Summary information

PDB id
2n21
Class
hydrolase-DNA
Method
NMR
Summary
Solution structure of complex between DNA g-quadruplex and g-quadruplex recognition domain of rhau
Reference
Heddi B, Cheong VV, Martadinata H, Phan AT (2015): "Insights into G-quadruplex specific recognition by the DEAH-box helicase RHAU: Solution structure of a peptide-quadruplex complex." Proc.Natl.Acad.Sci.USA, 112, 9608-9613. doi: 10.1073/pnas.1422605112.
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, 3(-P-P-P), parallel(4+0), UUUU

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 3 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.225 type=other  nts=4 GGGG B.DG3,B.DG7,B.DG11,B.DG15
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.150 type=planar nts=4 GGGG B.DG4,B.DG8,B.DG12,B.DG16
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.194 type=other  nts=4 GGGG B.DG5,B.DG9,B.DG13,B.DG17

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=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG11,B.DG15
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG4,B.DG8,B.DG12,B.DG16
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG5,B.DG9,B.DG13,B.DG17
  step#1  pm(>>,forward)  area=9.62  rise=3.35 twist=33.8
  step#2  pm(>>,forward)  area=14.15 rise=3.35 twist=31.4
  strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG3,B.DG4,B.DG5
  strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG7,B.DG8,B.DG9
  strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG11,B.DG12,B.DG13
  strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG15,B.DG16,B.DG17

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2 stacking diagrams 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG11,B.DG15
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG4,B.DG8,B.DG12,B.DG16
  step#1  pm(>>,forward)  area=9.62  rise=3.35 twist=33.8

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 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG4,B.DG8,B.DG12,B.DG16
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG5,B.DG9,B.DG13,B.DG17
  step#2  pm(>>,forward)  area=14.15 rise=3.35 twist=31.4

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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, UUUU, parallel, 3(-P-P-P), parallel(4+0)

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG11,B.DG15
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG4,B.DG8,B.DG12,B.DG16
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG5,B.DG9,B.DG13,B.DG17
  step#1  pm(>>,forward)  area=9.62  rise=3.35 twist=33.8
  step#2  pm(>>,forward)  area=14.15 rise=3.35 twist=31.4
  strand#1  U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG3,B.DG4,B.DG5
  strand#2  U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG7,B.DG8,B.DG9
  strand#3  U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG11,B.DG12,B.DG13
  strand#4  U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG15,B.DG16,B.DG17
  loop#1 type=propeller strands=[#1,#2] nts=1 T B.DT6
  loop#2 type=propeller strands=[#2,#3] nts=1 T B.DT10
  loop#3 type=propeller strands=[#3,#4] nts=1 T B.DT14

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