Summary information

PDB id
2m27
Class
DNA
Method
NMR
Summary
Major g-quadruplex structure formed in human vegf promoter, a monomeric parallel-stranded quadruplex
Reference
Agrawal P, Hatzakis E, Guo K, Carver M, Yang D (2013): "Solution structure of the major G-quadruplex formed in the human VEGF promoter in K+: insights into loop interactions of the parallel G-quadruplexes." Nucleic Acids Res., 41, 10584-10592. doi: 10.1093/nar/gkt784.
Abstract
 
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=0.062 type=planar nts=4 GGGG A.DG3,A.DG7,A.DG14,A.DG18
 2 glyco-bond=---- sugar=.... groove=---- planarity=0.032 type=planar nts=4 GGGG A.DG4,A.DG8,A.DG15,A.DG19
 3 glyco-bond=---- sugar=.... groove=---- planarity=0.089 type=planar nts=4 GGGG A.DG5,A.DG9,A.DG16,A.DG20

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.DG7,A.DG14,A.DG18
 2  glyco-bond=---- sugar=.... groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG15,A.DG19
 3  glyco-bond=---- sugar=.... groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG16,A.DG20
  step#1  pm(>>,forward)  area=19.04 rise=3.68 twist=22.8
  step#2  pm(>>,forward)  area=12.12 rise=3.75 twist=27.8
  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.DG7,A.DG8,A.DG9
  strand#3 DNA glyco-bond=--- sugar=... nts=3 GGG A.DG14,A.DG15,A.DG16
  strand#4 DNA glyco-bond=--- sugar=... nts=3 GGG A.DG18,A.DG19,A.DG20

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2 stacking diagrams 
 1  glyco-bond=---- sugar=.... groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG14,A.DG18
 2  glyco-bond=---- sugar=.... groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG15,A.DG19
  step#1  pm(>>,forward)  area=19.04 rise=3.68 twist=22.8

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 2  glyco-bond=---- sugar=.... groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG15,A.DG19
 3  glyco-bond=---- sugar=.... groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG16,A.DG20
  step#2  pm(>>,forward)  area=12.12 rise=3.75 twist=27.8

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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, 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.DG7,A.DG14,A.DG18
 2  glyco-bond=---- sugar=.... groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG15,A.DG19
 3  glyco-bond=---- sugar=.... groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG16,A.DG20
  step#1  pm(>>,forward)  area=19.04 rise=3.68 twist=22.8
  step#2  pm(>>,forward)  area=12.12 rise=3.75 twist=27.8
  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.DG7,A.DG8,A.DG9
  strand#3  U DNA glyco-bond=--- sugar=... nts=3 GGG A.DG14,A.DG15,A.DG16
  strand#4  U DNA glyco-bond=--- sugar=... nts=3 GGG A.DG18,A.DG19,A.DG20
  loop#1 type=propeller strands=[#1,#2] nts=1 C A.DC6
  loop#2 type=propeller strands=[#2,#3] nts=4 CCTT A.DC10,A.DC11,A.DT12,A.DT13
  loop#3 type=propeller strands=[#3,#4] nts=1 C A.DC17

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