Summary information and primary citation

PDB-id
9imy
Class
DNA
Method
NMR
Summary
Solution structure of max1a g-quadruplex DNA
Reference
Hu X, Cao C: "Solution structure of MAX G-quadruplex DNA."
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, UUUD, hybrid2, 3+1, 3(-PD+Lw)

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

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List of 3 G-tetrads

 1 glyco-bond=---s sugar=.-.- groove=--wn planarity=0.171 type=other  N+ nts=4 GGGG A.DG2,A.DG6,A.DG21,A.DG15
 2 glyco-bond=---s sugar=.3.- groove=--wn planarity=0.214 type=other  N+ nts=4 GGGG A.DG3,A.DG7,A.DG22,A.DG14
 3 glyco-bond=---s sugar=--3- groove=--wn planarity=0.188 type=other  N+ nts=4 GGGG A.DG4,A.DG8,A.DG23,A.DG13

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 sugar=.-.- groove=--wn WC-->Major N+ nts=4 GGGG A.DG2,A.DG6,A.DG21,A.DG15
 2  glyco-bond=---s sugar=.3.- groove=--wn WC-->Major N+ nts=4 GGGG A.DG3,A.DG7,A.DG22,A.DG14
 3  glyco-bond=---s sugar=--3- groove=--wn WC-->Major N+ nts=4 GGGG A.DG4,A.DG8,A.DG23,A.DG13
  step#1  pm(>>,forward)  area=13.35 rise=3.53 twist=28.8
  step#2  pm(>>,forward)  area=16.10 rise=3.71 twist=26.5
  strand#1 DNA glyco-bond=--- sugar=..- nts=3 GGG A.DG2,A.DG3,A.DG4
  strand#2 DNA glyco-bond=--- sugar=-3- nts=3 GGG A.DG6,A.DG7,A.DG8
  strand#3 DNA glyco-bond=--- sugar=..3 nts=3 GGG A.DG21,A.DG22,A.DG23
  strand#4 DNA glyco-bond=sss sugar=--- nts=3 GGG A.DG15,A.DG14,A.DG13

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2 stacking diagrams 
 1  glyco-bond=---s sugar=.-.- groove=--wn WC-->Major N+ nts=4 GGGG A.DG2,A.DG6,A.DG21,A.DG15
 2  glyco-bond=---s sugar=.3.- groove=--wn WC-->Major N+ nts=4 GGGG A.DG3,A.DG7,A.DG22,A.DG14
  step#1  pm(>>,forward)  area=13.35 rise=3.53 twist=28.8

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 2  glyco-bond=---s sugar=.3.- groove=--wn WC-->Major N+ nts=4 GGGG A.DG3,A.DG7,A.DG22,A.DG14
 3  glyco-bond=---s sugar=--3- groove=--wn WC-->Major N+ nts=4 GGGG A.DG4,A.DG8,A.DG23,A.DG13
  step#2  pm(>>,forward)  area=16.10 rise=3.71 twist=26.5

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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-tetrads, 3 loops, INTRA-molecular, UUUD, hybrid2, 3+1, 3(-PD+Lw)
 1  glyco-bond=---s sugar=.-.- groove=--wn WC-->Major N+ nts=4 GGGG A.DG2,A.DG6,A.DG21,A.DG15
 2  glyco-bond=---s sugar=.3.- groove=--wn WC-->Major N+ nts=4 GGGG A.DG3,A.DG7,A.DG22,A.DG14
 3  glyco-bond=---s sugar=--3- groove=--wn WC-->Major N+ nts=4 GGGG A.DG4,A.DG8,A.DG23,A.DG13
  step#1  pm(>>,forward)  area=13.35 rise=3.53 twist=28.8
  step#2  pm(>>,forward)  area=16.10 rise=3.71 twist=26.5
  strand#1  U DNA glyco-bond=--- sugar=..- nts=3 GGG A.DG2,A.DG3,A.DG4
  strand#2  U DNA glyco-bond=--- sugar=-3- nts=3 GGG A.DG6,A.DG7,A.DG8
  strand#3  U DNA glyco-bond=--- sugar=..3 nts=3 GGG A.DG21,A.DG22,A.DG23
  strand#4  D DNA glyco-bond=sss sugar=--- nts=3 GGG A.DG15,A.DG14,A.DG13
  loop#1 type=propeller strands=[#1,#2] nts=1 A A.DA5
  loop#2 type=diagonal  strands=[#2,#4] nts=4 GAAG A.DG9,A.DA10,A.DA11,A.DG12
  loop#3 type=lateral   strands=[#4,#3] nts=5 TGAAG A.DT16,A.DG17,A.DA18,A.DA19,A.DG20

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