Summary information and primary citation

PDB-id
9wnm
Class
DNA
Method
NMR
Summary
A (3+1) hybrid g-quadruplex formed by the chicken DNA replication origin
Reference
Liu C, You Y, Suen C: "A (3+1) hybrid G-quadruplex with a cytosine-bulge formed by the chicken DNA replication origin."
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, UDUU, hybrid3, 3+1, 3(-Lw-Ln-P)

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

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List of 3 G-tetrads

 1 glyco-bond=-ss- sugar=3--- groove=w-n- planarity=0.032 type=planar O- nts=4 GGGG A.DG1,A.DG20,A.DG16,A.DG10
 2 glyco-bond=-s-- sugar=--.- groove=wn-- planarity=0.027 type=planar O+ nts=4 GGGG A.DG2,A.DG9,A.DG17,A.DG21
 3 glyco-bond=-s-- sugar=3.-- groove=wn-- planarity=0.026 type=planar O+ nts=4 GGGG A.DG3,A.DG7,A.DG18,A.DG22

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=-ss- sugar=3--- groove=w-n- WC-->Major O- nts=4 GGGG A.DG1,A.DG20,A.DG16,A.DG10
 2  glyco-bond=---s sugar=--.- groove=--nw Major-->WC O+ nts=4 GGGG A.DG2,A.DG21,A.DG17,A.DG9
 3  glyco-bond=---s sugar=3--. groove=--nw Major-->WC O+ nts=4 GGGG A.DG3,A.DG22,A.DG18,A.DG7
  step#1  mm(<>,outward)  area=8.75  rise=3.09 twist=24.8
  step#2  pm(>>,forward)  area=13.67 rise=2.88 twist=26.2
  strand#1 DNA glyco-bond=--- sugar=3-3 nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG20,A.DG21,A.DG22
  strand#3 DNA glyco-bond=s-- sugar=-.- nts=3 GGG A.DG16,A.DG17,A.DG18
  strand#4 DNA glyco-bond=-ss sugar=--. nts=3 GGG A.DG10,A.DG9,A.DG7

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2 stacking diagrams 
 1  glyco-bond=-ss- sugar=3--- groove=w-n- WC-->Major O- nts=4 GGGG A.DG1,A.DG20,A.DG16,A.DG10
 2  glyco-bond=---s sugar=--.- groove=--nw Major-->WC O+ nts=4 GGGG A.DG2,A.DG21,A.DG17,A.DG9
  step#1  mm(<>,outward)  area=8.75  rise=3.09 twist=24.8

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 2  glyco-bond=---s sugar=--.- groove=--nw Major-->WC O+ nts=4 GGGG A.DG2,A.DG21,A.DG17,A.DG9
 3  glyco-bond=---s sugar=3--. groove=--nw Major-->WC O+ nts=4 GGGG A.DG3,A.DG22,A.DG18,A.DG7
  step#2  pm(>>,forward)  area=13.67 rise=2.88 twist=26.2

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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, UDUU, hybrid3, WARNING, 3+1, 3(-Lw-Ln-P), WARNING
 1  glyco-bond=--ss sugar=3--- groove=-n-w Major-->WC O- nts=4 GGGG A.DG1,A.DG10,A.DG16,A.DG20
 2  glyco-bond=-s-- sugar=--.- groove=wn-- WC-->Major O+ nts=4 GGGG A.DG2,A.DG9,A.DG17,A.DG21
 3  glyco-bond=-s-- sugar=3.-- groove=wn-- WC-->Major O+ nts=4 GGGG A.DG3,A.DG7,A.DG18,A.DG22
  step#1  mm(<>,outward)  area=8.75  rise=3.09 twist=24.8
  step#2  pm(>>,forward)  area=13.67 rise=2.88 twist=26.2
  strand#1  U DNA glyco-bond=--- sugar=3-3 nts=3 GGG A.DG1,A.DG2,A.DG3
  strand#2* D DNA glyco-bond=-ss sugar=--. nts=3 GGG A.DG10,A.DG9,A.DG7 bulged-nts=1 C A.DC8
  strand#3  U DNA glyco-bond=s-- sugar=-.- nts=3 GGG A.DG16,A.DG17,A.DG18
  strand#4  U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG20,A.DG21,A.DG22
  loop#1 type=lateral   strands=[#1,#2] nts=3 AAC A.DA4,A.DA5,A.DC6
  loop#2 type=lateral   strands=[#2,#3] nts=5 CATCA A.DC11,A.DA12,A.DT13,A.DC14,A.DA15
  loop#3 type=propeller strands=[#3,#4] nts=1 T A.DT19

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