Summary information

PDB id
8p6b
Class
DNA
Method
X-ray (2.5 Å)
Summary
Ruthenium complex bound to an antiparallel g-quadruplex
Reference
McQuaid KT, Cardin CJ: "Ruthenium complex bound to an antiparallel G-quadruplex."
Abstract
 
G4 notes
2 G-tetrads, 1 G4 helix

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 2 G-tetrads

 1 glyco-bond=s-s- sugar=33-- groove=wnwn planarity=0.427 type=saddle nts=4 GGGG A.DG1,A.DG9,A.DG13,A.DG21
 2 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.740 type=bowl   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, 2 G-tetrad layers, INTRA-molecular

 1  glyco-bond=s-s- sugar=33-- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG9,A.DG13,A.DG21
 2  glyco-bond=-s-s sugar=---- groove=nwnw Major-->WC nts=4 GGGG A.DG3,A.DG19,A.DG15,A.DG7
  step#1  mm(<>,outward)  area=0.00  rise=7.04 twist=-45.7
  strand#1 DNA glyco-bond=s- sugar=3- nts=2 GG A.DG1,A.DG3
  strand#2 DNA glyco-bond=-s sugar=3- nts=2 GG A.DG9,A.DG19
  strand#3 DNA glyco-bond=s- sugar=-- nts=2 GG A.DG13,A.DG15
  strand#4 DNA glyco-bond=-s sugar=-- nts=2 GG A.DG21,A.DG7

Download PDB file
Interactive view in 3Dmol.js
1 stacking diagram 
 1  glyco-bond=s-s- sugar=33-- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG9,A.DG13,A.DG21
 2  glyco-bond=-s-s sugar=---- groove=nwnw Major-->WC nts=4 GGGG A.DG3,A.DG19,A.DG15,A.DG7
  step#1  mm(<>,outward)  area=0.00  rise=7.04 twist=-45.7

Download PDB file
Interactive view in 3Dmol.js

List of 3 non-stem G4-loops (including the two closing Gs)

 1 type=lateral   helix=#1 nts=5 GTTTG A.DG3,A.DT4,A.DT5,A.DT6,A.DG7
 2 type=lateral   helix=#1 nts=5 GTTAG A.DG9,A.DT10,A.DT11,A.DA12,A.DG13
 3 type=lateral   helix=#1 nts=5 GTTAG A.DG15,A.DT16,A.DT17,A.DA18,A.DG19