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

PDB-id
3nz7
Class
DNA
Method
X-ray (1.1 Å)
Summary
A bimolecular anti-parallel-stranded oxytricha nova telomeric quadruplex in complex with a 3,6-disubstituted acridine ligand containing bis-3-fluoropyrrolidine end side chains
Reference
Campbell, N.H., Smith, D.L., Reszka, A.P., Neidle, S., O'Hagan, D.: (2011) "Fluorine in medicinal chemistry: beta-fluorination of peripheral pyrrolidines attached to acridine ligands affects their interactions with G-quadruplex DNA." Org.Biomol.Chem., 9, 1328-1331.
Abstract
Comparative X-ray structure studies reveal that C-F bond incorporation into the peripheral pyrrolidine moieties of the G-quadruplex DNA binding ligand BSU6039 leads to a distinct pyrrolidine ring conformation, relative to the non-fluorinated analogue, and with a different binding mode involving reversal of the pyrrolidinium N(+)-H orientation.
G4 notes
4 G-tetrads, 1 G4 helix, 1 G4 stem · (2+2), UDDU

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

PyMOL session file PDB file View in 3Dmol.js

List of 4 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=s--s groove=w-n- planarity=0.263 type=bowl   nts=4 GGGG A.DG1,B.DG4,A.DG12,B.DG9
 2 glyco-bond=-ss- groove=w-n- planarity=0.185 type=other  nts=4 GGGG A.DG2,B.DG3,A.DG11,B.DG10
 3 glyco-bond=s--s groove=w-n- planarity=0.173 type=other  nts=4 GGGG A.DG3,B.DG2,A.DG10,B.DG11
 4 glyco-bond=-ss- groove=w-n- planarity=0.204 type=other  nts=4 GGGG A.DG4,B.DG1,A.DG9,B.DG12

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

 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1,B.DG4,A.DG12,B.DG9
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG3,A.DG11,B.DG10
 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG2,A.DG10,B.DG11
 4  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG4,B.DG1,A.DG9,B.DG12
  step#1  mm(<>,outward)  area=14.20 rise=3.48 twist=16.7
  step#2  pp(><,inward)   area=19.00 rise=3.59 twist=36.8
  step#3  mm(<>,outward)  area=11.94 rise=3.46 twist=19.5
  strand#1 DNA glyco-bond=s-s- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4
  strand#2 DNA glyco-bond=-s-s nts=4 GGGG B.DG4,B.DG3,B.DG2,B.DG1
  strand#3 DNA glyco-bond=-s-s nts=4 GGGG A.DG12,A.DG11,A.DG10,A.DG9
  strand#4 DNA glyco-bond=s-s- nts=4 GGGG B.DG9,B.DG10,B.DG11,B.DG12

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3 stacking diagrams
 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1,B.DG4,A.DG12,B.DG9
2 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG3,A.DG11,B.DG10
step#1 mm(<>,outward) area=14.20 rise=3.48 twist=16.7

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 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG3,A.DG11,B.DG10
3 glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG2,A.DG10,B.DG11
step#2 pp(><,inward) area=19.00 rise=3.59 twist=36.8

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 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG2,A.DG10,B.DG11
4 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG4,B.DG1,A.DG9,B.DG12
step#3 mm(<>,outward) area=11.94 rise=3.46 twist=19.5

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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, 4 G-tetrad layers, 2 loops, inter-molecular, UDDU, anti-parallel, (2+2)

 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1,B.DG4,A.DG12,B.DG9
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG3,A.DG11,B.DG10
 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG2,A.DG10,B.DG11
 4  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG4,B.DG1,A.DG9,B.DG12
  step#1  mm(<>,outward)  area=14.20 rise=3.48 twist=16.7
  step#2  pp(><,inward)   area=19.00 rise=3.59 twist=36.8
  step#3  mm(<>,outward)  area=11.94 rise=3.46 twist=19.5
  strand#1  U DNA glyco-bond=s-s- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4
  strand#2  D DNA glyco-bond=-s-s nts=4 GGGG B.DG4,B.DG3,B.DG2,B.DG1
  strand#3  D DNA glyco-bond=-s-s nts=4 GGGG A.DG12,A.DG11,A.DG10,A.DG9
  strand#4  U DNA glyco-bond=s-s- nts=4 GGGG B.DG9,B.DG10,B.DG11,B.DG12
  loop#1 type=diagonal  strands=[#1,#3] nts=4 TTTT A.DT5,A.DT6,A.DT7,A.DT8
  loop#2 type=diagonal  strands=[#2,#4] nts=4 TTTT B.DT5,B.DT6,B.DT7,B.DT8

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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)