Summary information and primary citation

PDB-id
4wo3
Class
DNA
Method
X-ray (2.73 Å)
Summary
The second c-kit DNA quadruplex crystal structure
Reference
Wei D, Neidle S: "THE SECOND C-KIT1 DNA QUADRUPLEX CRYSTAL STRUCTURE."
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0, 2(-PX+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=0.175 type=other  O+ nts=4 GGGG 1:B.DG2,1:B.DG6,1:B.DG10,1:B.DG13
 2 glyco-bond=---- sugar=--3- groove=---- planarity=0.206 type=other  N+ nts=4 GGGG 1:B.DG3,1:B.DG7,1:B.DG21,1:B.DG14
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.332 type=bowl   N+ nts=4 GGGG 1:B.DG4,1:B.DG8,1:B.DG22,1:B.DG15

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 1:B.DG2,1:B.DG6,1:B.DG10,1:B.DG13
 2  glyco-bond=---- sugar=--3- groove=---- WC-->Major N+ nts=4 GGGG 1:B.DG3,1:B.DG7,1:B.DG21,1:B.DG14
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major N+ nts=4 GGGG 1:B.DG4,1:B.DG8,1:B.DG22,1:B.DG15
  step#1  pm(>>,forward)  area=14.54 rise=3.46 twist=28.8
  step#2  pm(>>,forward)  area=9.98  rise=3.36 twist=32.3
  strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG 1:B.DG2,1:B.DG3,1:B.DG4
  strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG 1:B.DG6,1:B.DG7,1:B.DG8
  strand#3 DNA glyco-bond=--- sugar=-3- nts=3 GGG 1:B.DG10,1:B.DG21,1:B.DG22
  strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG 1:B.DG13,1:B.DG14,1:B.DG15

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2 stacking diagrams 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:B.DG2,1:B.DG6,1:B.DG10,1:B.DG13
 2  glyco-bond=---- sugar=--3- groove=---- WC-->Major N+ nts=4 GGGG 1:B.DG3,1:B.DG7,1:B.DG21,1:B.DG14
  step#1  pm(>>,forward)  area=14.54 rise=3.46 twist=28.8

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 2  glyco-bond=---- sugar=--3- groove=---- WC-->Major N+ nts=4 GGGG 1:B.DG3,1:B.DG7,1:B.DG21,1:B.DG14
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major N+ nts=4 GGGG 1:B.DG4,1:B.DG8,1:B.DG22,1:B.DG15
  step#2  pm(>>,forward)  area=9.98  rise=3.36 twist=32.3

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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, 2 G-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 4+0, 2(-PX+P)
 1  glyco-bond=---- sugar=--3- groove=---- WC-->Major N+ nts=4 GGGG 1:B.DG3,1:B.DG7,1:B.DG21,1:B.DG14
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major N+ nts=4 GGGG 1:B.DG4,1:B.DG8,1:B.DG22,1:B.DG15
  step#1  pm(>>,forward)  area=9.98  rise=3.36 twist=32.3
  strand#1  U DNA glyco-bond=-- sugar=-- nts=2 GG 1:B.DG3,1:B.DG4
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG 1:B.DG7,1:B.DG8
  strand#3  U DNA glyco-bond=-- sugar=3- nts=2 GG 1:B.DG21,1:B.DG22
  strand#4  U DNA glyco-bond=-- sugar=-- nts=2 GG 1:B.DG14,1:B.DG15
  loop#1 type=propeller strands=[#1,#2] nts=2 AG 1:B.DA5,1:B.DG6
  loop#2 type=diag-prop strands=[#2,#4] nts=5 CGCTG 1:B.DC9,1:B.DG10,1:B.DC11,1:B.DT12,1:B.DG13
  loop#3 type=propeller strands=[#4,#3] nts=5 AGGAG 1:B.DA16,1:B.DG17,1:B.DG18,1:B.DA19,1:B.DG20

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List of 2 non-stem G4-loops (including the two closing Gs)

 1* type=V-shaped  helix=#1 nts=5 GGGCG 1:B.DG6,1:B.DG7,1:B.DG8,1:B.DC9,1:B.DG10
 2 type=lateral   helix=#1 nts=4 GCTG 1:B.DG10,1:B.DC11,1:B.DT12,1:B.DG13