Summary information

PDB id
8jic
Class
DNA
Method
NMR
Summary
Human telomere two-quartet g-quadruplex at ph 7.0
Reference
Galer P, Wang B, Plavec J, Sket P (2023): "Unveiling the structural mechanism of a G-quadruplex pH-Driven switch." Biochimie, 214, 73-82. doi: 10.1016/j.biochi.2023.08.002.
Abstract
 
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem, 2(-LwD+Ln), basket(2+2), UDDU

Base-block schematics in six views

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List of 2 G-tetrads

 1 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.136 type=planar nts=4 GGGG A.DG3,A.DG10,A.DG22,A.DG16
 2 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.156 type=planar nts=4 GGGG A.DG4,A.DG9,A.DG21,A.DG17

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, with 1 stem

 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG3,A.DG10,A.DG22,A.DG16
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG4,A.DG9,A.DG21,A.DG17
  step#1  mm(<>,outward)  area=15.17 rise=3.38 twist=17.8
  strand#1 DNA glyco-bond=s- sugar=-- nts=2 GG A.DG3,A.DG4
  strand#2 DNA glyco-bond=-s sugar=-- nts=2 GG A.DG10,A.DG9
  strand#3 DNA glyco-bond=-s sugar=-- nts=2 GG A.DG22,A.DG21
  strand#4 DNA glyco-bond=s- sugar=-- nts=2 GG A.DG16,A.DG17

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1 stacking diagram 
 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG3,A.DG10,A.DG22,A.DG16
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG4,A.DG9,A.DG21,A.DG17
  step#1  mm(<>,outward)  area=15.17 rise=3.38 twist=17.8

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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, 2 G-tetrad layers, 3 loops, INTRA-molecular, UDDU, anti-parallel, 2(-LwD+Ln), basket(2+2)

 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG A.DG3,A.DG10,A.DG22,A.DG16
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG A.DG4,A.DG9,A.DG21,A.DG17
  step#1  mm(<>,outward)  area=15.17 rise=3.38 twist=17.8
  strand#1  U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG3,A.DG4
  strand#2  D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG10,A.DG9
  strand#3  D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG22,A.DG21
  strand#4  U DNA glyco-bond=s- sugar=-- nts=2 GG A.DG16,A.DG17
  loop#1 type=lateral   strands=[#1,#2] nts=4 GTTA A.DG5,A.DT6,A.DT7,A.DA8
  loop#2 type=diagonal  strands=[#2,#4] nts=5 GTTAG A.DG11,A.DT12,A.DT13,A.DA14,A.DG15
  loop#3 type=lateral   strands=[#4,#3] nts=3 TTA A.DT18,A.DT19,A.DA20

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