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

PDB-id
6rnl
Class
DNA
Method
X-ray (1.88 Å)
Summary
L-[ru(tap)2(dppz)]2+ bound to the G-quadruplex forming sequence d(tagggtt)
Reference
McQuaid, K., Hall, J.P., Baumgaertner, L., Cardin, D.J., Cardin, C.J.: (2019) "Three thymine/adenine binding modes of the ruthenium complex Lambda-[Ru(TAP)2(dppz)]2+to the G-quadruplex forming sequence d(TAGGGTT) shown by X-ray crystallography." Chem.Commun.(Camb.), 55, 9116-9119.
Abstract
Λ-[Ru(TAP)2(dppz)]2+ was crystallised with the G-quadruplex-forming heptamer d(TAGGGTT). Surprisingly, even though there are four unique binding sites, the complex is not in contact with any G-quartet surface. Two complexes stabilise cavities formed from terminal T·A and T·T mismatched pairs. A third shows kinking by a TAP ligand between T·T linkages, while the fourth shows sandwiching of a dppz ligand between a T·A/T·A quadruplex and a T·T mismatch, stabilised by an additional T·A base pair stacking interaction on a TAP surface. Overall, the structure shows an unexpected affinity for thymine, and suggests models for G-quadruplex loop binding.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem · parallel(4+0), UUUU

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

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List of 3 G-tetrads [summary · schematics · helices · stems · costacks · homepage]

 1 glyco-bond=---- groove=---- planarity=0.175 type=other  nts=4 GGGG A.DG3,B.DG3,C.DG3,D.DG3
 2 glyco-bond=---- groove=---- planarity=0.192 type=other  nts=4 GGGG A.DG4,B.DG4,C.DG4,D.DG4
 3 glyco-bond=---- groove=---- planarity=0.302 type=bowl   nts=4 GGGG A.DG5,B.DG5,C.DG5,D.DG5

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,B.DG3,C.DG3,D.DG3
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,B.DG4,C.DG4,D.DG4
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,B.DG5,C.DG5,D.DG5
  step#1  pm(>>,forward)  area=11.51 rise=3.32 twist=28.4
  step#2  pm(>>,forward)  area=11.84 rise=3.43 twist=26.5
  strand#1 DNA glyco-bond=--- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2 DNA glyco-bond=--- nts=3 GGG B.DG3,B.DG4,B.DG5
  strand#3 DNA glyco-bond=--- nts=3 GGG C.DG3,C.DG4,C.DG5
  strand#4 DNA glyco-bond=--- nts=3 GGG D.DG3,D.DG4,D.DG5

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2 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,B.DG3,C.DG3,D.DG3
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,B.DG4,C.DG4,D.DG4
step#1 pm(>>,forward) area=11.51 rise=3.32 twist=28.4

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,B.DG4,C.DG4,D.DG4
3 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,B.DG5,C.DG5,D.DG5
step#2 pm(>>,forward) area=11.84 rise=3.43 twist=26.5

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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, 3 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,B.DG3,C.DG3,D.DG3
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,B.DG4,C.DG4,D.DG4
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG5,B.DG5,C.DG5,D.DG5
  step#1  pm(>>,forward)  area=11.51 rise=3.32 twist=28.4
  step#2  pm(>>,forward)  area=11.84 rise=3.43 twist=26.5
  strand#1  U DNA glyco-bond=--- nts=3 GGG A.DG3,A.DG4,A.DG5
  strand#2  U DNA glyco-bond=--- nts=3 GGG B.DG3,B.DG4,B.DG5
  strand#3  U DNA glyco-bond=--- nts=3 GGG C.DG3,C.DG4,C.DG5
  strand#4  U DNA glyco-bond=--- nts=3 GGG D.DG3,D.DG4,D.DG5

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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)