Summary information

PDB id
3eru
Class
DNA
Method
X-ray (2.0 Å)
Summary
A bimolecular anti-parallel-stranded oxytricha nova telomeric quadruplex in complex with a 3,6-disubstituted acridine bsu-6045
Reference
Campbell NH, Patel M, Tofa AB, Ghosh R, Parkinson GN, Neidle S (2009): "Selectivity in Ligand Recognition of G-Quadruplex Loops." Biochemistry, 48, 1675-1680. doi: 10.1021/bi802233v.
Abstract
A series of disubstituted acridine ligands have been cocrystallized with a bimolecular DNA G-quadruplex. The ligands have a range of cyclic amino end groups of varying size. The crystal structures show that the diagonal loop in this quadruplex results in a large cavity for these groups, in contrast to the steric constraints imposed by propeller loops in human telomeric quadruplexes. We conclude that the nature of the loop has a significant influence on ligand selectivity for particular quadruplex folds.
G4 notes
4 G-tetrads, 1 G4 helix, 1 G4 stem, (2+2), UDDU

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=w-n- planarity=0.277 type=bowl   nts=4 GGGG A.DG1,B.DG16,A.DG12,B.DG21
 2 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.184 type=other  nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22
 3 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.163 type=other  nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23
 4 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.198 type=other  nts=4 GGGG A.DG4,B.DG13,A.DG9,B.DG24

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 1 stem

 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG1,B.DG16,A.DG12,B.DG21
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22
 3  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23
 4  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG4,B.DG13,A.DG9,B.DG24
  step#1  mm(<>,outward)  area=14.26 rise=3.46 twist=16.9
  step#2  pp(><,inward)   area=18.92 rise=3.56 twist=37.1
  step#3  mm(<>,outward)  area=12.55 rise=3.46 twist=19.3
  strand#1 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4
  strand#2 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG B.DG16,B.DG15,B.DG14,B.DG13
  strand#3 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG A.DG12,A.DG11,A.DG10,A.DG9
  strand#4 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG B.DG21,B.DG22,B.DG23,B.DG24

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3 stacking diagrams 
 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG1,B.DG16,A.DG12,B.DG21
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22
  step#1  mm(<>,outward)  area=14.26 rise=3.46 twist=16.9

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 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22
 3  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23
  step#2  pp(><,inward)   area=18.92 rise=3.56 twist=37.1

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 3  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23
 4  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG4,B.DG13,A.DG9,B.DG24
  step#3  mm(<>,outward)  area=12.55 rise=3.46 twist=19.3

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

 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG1,B.DG16,A.DG12,B.DG21
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22
 3  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23
 4  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG4,B.DG13,A.DG9,B.DG24
  step#1  mm(<>,outward)  area=14.26 rise=3.46 twist=16.9
  step#2  pp(><,inward)   area=18.92 rise=3.56 twist=37.1
  step#3  mm(<>,outward)  area=12.55 rise=3.46 twist=19.3
  strand#1  U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4
  strand#2  D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG B.DG16,B.DG15,B.DG14,B.DG13
  strand#3  D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG A.DG12,A.DG11,A.DG10,A.DG9
  strand#4  U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG B.DG21,B.DG22,B.DG23,B.DG24
  loop#1 type=diagonal  strands=[#1,#3] nts=4 TTTT A.DT5,A.DT6,A.DT7,A.DT8
  loop#2 type=diagonal  strands=[#2,#4] nts=4 TTTT B.DT17,B.DT18,B.DT19,B.DT20

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