Summary information and primary citation

PDB-id
8p6b
Class
DNA
Method
X-ray (2.5 Å)
Summary
Ruthenium complex bound to a modified human telomeric sequence giving an antiparallel g-quadruplex
Reference
McQuaid KT, Cardin CJ: "Ruthenium complex bound to an antiparallel G-quadruplex."
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, UDUD, anti-parallel:chair, 2+2, 3(+Lm+Ln+Lw)

Cartoon-block schematics in six views (download the tarball)

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List of 3 G-tetrads

 1 glyco-bond=--s- sugar=.3-- groove=-nw- planarity=0.427 type=saddle O- nts=4 GGGG A.DG1,A.DG9,A.DG13,A.DG21
 2 glyco-bond=---s sugar=--3- groove=--wn planarity=0.644 type=other  -- nts=4 GGGG A.DG2,A.DG8,A.DG14,A.DG20
 3 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.740 type=bowl   O+ nts=4 GGGG A.DG3,A.DG7,A.DG15,A.DG19

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-tetrads, INTRA-molecular, with 1 stem
 1  glyco-bond=--s- sugar=.3-- groove=-nw- Major-->WC O- nts=4 GGGG A.DG1,A.DG9,A.DG13,A.DG21
 2  glyco-bond=---s sugar=--3- groove=--wn     --     -- nts=4 GGGG A.DG2,A.DG8,A.DG14,A.DG20
 3  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major O+ nts=4 GGGG A.DG3,A.DG7,A.DG15,A.DG19
  step#1  mm(<>,outward)  area=11.00 rise=3.48 twist=22.3
  step#2  pm(>>,forward)  area=17.23 rise=3.55 twist=22.1
  strand#1 DNA glyco-bond=--- sugar=.-- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2 DNA glyco-bond=--s sugar=3-- nts=3 GGG A.DG9,A.DG8,A.DG7
  strand#3 DNA glyco-bond=s-- sugar=-3- nts=3 GGG A.DG13,A.DG14,A.DG15
  strand#4 DNA glyco-bond=-ss sugar=--- nts=3 GGG A.DG21,A.DG20,A.DG19

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2 stacking diagrams 
 1  glyco-bond=--s- sugar=.3-- groove=-nw- Major-->WC O- nts=4 GGGG A.DG1,A.DG9,A.DG13,A.DG21
 2  glyco-bond=---s sugar=--3- groove=--wn     --     -- nts=4 GGGG A.DG2,A.DG8,A.DG14,A.DG20
  step#1  mm(<>,outward)  area=11.00 rise=3.48 twist=22.3

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 2  glyco-bond=---s sugar=--3- groove=--wn     --     -- nts=4 GGGG A.DG2,A.DG8,A.DG14,A.DG20
 3  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major O+ nts=4 GGGG A.DG3,A.DG7,A.DG15,A.DG19
  step#2  pm(>>,forward)  area=17.23 rise=3.55 twist=22.1

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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-tetrads, 3 loops, INTRA-molecular, UDUD, anti-parallel:chair, WARNING, 2+2, 3(+Lm+Ln+Lw), WARNING
 1  glyco-bond=--s- sugar=.--3 groove=-wn- WC-->Major O- nts=4 GGGG A.DG1,A.DG21,A.DG13,A.DG9
 2  glyco-bond=-s-- sugar=--3- groove=nw--     --     -- nts=4 GGGG A.DG2,A.DG20,A.DG14,A.DG8
 3  glyco-bond=-s-s sugar=---- groove=nwnw Major-->WC O+ nts=4 GGGG A.DG3,A.DG19,A.DG15,A.DG7
  step#1  mm(<>,outward)  area=11.00 rise=3.48 twist=22.3
  step#2  pm(>>,forward)  area=17.23 rise=3.55 twist=22.1
  strand#1  U DNA glyco-bond=--- sugar=.-- nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2  D DNA glyco-bond=-ss sugar=--- nts=3 GGG A.DG21,A.DG20,A.DG19
  strand#3  U DNA glyco-bond=s-- sugar=-3- nts=3 GGG A.DG13,A.DG14,A.DG15
  strand#4  D DNA glyco-bond=--s sugar=3-- nts=3 GGG A.DG9,A.DG8,A.DG7
  loop#1 type=lateral   strands=[#1,#4] nts=3 TTT A.DT4,A.DT5,A.DT6
  loop#2 type=lateral   strands=[#4,#3] nts=3 TTA A.DT10,A.DT11,A.DA12
  loop#3 type=lateral   strands=[#3,#2] nts=3 TTA A.DT16,A.DT17,A.DA18

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