(GGGTTA) in K+ or Na+ solution." To be published
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · (2+2), UDUD

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=s-s- groove=wnwn planarity=0.285 type=other  nts=4 GGGG A.DG1,D.DG3,B.DG1,C.DG3
 2 glyco-bond=-s-s groove=wnwn planarity=0.222 type=other  nts=4 GGGG A.DG2,D.DG2,B.DG2,C.DG2
 3 glyco-bond=-s-s groove=wnwn planarity=0.321 type=other  nts=4 GGGG A.DG3,D.DG1,B.DG3,C.DG1

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, 3 G-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG1,D.DG3,B.DG1,C.DG3
 2  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG2,D.DG2,B.DG2,C.DG2
 3  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG3,D.DG1,B.DG3,C.DG1
  step#1  mm(<>,outward)  area=6.65  rise=4.71 twist=17.6
  step#2  pm(>>,forward)  area=3.75  rise=4.94 twist=24.4
  strand#1 DNA glyco-bond=s-- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2 DNA glyco-bond=-ss nts=3 GGG D.DG3,D.DG2,D.DG1
  strand#3 DNA glyco-bond=s-- nts=3 GGG B.DG1,B.DG2,B.DG3
  strand#4 DNA glyco-bond=-ss nts=3 GGG C.DG3,C.DG2,C.DG1

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2 stacking diagrams
 1  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG1,D.DG3,B.DG1,C.DG3
2 glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG2,D.DG2,B.DG2,C.DG2
step#1 mm(<>,outward) area=6.65 rise=4.71 twist=17.6

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 2  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG2,D.DG2,B.DG2,C.DG2
3 glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG3,D.DG1,B.DG3,C.DG1
step#2 pm(>>,forward) area=3.75 rise=4.94 twist=24.4

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List of 1 G4-stem [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, 3 G-tetrad layers, 0 loops, inter-molecular, UDUD, anti-parallel, (2+2)

 1  glyco-bond=s-s- groove=wnwn Major-->WC nts=4 GGGG A.DG1,D.DG3,B.DG1,C.DG3
 2  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG2,D.DG2,B.DG2,C.DG2
 3  glyco-bond=-s-s groove=wnwn WC-->Major nts=4 GGGG A.DG3,D.DG1,B.DG3,C.DG1
  step#1  mm(<>,outward)  area=6.65  rise=4.71 twist=17.6
  step#2  pm(>>,forward)  area=3.75  rise=4.94 twist=24.4
  strand#1  U DNA glyco-bond=s-- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2  D DNA glyco-bond=-ss nts=3 GGG D.DG3,D.DG2,D.DG1
  strand#3  U DNA glyco-bond=s-- nts=3 GGG B.DG1,B.DG2,B.DG3
  strand#4  D DNA glyco-bond=-ss nts=3 GGG C.DG3,C.DG2,C.DG1

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List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

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