Summary information and primary citation

PDB-id
9u89
Class
DNA
Method
NMR
Summary
Structure of aa(gggtt)3gggaa g-quadruplex in the presence of potassium ions
Reference
Negi D, Sannapureddi RKR, Sathyamoorthy B: "Molecular Interactions of a Frustrated G-Rich Sequence: Atomistic Insights into Folding of DNA G-Quadruplexes."
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0, 3(-P-P-P)

Cartoon-block schematics in six views (download the tarball)

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List of 3 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.136 type=planar O+ nts=4 GGGG A.DG3,A.DG8,A.DG13,A.DG18
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.203 type=other  O+ nts=4 GGGG A.DG4,A.DG9,A.DG14,A.DG19
 3 glyco-bond=---- sugar=.--. groove=---- planarity=0.167 type=other  O+ nts=4 GGGG A.DG5,A.DG10,A.DG15,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-tetrads, INTRA-molecular, with 1 stem
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG8,A.DG13,A.DG18
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG9,A.DG14,A.DG19
 3  glyco-bond=---- sugar=.--. groove=---- WC-->Major O+ nts=4 GGGG A.DG5,A.DG10,A.DG15,A.DG20
  step#1  pm(>>,forward)  area=14.23 rise=3.33 twist=26.2
  step#2  pm(>>,forward)  area=14.19 rise=3.31 twist=23.7
  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.DG8,A.DG9,A.DG10
  strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG13,A.DG14,A.DG15
  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 O+ nts=4 GGGG A.DG3,A.DG8,A.DG13,A.DG18
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG9,A.DG14,A.DG19
  step#1  pm(>>,forward)  area=14.23 rise=3.33 twist=26.2

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 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG9,A.DG14,A.DG19
 3  glyco-bond=---- sugar=.--. groove=---- WC-->Major O+ nts=4 GGGG A.DG5,A.DG10,A.DG15,A.DG20
  step#2  pm(>>,forward)  area=14.19 rise=3.31 twist=23.7

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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-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 3(-P-P-P)
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG3,A.DG8,A.DG13,A.DG18
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG9,A.DG14,A.DG19
 3  glyco-bond=---- sugar=.--. groove=---- WC-->Major O+ nts=4 GGGG A.DG5,A.DG10,A.DG15,A.DG20
  step#1  pm(>>,forward)  area=14.23 rise=3.33 twist=26.2
  step#2  pm(>>,forward)  area=14.19 rise=3.31 twist=23.7
  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.DG8,A.DG9,A.DG10
  strand#3  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG13,A.DG14,A.DG15
  strand#4  U DNA glyco-bond=--- sugar=--. nts=3 GGG A.DG18,A.DG19,A.DG20
  loop#1 type=propeller strands=[#1,#2] nts=2 TT A.DT6,A.DT7
  loop#2 type=propeller strands=[#2,#3] nts=2 TT A.DT11,A.DT12
  loop#3 type=propeller strands=[#3,#4] nts=2 TT A.DT16,A.DT17

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