Summary information

PDB id
6jjg
Class
DNA
Method
X-ray (1.969 Å)
Summary
Crystal structure of a two-quartet DNA mixed-parallel-antiparallel g-quadruplex
Reference
Zhang YS, Parkinson GN, Wagner A, Wei DG: "Crystal structure of a two-quartet DNA mixed-parallel/antiparallel G-quadruplex."
Abstract
 
G4 notes
4 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, (2+2), UDUD; parallel(4+0), UUUU, coaxial interfaces: mixed

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 4 G-tetrads

 1 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.067 type=planar nts=4 GGGG A.DG1,A.DG7,B.DG1,B.DG7
 2 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.200 type=other  nts=4 GGGG A.DG2,A.DG6,B.DG2,B.DG6
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.093 type=planar nts=4 GGGG A.DG9,A.DG12,B.DG9,B.DG12
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.219 type=other  nts=4 GGGG A.DG10,A.DG13,B.DG10,B.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, 4 G-tetrad layers, inter-molecular, with 2 stems

 1  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG6,B.DG2,B.DG6
 2* glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG7,B.DG1,B.DG7
 3  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG9,B.DG12,B.DG9,A.DG12
 4  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG10,B.DG13,B.DG10,A.DG13
  step#1  mm(<>,outward)  area=17.37 rise=3.49 twist=13.1
  step#2  pm(>>,forward)  area=7.07  rise=3.25 twist=-37.6
  step#3  pm(>>,forward)  area=8.32  rise=3.24 twist=36.0
  strand#1 DNA glyco-bond=-s-- sugar=---- nts=4 GGGG A.DG2,A.DG1,A.DG9,A.DG10
  strand#2 DNA glyco-bond=s--- sugar=---- nts=4 GGGG A.DG6,A.DG7,B.DG12,B.DG13
  strand#3 DNA glyco-bond=-s-- sugar=---- nts=4 GGGG B.DG2,B.DG1,B.DG9,B.DG10
  strand#4 DNA glyco-bond=s--- sugar=---- nts=4 GGGG B.DG6,B.DG7,A.DG12,A.DG13

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3 stacking diagrams
 1  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG6,B.DG2,B.DG6
2* glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG7,B.DG1,B.DG7
step#1 mm(<>,outward) area=17.37 rise=3.49 twist=13.1

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 2* glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG7,B.DG1,B.DG7
3 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG9,B.DG12,B.DG9,A.DG12
step#2 pm(>>,forward) area=7.07 rise=3.25 twist=-37.6

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 3  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG9,B.DG12,B.DG9,A.DG12
4 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG10,B.DG13,B.DG10,A.DG13
step#3 pm(>>,forward) area=8.32 rise=3.24 twist=36.0

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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, 2 G-tetrad layers, 2 loops, inter-molecular, UDUD, anti-parallel, (2+2)

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG7,B.DG1,B.DG7
 2  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG6,B.DG2,B.DG6
  step#1  mm(<>,outward)  area=17.37 rise=3.49 twist=13.1
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG1,A.DG2
  strand#2  D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG7,A.DG6
  strand#3  U DNA glyco-bond=s- sugar=-- nts=2 GG B.DG1,B.DG2
  strand#4  D DNA glyco-bond=-s sugar=-- nts=2 GG B.DG7,B.DG6
  loop#1 type=lateral   strands=[#1,#2] nts=3 CTC A.DC3,A.DT4,A.DC5
  loop#2 type=lateral   strands=[#3,#4] nts=3 CTC B.DC3,B.DT4,B.DC5

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

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG9,A.DG12,B.DG9,B.DG12
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG10,A.DG13,B.DG10,B.DG13
  step#1  pm(>>,forward)  area=8.32  rise=3.24 twist=36.0
  strand#1  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG9,A.DG10
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG12,A.DG13
  strand#3  U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG9,B.DG10
  strand#4  U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG12,B.DG13
  loop#1 type=propeller strands=[#1,#2] nts=1 C A.DC11
  loop#2 type=propeller strands=[#3,#4] nts=1 C B.DC11

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List of 1 G4 coaxial stack

 1 G4 helix#1 contains 2 G4 stems: [#1,#2]  [mixed]