Summary information and primary citation

PDB-id
21cc
Class
RNA
Method
NMR
Summary
A solution NMR model of l-RNA r(uaggguuagggu) bounding protoporphyrin ix ligand
Reference
Iwakiri R, Wang SY, Xu Y: "A solution NMR model of L-RNA r(UAGGGUUAGGGU) bounding Protoporphyrin IX ligand."
Abstract
 
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0, negative twist

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

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List of 3 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.323 type=bowl   -- nts=4 GGGG A.G3,A.G9,B.G15,B.G21
 2 glyco-bond=---- sugar=3333 groove=---- planarity=0.177 type=other  -- nts=4 GGGG A.G4,A.G10,B.G16,B.G22
 3 glyco-bond=---- sugar=-3-3 groove=---- planarity=0.188 type=other  -- nts=4 GGGG A.G5,A.G11,B.G17,B.G23

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, inter-molecular, with 1 stem
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.G3,A.G9,B.G15,B.G21
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG A.G4,A.G10,B.G16,B.G22
 3  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major -- nts=4 GGGG A.G5,A.G11,B.G17,B.G23
  step#1  mp(<<,backward) area=8.13  rise=3.70 twist=-33.4
  step#2  mp(<<,backward) area=13.01 rise=3.43 twist=-27.0
  strand#1 RNA glyco-bond=--- sugar=-3- nts=3 GGG A.G3,A.G4,A.G5
  strand#2 RNA glyco-bond=--- sugar=-33 nts=3 GGG A.G9,A.G10,A.G11
  strand#3 RNA glyco-bond=--- sugar=-3- nts=3 GGG B.G15,B.G16,B.G17
  strand#4 RNA glyco-bond=--- sugar=-33 nts=3 GGG B.G21,B.G22,B.G23

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2 stacking diagrams 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major -- nts=4 GGGG A.G3,A.G9,B.G15,B.G21
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG A.G4,A.G10,B.G16,B.G22
  step#1  mp(<<,backward) area=8.13  rise=3.70 twist=-33.4

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 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major -- nts=4 GGGG A.G4,A.G10,B.G16,B.G22
 3  glyco-bond=---- sugar=-3-3 groove=---- WC-->Major -- nts=4 GGGG A.G5,A.G11,B.G17,B.G23
  step#2  mp(<<,backward) area=13.01 rise=3.43 twist=-27.0

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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, 2 loops, inter-molecular, UUUU, parallel, WARNING, 4+0, WARNING
 1  glyco-bond=---- sugar=---- groove=---- Major-->WC -- nts=4 GGGG A.G3,B.G21,B.G15,A.G9
 2  glyco-bond=---- sugar=3333 groove=---- Major-->WC -- nts=4 GGGG A.G4,B.G22,B.G16,A.G10
 3  glyco-bond=---- sugar=-3-3 groove=---- Major-->WC -- nts=4 GGGG A.G5,B.G23,B.G17,A.G11
  step#1  mp(<<,backward) area=8.13  rise=3.70 twist=-33.4
  step#2  mp(<<,backward) area=13.01 rise=3.43 twist=-27.0
  strand#1  U RNA glyco-bond=--- sugar=-3- nts=3 GGG A.G3,A.G4,A.G5
  strand#2  U RNA glyco-bond=--- sugar=-33 nts=3 GGG B.G21,B.G22,B.G23
  strand#3  U RNA glyco-bond=--- sugar=-3- nts=3 GGG B.G15,B.G16,B.G17
  strand#4  U RNA glyco-bond=--- sugar=-33 nts=3 GGG A.G9,A.G10,A.G11
  loop#1 type=propeller strands=[#1,#4] nts=3 UUA A.U6,A.U7,A.A8
  loop#2 type=propeller strands=[#3,#2] nts=3 UUA B.U18,B.U19,B.A20

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