Summary information

PDB id
8taa
Class
DNA
Method
X-ray (1.45 Å)
Summary
Right-left hybrid parallel g-quadruplex in complex with n-methyl mesoporphyrin
Reference
Seth PC, Yatsunyk LA: "Right-left hybrid parallel G-quadruplex in complex with N-methyl mesoporphyrin."
Abstract
 
G4 notes
4 G-tetrads, 1 G4 helix, 1 G4 stem, 2(-P-P-P), parallel(4+0), UUUU

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 4 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.120 type=planar nts=4 GGGG A.DG1,A.DG4,A.DG7,A.DG10
 2 glyco-bond=---- sugar=---- groove=---- planarity=0.184 type=other  nts=4 GGGG A.DG3,A.DG6,A.DG9,A.DG12
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.088 type=planar nts=4 GGGG A.DG15,A.DG18,A.DG21,A.DG24
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.126 type=planar nts=4 GGGG A.DG16,A.DG19,A.DG22,A.DG25

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, 4 G-tetrad layers, INTRA-molecular, with 1 stem

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG6,A.DG9,A.DG12
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG7,A.DG10,A.DG1
 3  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG21,A.DG18,A.DG15,A.DG24
 4  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG22,A.DG19,A.DG16,A.DG25
  step#1  mp(<<,backward) area=11.76 rise=3.25 twist=-26.4
  step#2  mm(<>,outward)  area=28.59 rise=3.29 twist=-10.0
  step#3  pm(>>,forward)  area=8.31  rise=3.35 twist=32.9
  strand#1 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG3,A.DG4,A.DG21,A.DG22
  strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG6,A.DG7,A.DG18,A.DG19
  strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG9,A.DG10,A.DG15,A.DG16
  strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG12,A.DG1,A.DG24,A.DG25

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3 stacking diagrams 
 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG6,A.DG9,A.DG12
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG7,A.DG10,A.DG1
  step#1  mp(<<,backward) area=11.76 rise=3.25 twist=-26.4

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 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG7,A.DG10,A.DG1
 3  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG21,A.DG18,A.DG15,A.DG24
  step#2  mm(<>,outward)  area=28.59 rise=3.29 twist=-10.0

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 3  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG21,A.DG18,A.DG15,A.DG24
 4  glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG22,A.DG19,A.DG16,A.DG25
  step#3  pm(>>,forward)  area=8.31  rise=3.35 twist=32.9

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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-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG15,A.DG18,A.DG21,A.DG24
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG16,A.DG19,A.DG22,A.DG25
  step#1  pm(>>,forward)  area=8.31  rise=3.35 twist=32.9
  strand#1  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG15,A.DG16
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG18,A.DG19
  strand#3  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG21,A.DG22
  strand#4  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG24,A.DG25
  loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT17
  loop#2 type=propeller strands=[#2,#3] nts=1 T A.DT20
  loop#3 type=propeller strands=[#3,#4] nts=1 T A.DT23

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

 1 type=V-shaped  helix=#1 nts=4 GTGG A.DG1,A.DT2,A.DG3,A.DG4
 2* type=V-shaped  helix=#1 nts=4 GGTG A.DG9,A.DG10,A.DT11,A.DG12