Summary information

PDB id
7w0x
Class
DNA
Method
NMR
Summary
Tetrameric antiparallel g-quadruplex formed by natural human telomeric sequence
Reference
Zhang N, Jing HT, Fu WQ: "NMR structure of an alternating antiparallel tetrameric G-quadruplex assembled by the single-repeat of human telomeric DNA d(GGGTTA)."
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, (2+2), UDUD

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads

 1 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.399 type=other  nts=4 GGGG A.DG1,D.DG21,B.DG7,C.DG15
 2 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.438 type=other  nts=4 GGGG A.DG2,D.DG20,B.DG8,C.DG14
 3 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.559 type=other  nts=4 GGGG A.DG3,D.DG19,B.DG9,C.DG13

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

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,D.DG21,B.DG7,C.DG15
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG2,D.DG20,B.DG8,C.DG14
 3  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG3,D.DG19,B.DG9,C.DG13
  step#1  mm(<>,outward)  area=13.20 rise=3.81 twist=19.5
  step#2  pm(>>,forward)  area=14.75 rise=3.92 twist=27.3
  strand#1 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2 DNA glyco-bond=-ss sugar=--- nts=3 GGG D.DG21,D.DG20,D.DG19
  strand#3 DNA glyco-bond=s-- sugar=--- nts=3 GGG B.DG7,B.DG8,B.DG9
  strand#4 DNA glyco-bond=-ss sugar=--- nts=3 GGG C.DG15,C.DG14,C.DG13

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2 stacking diagrams 
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,D.DG21,B.DG7,C.DG15
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG2,D.DG20,B.DG8,C.DG14
  step#1  mm(<>,outward)  area=13.20 rise=3.81 twist=19.5

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 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG2,D.DG20,B.DG8,C.DG14
 3  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG3,D.DG19,B.DG9,C.DG13
  step#2  pm(>>,forward)  area=14.75 rise=3.92 twist=27.3

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List of 1 G4-stem

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- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,D.DG21,B.DG7,C.DG15
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG2,D.DG20,B.DG8,C.DG14
 3  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG3,D.DG19,B.DG9,C.DG13
  step#1  mm(<>,outward)  area=13.20 rise=3.81 twist=19.5
  step#2  pm(>>,forward)  area=14.75 rise=3.92 twist=27.3
  strand#1  U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2  D DNA glyco-bond=-ss sugar=--- nts=3 GGG D.DG21,D.DG20,D.DG19
  strand#3  U DNA glyco-bond=s-- sugar=--- nts=3 GGG B.DG7,B.DG8,B.DG9
  strand#4  D DNA glyco-bond=-ss sugar=--- nts=3 GGG C.DG15,C.DG14,C.DG13

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