Summary information and primary citation

PDB-id
9kg4
Class
DNA
Method
NMR
Summary
Solution structure of free htert promoter g-quadruplex
Reference
Zhang YQ, Gu W, He SH, Cheng RS, Chen ZY, Yan TD, Kong LY, Wang KB: "G146A Mutation in hTERT Promoter Induces a Distinct G-Quadruplex That Activates hTERT Transcription: Structure Determination and Its Potential as a Drug Target."
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=0.212 type=other  O+ nts=4 GGGG X.DG8,X.DG13,X.DG19,X.DG23
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.382 type=bowl   O+ nts=4 GGGG X.DG9,X.DG14,X.DG20,X.DG24
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.392 type=bowl   O+ nts=4 GGGG X.DG10,X.DG15,X.DG21,X.DG25

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.DG8,X.DG13,X.DG19,X.DG23
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG9,X.DG14,X.DG20,X.DG24
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG10,X.DG15,X.DG21,X.DG25
  step#1  pm(>>,forward)  area=18.63 rise=3.47 twist=18.5
  step#2  pm(>>,forward)  area=10.13 rise=3.39 twist=29.2
  strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG8,X.DG9,X.DG10
  strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG13,X.DG14,X.DG15
  strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG19,X.DG20,X.DG21
  strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG23,X.DG24,X.DG25

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2 stacking diagrams 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG8,X.DG13,X.DG19,X.DG23
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG9,X.DG14,X.DG20,X.DG24
  step#1  pm(>>,forward)  area=18.63 rise=3.47 twist=18.5

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 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG9,X.DG14,X.DG20,X.DG24
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG10,X.DG15,X.DG21,X.DG25
  step#2  pm(>>,forward)  area=10.13 rise=3.39 twist=29.2

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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.DG8,X.DG13,X.DG19,X.DG23
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG9,X.DG14,X.DG20,X.DG24
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG10,X.DG15,X.DG21,X.DG25
  step#1  pm(>>,forward)  area=18.63 rise=3.47 twist=18.5
  step#2  pm(>>,forward)  area=10.13 rise=3.39 twist=29.2
  strand#1  U DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG8,X.DG9,X.DG10
  strand#2  U DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG13,X.DG14,X.DG15
  strand#3  U DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG19,X.DG20,X.DG21
  strand#4  U DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG23,X.DG24,X.DG25
  loop#1 type=propeller strands=[#1,#2] nts=2 TC X.DT11,X.DC12
  loop#2 type=propeller strands=[#2,#3] nts=3 ACT X.DA16,X.DC17,X.DT18
  loop#3 type=propeller strands=[#3,#4] nts=1 C X.DC22

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