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

PDB-id
3eui
Class
DNA
Method
X-ray (2.2 Å)
Summary
A bimolecular anti-parallel-stranded oxytricha nova telomeric quadruplex in complex with a 3,6-disubstituted acridine bsu-6042 in a large unit cell
Reference
Campbell, N.H., Patel, M., Tofa, A.B., Ghosh, R., Parkinson, G.N., Neidle, S.: (2009) "Selectivity in Ligand Recognition of G-Quadruplex Loops." Biochemistry, 48, 1675-1680.
Abstract
A series of disubstituted acridine ligands have been cocrystallized with a bimolecular DNA G-quadruplex. The ligands have a range of cyclic amino end groups of varying size. The crystal structures show that the diagonal loop in this quadruplex results in a large cavity for these groups, in contrast to the steric constraints imposed by propeller loops in human telomeric quadruplexes. We conclude that the nature of the loop has a significant influence on ligand selectivity for particular quadruplex folds.
G4 notes
8 G-tetrads, 2 G4 helices, 2 G4 stems · (2+2), UDDU

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

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List of 8 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=s--s groove=w-n- planarity=0.246 type=bowl   nts=4 GGGG A.DG1,B.DG16,A.DG12,B.DG21
 2 glyco-bond=-ss- groove=w-n- planarity=0.176 type=other  nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22
 3 glyco-bond=s--s groove=w-n- planarity=0.174 type=other  nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23
 4 glyco-bond=-ss- groove=w-n- planarity=0.190 type=other  nts=4 GGGG A.DG4,B.DG13,A.DG9,B.DG24
 5 glyco-bond=s--s groove=w-n- planarity=0.277 type=bowl   nts=4 GGGG C.DG25,D.DG40,C.DG36,D.DG45
 6 glyco-bond=-ss- groove=w-n- planarity=0.209 type=other  nts=4 GGGG C.DG26,D.DG39,C.DG35,D.DG46
 7 glyco-bond=s--s groove=w-n- planarity=0.179 type=other  nts=4 GGGG C.DG27,D.DG38,C.DG34,D.DG47
 8 glyco-bond=-ss- groove=w-n- planarity=0.211 type=other  nts=4 GGGG C.DG28,D.DG37,C.DG33,D.DG48

List of 2 G4-helices [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.DG16,A.DG12,B.DG21
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22
 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23
 4  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG4,B.DG13,A.DG9,B.DG24
  step#1  mm(<>,outward)  area=14.07 rise=3.50 twist=17.6
  step#2  pp(><,inward)   area=20.62 rise=3.59 twist=36.4
  step#3  mm(<>,outward)  area=12.65 rise=3.45 twist=19.6
  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.DG16,B.DG15,B.DG14,B.DG13
  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.DG21,B.DG22,B.DG23,B.DG24

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3 stacking diagrams
 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG1,B.DG16,A.DG12,B.DG21
2 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22
step#1 mm(<>,outward) area=14.07 rise=3.50 twist=17.6

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 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22
3 glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23
step#2 pp(><,inward) area=20.62 rise=3.59 twist=36.4

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 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23
4 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG4,B.DG13,A.DG9,B.DG24
step#3 mm(<>,outward) area=12.65 rise=3.45 twist=19.6

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Helix#2, 4 G-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG C.DG25,D.DG40,C.DG36,D.DG45
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG C.DG26,D.DG39,C.DG35,D.DG46
 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG C.DG27,D.DG38,C.DG34,D.DG47
 4  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG C.DG28,D.DG37,C.DG33,D.DG48
  step#1  mm(<>,outward)  area=13.12 rise=3.50 twist=18.7
  step#2  pp(><,inward)   area=19.86 rise=3.54 twist=35.8
  step#3  mm(<>,outward)  area=12.56 rise=3.47 twist=19.5
  strand#1 DNA glyco-bond=s-s- nts=4 GGGG C.DG25,C.DG26,C.DG27,C.DG28
  strand#2 DNA glyco-bond=-s-s nts=4 GGGG D.DG40,D.DG39,D.DG38,D.DG37
  strand#3 DNA glyco-bond=-s-s nts=4 GGGG C.DG36,C.DG35,C.DG34,C.DG33
  strand#4 DNA glyco-bond=s-s- nts=4 GGGG D.DG45,D.DG46,D.DG47,D.DG48

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3 stacking diagrams
 1  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG C.DG25,D.DG40,C.DG36,D.DG45
2 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG C.DG26,D.DG39,C.DG35,D.DG46
step#1 mm(<>,outward) area=13.12 rise=3.50 twist=18.7

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 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG C.DG26,D.DG39,C.DG35,D.DG46
3 glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG C.DG27,D.DG38,C.DG34,D.DG47
step#2 pp(><,inward) area=19.86 rise=3.54 twist=35.8

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 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG C.DG27,D.DG38,C.DG34,D.DG47
4 glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG C.DG28,D.DG37,C.DG33,D.DG48
step#3 mm(<>,outward) area=12.56 rise=3.47 twist=19.5

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List of 2 G4-stems [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.DG16,A.DG12,B.DG21
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22
 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23
 4  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG A.DG4,B.DG13,A.DG9,B.DG24
  step#1  mm(<>,outward)  area=14.07 rise=3.50 twist=17.6
  step#2  pp(><,inward)   area=20.62 rise=3.59 twist=36.4
  step#3  mm(<>,outward)  area=12.65 rise=3.45 twist=19.6
  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.DG16,B.DG15,B.DG14,B.DG13
  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.DG21,B.DG22,B.DG23,B.DG24
  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.DT17,B.DT18,B.DT19,B.DT20

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Stem#2, 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 C.DG25,D.DG40,C.DG36,D.DG45
 2  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG C.DG26,D.DG39,C.DG35,D.DG46
 3  glyco-bond=s--s groove=w-n- Major-->WC nts=4 GGGG C.DG27,D.DG38,C.DG34,D.DG47
 4  glyco-bond=-ss- groove=w-n- WC-->Major nts=4 GGGG C.DG28,D.DG37,C.DG33,D.DG48
  step#1  mm(<>,outward)  area=13.12 rise=3.50 twist=18.7
  step#2  pp(><,inward)   area=19.86 rise=3.54 twist=35.8
  step#3  mm(<>,outward)  area=12.56 rise=3.47 twist=19.5
  strand#1  U DNA glyco-bond=s-s- nts=4 GGGG C.DG25,C.DG26,C.DG27,C.DG28
  strand#2  D DNA glyco-bond=-s-s nts=4 GGGG D.DG40,D.DG39,D.DG38,D.DG37
  strand#3  D DNA glyco-bond=-s-s nts=4 GGGG C.DG36,C.DG35,C.DG34,C.DG33
  strand#4  U DNA glyco-bond=s-s- nts=4 GGGG D.DG45,D.DG46,D.DG47,D.DG48
  loop#1 type=diagonal  strands=[#1,#3] nts=4 TTTT C.DT29,C.DT30,C.DT31,C.DT32
  loop#2 type=diagonal  strands=[#2,#4] nts=4 TTTT D.DT41,D.DT42,D.DT43,D.DT44

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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)