Summary information [schematics · tetrads · helices · stems · costacks · homepage]

PDB-id
2mfu
Class
DNA
Method
NMR
Summary
Solution NMR structure of quadruplex d(tgggtttgggttgggtttggg) in sodium conditions
Reference
Karsisiotis, A., Dillon, P., Webba da Silva, M.: "Solution NMR structure of quadruplex d(TGGGTTTGGGTTGGGTTTGGG) in sodium conditions." To be published
Abstract
 
G4 notes
2 G-tetrads, 1 G4 helix, 1 G4 stem · 2(-Lw-Ln-P), hybrid-2(3+1), UDUU

Base-block schematics in six views [summary · tetrads · helices · stems · costacks · homepage]

PyMOL session file PDB file View in 3Dmol.js

List of 2 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=s-.s groove=w..- planarity=0.123 type=planar nts=4 GGGG A.DG3,A.DG10,A.DG14,A.DG19
 2 glyco-bond=-s-- groove=wn-- planarity=0.226 type=other  nts=4 GGGG A.DG4,A.DG9,A.DG15,A.DG20

List of 1 G4-helix [summary · schematics · tetrads · stems · costacks · homepage]

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

 1  glyco-bond=s-.s groove=w..- Major-->WC nts=4 GGGG A.DG3,A.DG10,A.DG14,A.DG19
 2  glyco-bond=-s-- groove=wn-- WC-->Major nts=4 GGGG A.DG4,A.DG9,A.DG15,A.DG20
  step#1  mm(<>,outward)  area=11.85 rise=3.15 twist=18.1
  strand#1 DNA glyco-bond=s- nts=2 GG A.DG3,A.DG4
  strand#2 DNA glyco-bond=-s nts=2 GG A.DG10,A.DG9
  strand#3 DNA glyco-bond=.- nts=2 GG A.DG14,A.DG15
  strand#4 DNA glyco-bond=s- nts=2 GG A.DG19,A.DG20

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1 stacking diagram
 1  glyco-bond=s-.s groove=w..- Major-->WC nts=4 GGGG A.DG3,A.DG10,A.DG14,A.DG19
2 glyco-bond=-s-- groove=wn-- WC-->Major nts=4 GGGG A.DG4,A.DG9,A.DG15,A.DG20
step#1 mm(<>,outward) area=11.85 rise=3.15 twist=18.1

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List of 1 G4-stem [summary · schematics · tetrads · helices · costacks · homepage]

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, UDUU, anti-parallel, 2(-Lw-Ln-P), hybrid-2(3+1)

 1  glyco-bond=s-.s groove=w..- Major-->WC nts=4 GGGG A.DG3,A.DG10,A.DG14,A.DG19
 2  glyco-bond=-s-- groove=wn-- WC-->Major nts=4 GGGG A.DG4,A.DG9,A.DG15,A.DG20
  step#1  mm(<>,outward)  area=11.85 rise=3.15 twist=18.1
  strand#1  U DNA glyco-bond=s- nts=2 GG A.DG3,A.DG4
  strand#2  D DNA glyco-bond=-s nts=2 GG A.DG10,A.DG9
  strand#3  U DNA glyco-bond=.- nts=2 GG A.DG14,A.DG15
  strand#4  U DNA glyco-bond=s- nts=2 GG A.DG19,A.DG20
  loop#1 type=lateral   strands=[#1,#2] nts=4 TTTG A.DT5,A.DT6,A.DT7,A.DG8
  loop#2 type=lateral   strands=[#2,#3] nts=3 TTG A.DT11,A.DT12,A.DG13
  loop#3 type=propeller strands=[#3,#4] nts=3 TTT A.DT16,A.DT17,A.DT18

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List of 0 G4 coaxial stacks [summary · schematics · tetrads · helices · stems · homepage]

List of 0 non-stem G4-loops (including the two closing Gs)