DSSR-curated G4 structure: PDB entry 6xcl

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 AM, Chen M, Liang Y, Jia Z, Mergny JL, Petitjean A (2021): "Going Platinum to the Tune of a Remarkable Guanine Quadruplex Binder: Solution- and Solid-State Investigations." Angew.Chem.Int.Ed.Engl., 60, 2500-2507. 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

PyMOL session file	PDB file	View in 3Dmol.js

List of 6 G-tetrads

 1 glyco-bond=---- sugar=---- groove=---- planarity=0.084 type=planar nts=4 GGGG A.DG2,A.DG8,A.DG14,A.DG20
 2 glyco-bond=---- sugar=.--- groove=---- planarity=0.133 type=planar nts=4 GGGG A.DG3,A.DG9,A.DG15,A.DG21
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.238 type=bowl   nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.106 type=planar nts=4 GGGG B.DG2,B.DG8,B.DG14,B.DG20
 5 glyco-bond=---- sugar=.--- groove=---- planarity=0.148 type=planar nts=4 GGGG B.DG3,B.DG9,B.DG15,B.DG21
 6 glyco-bond=---- sugar=---- 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=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22 2 glyco-bond=---- sugar=.--- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG15,A.DG21 3* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,A.DG14,A.DG20 4 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.DG2,B.DG20,B.DG14,B.DG8 5 glyco-bond=---- sugar=.--- groove=---- Major-->WC nts=4 GGGG B.DG3,B.DG21,B.DG15,B.DG9 6 glyco-bond=---- sugar=---- 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=------ sugar=-.--.- nts=6 GGGGGG A.DG4,A.DG3,A.DG2,B.DG2,B.DG3,B.DG4 strand#2 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG A.DG10,A.DG9,A.DG8,B.DG20,B.DG21,B.DG22 strand#3 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG A.DG16,A.DG15,A.DG14,B.DG14,B.DG15,B.DG16 strand#4 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG A.DG22,A.DG21,A.DG20,B.DG8,B.DG9,B.DG10 Download PDB file Interactive view in 3Dmol.js
5 stacking diagrams
	1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22 2 glyco-bond=---- sugar=.--- 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 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---- sugar=.--- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG15,A.DG21 3* glyco-bond=---- sugar=---- 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 Download PDB file Interactive view in 3Dmol.js
	3* glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,A.DG14,A.DG20 4 glyco-bond=---- sugar=---- 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 Download PDB file Interactive view in 3Dmol.js
	4 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG B.DG2,B.DG20,B.DG14,B.DG8 5 glyco-bond=---- sugar=.--- 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 Download PDB file Interactive view in 3Dmol.js
	5 glyco-bond=---- sugar=.--- groove=---- Major-->WC nts=4 GGGG B.DG3,B.DG21,B.DG15,B.DG9 6 glyco-bond=---- sugar=---- 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 Download PDB file Interactive view in 3Dmol.js

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=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG8,A.DG14,A.DG20
 2  glyco-bond=---- sugar=.--- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG9,A.DG15,A.DG21
 3  glyco-bond=---- sugar=---- 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=--- sugar=-.- nts=3 GGG A.DG2,A.DG3,A.DG4
  strand#2  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG8,A.DG9,A.DG10
  strand#3  U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG14,A.DG15,A.DG16
  strand#4  U DNA glyco-bond=--- sugar=--- 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

Download PDB file
Interactive view in 3Dmol.js

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

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG2,B.DG8,B.DG14,B.DG20
 2  glyco-bond=---- sugar=.--- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG9,B.DG15,B.DG21
 3  glyco-bond=---- sugar=---- 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=--- sugar=-.- nts=3 GGG B.DG2,B.DG3,B.DG4
  strand#2  U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG8,B.DG9,B.DG10
  strand#3  U DNA glyco-bond=--- sugar=--- nts=3 GGG B.DG14,B.DG15,B.DG16
  strand#4  U DNA glyco-bond=--- sugar=--- 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