Summary information and primary citation

PDB-id
8wa4
Class
DNA
Method
NMR
Summary
Solution structure of free atf4 promoter g-quadruplex
Reference
Xiao CM, Li YP, Liu YS, Dong RF, He XY, Lin Q, Zang X, Wang KB, Xia YZ, Kong LY: "Stabilizing ATF4 promoter G-quadruplex overcomes the resistance of glutamine-restricted cancer therapy."
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=0.255 type=other  O+ nts=4 GGGG X.DG4,X.DG8,X.DG12,X.DG17
 2 glyco-bond=---- sugar=---. groove=---- planarity=0.261 type=other  O+ nts=4 GGGG X.DG5,X.DG9,X.DG13,X.DG18
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.289 type=other  O+ nts=4 GGGG X.DG6,X.DG10,X.DG14,X.DG19

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 X.DG4,X.DG8,X.DG12,X.DG17
 2  glyco-bond=---- sugar=---. groove=---- WC-->Major O+ nts=4 GGGG X.DG5,X.DG9,X.DG13,X.DG18
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG6,X.DG10,X.DG14,X.DG19
  step#1  pm(>>,forward)  area=15.39 rise=3.33 twist=24.0
  step#2  pm(>>,forward)  area=11.68 rise=3.38 twist=30.1
  strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG4,X.DG5,X.DG6
  strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG8,X.DG9,X.DG10
  strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG12,X.DG13,X.DG14
  strand#4 DNA glyco-bond=--- sugar=-.- nts=3 GGG X.DG17,X.DG18,X.DG19

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2 stacking diagrams 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG4,X.DG8,X.DG12,X.DG17
 2  glyco-bond=---- sugar=---. groove=---- WC-->Major O+ nts=4 GGGG X.DG5,X.DG9,X.DG13,X.DG18
  step#1  pm(>>,forward)  area=15.39 rise=3.33 twist=24.0

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 2  glyco-bond=---- sugar=---. groove=---- WC-->Major O+ nts=4 GGGG X.DG5,X.DG9,X.DG13,X.DG18
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG6,X.DG10,X.DG14,X.DG19
  step#2  pm(>>,forward)  area=11.68 rise=3.38 twist=30.1

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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 X.DG4,X.DG8,X.DG12,X.DG17
 2  glyco-bond=---- sugar=---. groove=---- WC-->Major O+ nts=4 GGGG X.DG5,X.DG9,X.DG13,X.DG18
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG6,X.DG10,X.DG14,X.DG19
  step#1  pm(>>,forward)  area=15.39 rise=3.33 twist=24.0
  step#2  pm(>>,forward)  area=11.68 rise=3.38 twist=30.1
  strand#1  U DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG4,X.DG5,X.DG6
  strand#2  U DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG8,X.DG9,X.DG10
  strand#3  U DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG12,X.DG13,X.DG14
  strand#4  U DNA glyco-bond=--- sugar=-.- nts=3 GGG X.DG17,X.DG18,X.DG19
  loop#1 type=propeller strands=[#1,#2] nts=1 A X.DA7
  loop#2 type=propeller strands=[#2,#3] nts=1 A X.DA11
  loop#3 type=propeller strands=[#3,#4] nts=2 AA X.DA15,X.DA16

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