Summary information

PDB id
6xcl
Class
DNA
Method
X-ray (2.7 Å)
Summary
Crystal structure of human telomeric DNA g-quadruplex in complex with a novel platinum(ii) complex.
Reference
Miron CE, van Staalduinen L, Rangaswamy AMM, Chen M, Liang Y, Jia Z, Mergny JL, Petitjean A (2020): "Going Platinum to the Tune of a Remarkable Guanine Quadruplex Binder: Solution- and Solid-State Investigations." Angew.Chem.Int.Ed.Engl. doi: 10.1002/anie.202012520.
Abstract
Guanine quadruplex recognition has gained increasing attention, inspired by the growing awareness of the key roles played by these non-canonical nucleic acid architectures in cellular regulatory processes. We report here the solution and solid-state studies of a novel planar platinum(II) complex that is easily assembled from a simple ligand, and exhibits notable binding affinity for guanine quadruplex structures, while maintaining good selectivity for guanine quadruplex over duplex structures. A crystal structure of this ligand complexed with a telomeric quadruplex confirms double end-capping, with dimerization at the 5' interface.
G4 notes
6 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, 3(-P-P-P), parallel(4+0), UUUU, coaxial interfaces: 5'/5'

Base-block schematics in six views

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List of 6 G-tetrads

 1 glyco-bond=---- groove=---- planarity=0.084 type=planar nts=4 GGGG A.DG2,A.DG8,A.DG14,A.DG20
 2 glyco-bond=---- groove=---- planarity=0.133 type=planar nts=4 GGGG A.DG3,A.DG9,A.DG15,A.DG21
 3 glyco-bond=---- groove=---- planarity=0.238 type=bowl   nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22
 4 glyco-bond=---- groove=---- planarity=0.106 type=planar nts=4 GGGG B.DG2,B.DG8,B.DG14,B.DG20
 5 glyco-bond=---- groove=---- planarity=0.148 type=planar nts=4 GGGG B.DG3,B.DG9,B.DG15,B.DG21
 6 glyco-bond=---- groove=---- planarity=0.236 type=bowl   nts=4 GGGG B.DG4,B.DG10,B.DG16,B.DG22

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, 6 G-tetrad layers, inter-molecular, with 2 stems

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG15,A.DG21
 3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,A.DG14,A.DG20
 4  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG2,B.DG20,B.DG14,B.DG8
 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG3,B.DG21,B.DG15,B.DG9
 6  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG4,B.DG22,B.DG16,B.DG10
  step#1  mp(<<,backward) area=11.88 rise=3.43 twist=27.9
  step#2  mp(<<,backward) area=10.86 rise=3.31 twist=29.1
  step#3  mm(<>,outward)  area=0.00  rise=6.66 twist=-101.8
  step#4  pm(>>,forward)  area=10.14 rise=3.30 twist=29.1
  step#5  pm(>>,forward)  area=11.61 rise=3.43 twist=28.1
  strand#1 DNA glyco-bond=------ nts=6 GGGGGG A.DG4,A.DG3,A.DG2,B.DG2,B.DG3,B.DG4
  strand#2 DNA glyco-bond=------ nts=6 GGGGGG A.DG10,A.DG9,A.DG8,B.DG20,B.DG21,B.DG22
  strand#3 DNA glyco-bond=------ nts=6 GGGGGG A.DG16,A.DG15,A.DG14,B.DG14,B.DG15,B.DG16
  strand#4 DNA glyco-bond=------ nts=6 GGGGGG A.DG22,A.DG21,A.DG20,B.DG8,B.DG9,B.DG10

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5 stacking diagrams
 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22
2 glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG15,A.DG21
step#1 mp(<<,backward) area=11.88 rise=3.43 twist=27.9

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 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG15,A.DG21
3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,A.DG14,A.DG20
step#2 mp(<<,backward) area=10.86 rise=3.31 twist=29.1

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 3* glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,A.DG14,A.DG20
4 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG2,B.DG20,B.DG14,B.DG8
step#3 mm(<>,outward) area=0.00 rise=6.66 twist=-101.8

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 4  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG2,B.DG20,B.DG14,B.DG8
5 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG3,B.DG21,B.DG15,B.DG9
step#4 pm(>>,forward) area=10.14 rise=3.30 twist=29.1

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 5  glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG3,B.DG21,B.DG15,B.DG9
6 glyco-bond=---- groove=---- Major-->WC nts=4 GGGG B.DG4,B.DG22,B.DG16,B.DG10
step#5 pm(>>,forward) area=11.61 rise=3.43 twist=28.1

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List of 2 G4-stems

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,A.DG14,A.DG20
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG15,A.DG21
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22
  step#1  pm(>>,forward)  area=10.86 rise=3.31 twist=29.1
  step#2  pm(>>,forward)  area=11.88 rise=3.43 twist=27.9
  strand#1  U DNA glyco-bond=--- nts=3 GGG A.DG2,A.DG3,A.DG4
  strand#2  U DNA glyco-bond=--- nts=3 GGG A.DG8,A.DG9,A.DG10
  strand#3  U DNA glyco-bond=--- nts=3 GGG A.DG14,A.DG15,A.DG16
  strand#4  U DNA glyco-bond=--- nts=3 GGG A.DG20,A.DG21,A.DG22
  loop#1 type=propeller strands=[#1,#2] nts=3 TTA A.DT5,A.DT6,A.DA7
  loop#2 type=propeller strands=[#2,#3] nts=3 TTA A.DT11,A.DT12,A.DA13
  loop#3 type=propeller strands=[#3,#4] nts=3 TTA A.DT17,A.DT18,A.DA19

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

 1  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG2,B.DG8,B.DG14,B.DG20
 2  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG9,B.DG15,B.DG21
 3  glyco-bond=---- groove=---- WC-->Major nts=4 GGGG B.DG4,B.DG10,B.DG16,B.DG22
  step#1  pm(>>,forward)  area=10.14 rise=3.30 twist=29.1
  step#2  pm(>>,forward)  area=11.61 rise=3.43 twist=28.1
  strand#1  U DNA glyco-bond=--- nts=3 GGG B.DG2,B.DG3,B.DG4
  strand#2  U DNA glyco-bond=--- nts=3 GGG B.DG8,B.DG9,B.DG10
  strand#3  U DNA glyco-bond=--- nts=3 GGG B.DG14,B.DG15,B.DG16
  strand#4  U DNA glyco-bond=--- nts=3 GGG B.DG20,B.DG21,B.DG22
  loop#1 type=propeller strands=[#1,#2] nts=3 TTA B.DT5,B.DT6,B.DA7
  loop#2 type=propeller strands=[#2,#3] nts=3 TTA B.DT11,B.DT12,B.DA13
  loop#3 type=propeller strands=[#3,#4] nts=3 TTA B.DT17,B.DT18,B.DA19

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List of 1 G4 coaxial stack

 1 G4 helix#1 contains 2 G4 stems: [#1,#2]  [5'/5']