Summary information

PDB id
7qvq
Class
DNA
Method
X-ray (2.4 Å)
Summary
Human telomeric DNA g-quadruplex of a gold(iii) complex containing the 2,4,6-tris (2-pyrimidyl)-1,3,5-triazine ligand
Reference
Bazzicalupi C, Bonardi A, Biver T, Ferraroni M, Papi F, Savastano M, Lombardi P, Gratteri P (2022): "Probing the Efficiency of 13-Pyridylalkyl Berberine Derivatives to Human Telomeric G-Quadruplexes Binding: Spectroscopic, Solid State and In Silico Analysis." Int J Mol Sci, 23. doi: 10.3390/ijms232214061.
Abstract
The interaction between the series of berberine derivatives
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, 3(-P-P-P), parallel(4+0), UUUU

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.089 type=planar nts=4 GGGG A.DG3,A.DG9,A.DG15,A.DG21
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.084 type=planar nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.167 type=other  nts=4 GGGG A.DG5,A.DG11,A.DG17,A.DG23

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-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG15,A.DG21
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG11,A.DG17,A.DG23
  step#1  pm(>>,forward)  area=9.53  rise=3.30 twist=34.4
  step#2  pm(>>,forward)  area=14.88 rise=3.35 twist=25.5
  strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG9,A.DG10,A.DG11
  strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG15,A.DG16,A.DG17
  strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG21,A.DG22,A.DG23

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2 stacking diagrams 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG15,A.DG21
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22
  step#1  pm(>>,forward)  area=9.53  rise=3.30 twist=34.4

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 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG11,A.DG17,A.DG23
  step#2  pm(>>,forward)  area=14.88 rise=3.35 twist=25.5

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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-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG15,A.DG21
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG11,A.DG17,A.DG23
  step#1  pm(>>,forward)  area=9.53  rise=3.30 twist=34.4
  step#2  pm(>>,forward)  area=14.88 rise=3.35 twist=25.5
  strand#1  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG9,A.DG10,A.DG11
  strand#3  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG15,A.DG16,A.DG17
  strand#4  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG21,A.DG22,A.DG23
  loop#1 type=propeller strands=[#1,#2] nts=3 TTA A.DT6,A.DT7,A.DA8
  loop#2 type=propeller strands=[#2,#3] nts=3 TTA A.DT12,A.DT13,A.DA14
  loop#3 type=propeller strands=[#3,#4] nts=3 TTA A.DT18,A.DT19,A.DA20

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