Summary information and primary citation

PDB-id
9u83
Class
DNA
Method
NMR
Summary
Structure of aa(gggtt)3gggaa g-quadruplex in the presence of sodium 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, UDUU, hybrid3, 3+1, 3(-Lw-Ln-P)

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

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List of 3 G-tetrads

 1 glyco-bond=s-ss sugar=.--- groove=wn-- planarity=0.390 type=bowl   O- nts=4 GGGG A.DG3,A.DG10,A.DG13,A.DG18
 2 glyco-bond=-s-- sugar=3--3 groove=wn-- planarity=0.386 type=other  O+ nts=4 GGGG A.DG4,A.DG9,A.DG14,A.DG19
 3 glyco-bond=-s-- sugar=---- groove=wn-- planarity=0.606 type=bowl   O+ nts=4 GGGG A.DG5,A.DG8,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=s-ss sugar=.--- groove=wn-- Major-->WC O- nts=4 GGGG A.DG3,A.DG10,A.DG13,A.DG18
 2  glyco-bond=-s-- sugar=3--3 groove=wn-- WC-->Major O+ nts=4 GGGG A.DG4,A.DG9,A.DG14,A.DG19
 3  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG A.DG5,A.DG8,A.DG15,A.DG20
  step#1  mm(<>,outward)  area=17.02 rise=3.63 twist=12.9
  step#2  pm(>>,forward)  area=14.32 rise=3.74 twist=19.0
  strand#1 DNA glyco-bond=s-- sugar=.3- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2 DNA glyco-bond=-ss sugar=--- nts=3 GGG A.DG10,A.DG9,A.DG8
  strand#3 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG13,A.DG14,A.DG15
  strand#4 DNA glyco-bond=s-- sugar=-3- nts=3 GGG A.DG18,A.DG19,A.DG20

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2 stacking diagrams 
 1  glyco-bond=s-ss sugar=.--- groove=wn-- Major-->WC O- nts=4 GGGG A.DG3,A.DG10,A.DG13,A.DG18
 2  glyco-bond=-s-- sugar=3--3 groove=wn-- WC-->Major O+ nts=4 GGGG A.DG4,A.DG9,A.DG14,A.DG19
  step#1  mm(<>,outward)  area=17.02 rise=3.63 twist=12.9

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 2  glyco-bond=-s-- sugar=3--3 groove=wn-- WC-->Major O+ nts=4 GGGG A.DG4,A.DG9,A.DG14,A.DG19
 3  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG A.DG5,A.DG8,A.DG15,A.DG20
  step#2  pm(>>,forward)  area=14.32 rise=3.74 twist=19.0

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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, UDUU, hybrid3, 3+1, 3(-Lw-Ln-P)
 1  glyco-bond=s-ss sugar=.--- groove=wn-- Major-->WC O- nts=4 GGGG A.DG3,A.DG10,A.DG13,A.DG18
 2  glyco-bond=-s-- sugar=3--3 groove=wn-- WC-->Major O+ nts=4 GGGG A.DG4,A.DG9,A.DG14,A.DG19
 3  glyco-bond=-s-- sugar=---- groove=wn-- WC-->Major O+ nts=4 GGGG A.DG5,A.DG8,A.DG15,A.DG20
  step#1  mm(<>,outward)  area=17.02 rise=3.63 twist=12.9
  step#2  pm(>>,forward)  area=14.32 rise=3.74 twist=19.0
  strand#1  U DNA glyco-bond=s-- sugar=.3- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2  D DNA glyco-bond=-ss sugar=--- nts=3 GGG A.DG10,A.DG9,A.DG8
  strand#3  U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG13,A.DG14,A.DG15
  strand#4  U DNA glyco-bond=s-- sugar=-3- nts=3 GGG A.DG18,A.DG19,A.DG20
  loop#1 type=lateral   strands=[#1,#2] nts=2 TT A.DT6,A.DT7
  loop#2 type=lateral   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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