DSSR-curated G4 structure: PDB entry 4wo3

Summary information

PDB id: 4wo3
Class: DNA
Method: X-ray (2.73 Å)
Summary: The second c-kit DNA quadruplex crystal structure
Reference: Wei D, Neidle S: "THE SECOND C-KIT1 DNA QUADRUPLEX CRYSTAL STRUCTURE."
Abstract
G4 notes: 6 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, 2(-PX+P), parallel(4+0), UUUU, coaxial interfaces: 5'/5'-SEPARATED

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=0.175 type=other  nts=4 GGGG B.DG2,B.DG6,B.DG10,B.DG13
 2 glyco-bond=---- sugar=--3- groove=---- planarity=0.206 type=other  nts=4 GGGG B.DG3,B.DG7,B.DG21,B.DG14
 3 glyco-bond=---- sugar=---- groove=---- planarity=0.332 type=bowl   nts=4 GGGG B.DG4,B.DG8,B.DG22,B.DG15
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.156 type=planar nts=4 GGGG A.DG2,A.DG6,A.DG10,A.DG13
 5 glyco-bond=---- sugar=--.. groove=---- planarity=0.204 type=other  nts=4 GGGG A.DG3,A.DG7,A.DG21,A.DG14
 6 glyco-bond=---- sugar=---- groove=---- planarity=0.309 type=bowl   nts=4 GGGG A.DG4,A.DG8,A.DG22,A.DG15

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 B.DG4,B.DG8,B.DG22,B.DG15 2 glyco-bond=---- sugar=--3- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG21,B.DG14 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG2,B.DG6,B.DG10,B.DG13 4 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG13,A.DG10,A.DG6,A.DG2 5 glyco-bond=---- sugar=..-- groove=---- Major-->WC nts=4 GGGG A.DG14,A.DG21,A.DG7,A.DG3 6 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG15,A.DG22,A.DG8,A.DG4 step#1 mp(<<,backward) area=9.98 rise=3.36 twist=32.3 step#2 mp(<<,backward) area=14.54 rise=3.46 twist=28.8 step#3 mm(<>,outward) area=29.35 rise=3.32 twist=-10.5 step#4 pm(>>,forward) area=12.90 rise=3.39 twist=29.6 step#5 pm(>>,forward) area=9.86 rise=3.40 twist=32.9 strand#1 DNA glyco-bond=------ sugar=----.- nts=6 GGGGGG B.DG4,B.DG3,B.DG2,A.DG13,A.DG14,A.DG15 strand#2 DNA glyco-bond=------ sugar=----.- nts=6 GGGGGG B.DG8,B.DG7,B.DG6,A.DG10,A.DG21,A.DG22 strand#3 DNA glyco-bond=------ sugar=-3---- nts=6 GGGGGG B.DG22,B.DG21,B.DG10,A.DG6,A.DG7,A.DG8 strand#4 DNA glyco-bond=------ sugar=------ nts=6 GGGGGG B.DG15,B.DG14,B.DG13,A.DG2,A.DG3,A.DG4 Download PDB file Interactive view in 3Dmol.js
5 stacking diagrams
	1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG4,B.DG8,B.DG22,B.DG15 2 glyco-bond=---- sugar=--3- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG21,B.DG14 step#1 mp(<<,backward) area=9.98 rise=3.36 twist=32.3 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---- sugar=--3- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG21,B.DG14 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG2,B.DG6,B.DG10,B.DG13 step#2 mp(<<,backward) area=14.54 rise=3.46 twist=28.8 Download PDB file Interactive view in 3Dmol.js
	3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG2,B.DG6,B.DG10,B.DG13 4 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG13,A.DG10,A.DG6,A.DG2 step#3 mm(<>,outward) area=29.35 rise=3.32 twist=-10.5 Download PDB file Interactive view in 3Dmol.js
	4 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG13,A.DG10,A.DG6,A.DG2 5 glyco-bond=---- sugar=..-- groove=---- Major-->WC nts=4 GGGG A.DG14,A.DG21,A.DG7,A.DG3 step#4 pm(>>,forward) area=12.90 rise=3.39 twist=29.6 Download PDB file Interactive view in 3Dmol.js
	5 glyco-bond=---- sugar=..-- groove=---- Major-->WC nts=4 GGGG A.DG14,A.DG21,A.DG7,A.DG3 6 glyco-bond=---- sugar=---- groove=---- Major-->WC nts=4 GGGG A.DG15,A.DG22,A.DG8,A.DG4 step#5 pm(>>,forward) area=9.86 rise=3.40 twist=32.9 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, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-PX+P), parallel(4+0)

 1  glyco-bond=---- sugar=--3- groove=---- WC-->Major nts=4 GGGG B.DG3,B.DG7,B.DG21,B.DG14
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG B.DG4,B.DG8,B.DG22,B.DG15
  step#1  pm(>>,forward)  area=9.98  rise=3.36 twist=32.3
  strand#1  U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG3,B.DG4
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG7,B.DG8
  strand#3  U DNA glyco-bond=-- sugar=3- nts=2 GG B.DG21,B.DG22
  strand#4  U DNA glyco-bond=-- sugar=-- nts=2 GG B.DG14,B.DG15
  loop#1 type=propeller strands=[#1,#2] nts=2 AG B.DA5,B.DG6
  loop#2 type=diag-prop strands=[#2,#4] nts=5 CGCTG B.DC9,B.DG10,B.DC11,B.DT12,B.DG13
  loop#3 type=propeller strands=[#4,#3] nts=5 AGGAG B.DA16,B.DG17,B.DG18,B.DA19,B.DG20

Download PDB file
Interactive view in 3Dmol.js

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

 1  glyco-bond=---- sugar=--.. groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG21,A.DG14
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG22,A.DG15
  step#1  pm(>>,forward)  area=9.86  rise=3.40 twist=32.9
  strand#1  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG3,A.DG4
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG7,A.DG8
  strand#3  U DNA glyco-bond=-- sugar=.- nts=2 GG A.DG21,A.DG22
  strand#4  U DNA glyco-bond=-- sugar=.- nts=2 GG A.DG14,A.DG15
  loop#1 type=propeller strands=[#1,#2] nts=2 AG A.DA5,A.DG6
  loop#2 type=diag-prop strands=[#2,#4] nts=5 CGCTG A.DC9,A.DG10,A.DC11,A.DT12,A.DG13
  loop#3 type=propeller strands=[#4,#3] nts=5 AGGAG A.DA16,A.DG17,A.DG18,A.DA19,A.DG20