Summary information

PDB id
8ht7
Class
DNA binding protein
Method
NMR
Summary
The n-terminal region of cdc6 specifically recognizes human DNA g-quadruplex
Reference
Liu C, Zhu G, Geng Y, Xu N: "The N-terminal region of Cdc6 specifically recognizes human DNA G-quadruplex."
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, 3(+Ln+Lw+Ln), chair(2+2), UDUD

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads

 1 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.077 type=planar nts=4 GGGG A.DG1,A.DG21,A.DG13,A.DG9
 2 glyco-bond=-s-s sugar=3--3 groove=wnwn planarity=0.041 type=planar nts=4 GGGG A.DG2,A.DG20,A.DG14,A.DG8
 3 glyco-bond=-s-s sugar=3.-3 groove=wnwn planarity=0.218 type=bowl-2 nts=4 GGGG A.DG3,A.DG19,A.DG15,A.DG7

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-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG21,A.DG13,A.DG9
 2  glyco-bond=-s-s sugar=3--3 groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG20,A.DG14,A.DG8
 3  glyco-bond=-s-s sugar=3.-3 groove=wnwn WC-->Major nts=4 GGGG A.DG3,A.DG19,A.DG15,A.DG7
  step#1  mm(<>,outward)  area=9.53  rise=3.26 twist=23.2
  step#2  pm(>>,forward)  area=16.65 rise=3.76 twist=22.4
  strand#1 DNA glyco-bond=s-- sugar=-33 nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2 DNA glyco-bond=-ss sugar=--. nts=3 GGG A.DG21,A.DG20,A.DG19
  strand#3 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG13,A.DG14,A.DG15
  strand#4 DNA glyco-bond=-ss sugar=-33 nts=3 GGG A.DG9,A.DG8,A.DG7

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2 stacking diagrams 
 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG21,A.DG13,A.DG9
 2  glyco-bond=-s-s sugar=3--3 groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG20,A.DG14,A.DG8
  step#1  mm(<>,outward)  area=9.53  rise=3.26 twist=23.2

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 2  glyco-bond=-s-s sugar=3--3 groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG20,A.DG14,A.DG8
 3  glyco-bond=-s-s sugar=3.-3 groove=wnwn WC-->Major nts=4 GGGG A.DG3,A.DG19,A.DG15,A.DG7
  step#2  pm(>>,forward)  area=16.65 rise=3.76 twist=22.4

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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-tetrad layers, 3 loops, INTRA-molecular, UDUD, anti-parallel, 3(+Ln+Lw+Ln), chair(2+2)

 1  glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG1,A.DG21,A.DG13,A.DG9
 2  glyco-bond=-s-s sugar=3--3 groove=wnwn WC-->Major nts=4 GGGG A.DG2,A.DG20,A.DG14,A.DG8
 3  glyco-bond=-s-s sugar=3.-3 groove=wnwn WC-->Major nts=4 GGGG A.DG3,A.DG19,A.DG15,A.DG7
  step#1  mm(<>,outward)  area=9.53  rise=3.26 twist=23.2
  step#2  pm(>>,forward)  area=16.65 rise=3.76 twist=22.4
  strand#1  U DNA glyco-bond=s-- sugar=-33 nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2  D DNA glyco-bond=-ss sugar=--. nts=3 GGG A.DG21,A.DG20,A.DG19
  strand#3  U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG13,A.DG14,A.DG15
  strand#4  D DNA glyco-bond=-ss sugar=-33 nts=3 GGG A.DG9,A.DG8,A.DG7
  loop#1 type=lateral   strands=[#1,#4] nts=3 TTA A.DT4,A.DT5,A.DA6
  loop#2 type=lateral   strands=[#4,#3] nts=3 TTA A.DT10,A.DT11,A.DA12
  loop#3 type=lateral   strands=[#3,#2] nts=3 TTT A.DT16,A.DT17,A.DT18

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