DSSR-curated G4 structure: PDB entry 2n3m

Summary information

PDB id: 2n3m
Class: DNA
Method: NMR
Summary: G-quadruplex structure of an anti-proliferative DNA sequence
Reference: Do NQ, Chung WJ, Truong THA, Heddi B, Phan AT: "G-quadruplex structure of an anti-proliferative DNA sequence."
Abstract
G4 notes: 4 G-tetrads, 1 G4 helix, 2 G4 stems, 1 G4 coaxial stack, 2(-P-P-P), parallel(4+0), UUUU, coaxial interfaces: 3'/5'

Base-block schematics in six views

PyMOL session file	PDB file	View in 3Dmol.js

List of 4 G-tetrads

 1 glyco-bond=---- sugar=---. groove=---- planarity=0.180 type=other  nts=4 GGGG A.DG2,A.DG5,A.DG8,A.DG12
 2 glyco-bond=---- sugar=.--3 groove=---- planarity=0.189 type=other  nts=4 GGGG A.DG3,A.DG6,A.DG9,A.DG15
 3 glyco-bond=---- sugar=---. groove=---- planarity=0.141 type=planar nts=4 GGGG A.DG17,A.DG20,A.DG23,A.DG26
 4 glyco-bond=---- sugar=---- groove=---- planarity=0.229 type=other  nts=4 GGGG A.DG18,A.DG21,A.DG24,A.DG27

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, 4 G-tetrad layers, INTRA-molecular, with 2 stems

	1 glyco-bond=---- sugar=---. groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG5,A.DG8,A.DG12 2* glyco-bond=---- sugar=.--3 groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG6,A.DG9,A.DG15 3 glyco-bond=---- sugar=--.- groove=---- WC-->Major nts=4 GGGG A.DG20,A.DG23,A.DG26,A.DG17 4 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG21,A.DG24,A.DG27,A.DG18 step#1 pm(>>,forward) area=10.66 rise=3.17 twist=30.4 step#2 pm(>>,forward) area=18.14 rise=3.32 twist=21.7 step#3 pm(>>,forward) area=7.51 rise=3.26 twist=35.1 strand#1 DNA glyco-bond=---- sugar=-.-- nts=4 GGGG A.DG2,A.DG3,A.DG20,A.DG21 strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG5,A.DG6,A.DG23,A.DG24 strand#3 DNA glyco-bond=---- sugar=--.- nts=4 GGGG A.DG8,A.DG9,A.DG26,A.DG27 strand#4 DNA glyco-bond=---- sugar=.3-- nts=4 GGGG A.DG12,A.DG15,A.DG17,A.DG18 Download PDB file Interactive view in 3Dmol.js
3 stacking diagrams
	1 glyco-bond=---- sugar=---. groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG5,A.DG8,A.DG12 2* glyco-bond=---- sugar=.--3 groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG6,A.DG9,A.DG15 step#1 pm(>>,forward) area=10.66 rise=3.17 twist=30.4 Download PDB file Interactive view in 3Dmol.js
	2* glyco-bond=---- sugar=.--3 groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG6,A.DG9,A.DG15 3 glyco-bond=---- sugar=--.- groove=---- WC-->Major nts=4 GGGG A.DG20,A.DG23,A.DG26,A.DG17 step#2 pm(>>,forward) area=18.14 rise=3.32 twist=21.7 Download PDB file Interactive view in 3Dmol.js
	3 glyco-bond=---- sugar=--.- groove=---- WC-->Major nts=4 GGGG A.DG20,A.DG23,A.DG26,A.DG17 4 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG21,A.DG24,A.DG27,A.DG18 step#3 pm(>>,forward) area=7.51 rise=3.26 twist=35.1 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, 2 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)

 1  glyco-bond=---- sugar=---. groove=---- WC-->Major nts=4 GGGG A.DG2,A.DG5,A.DG8,A.DG12
 2  glyco-bond=---- sugar=.--3 groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG6,A.DG9,A.DG15
  step#1  pm(>>,forward)  area=10.66 rise=3.17 twist=30.4
  strand#1  U DNA glyco-bond=-- sugar=-. nts=2 GG A.DG2,A.DG3
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG5,A.DG6
  strand#3  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG8,A.DG9
  strand#4* U DNA glyco-bond=-- sugar=.3 nts=2 GG A.DG12,A.DG15 bulged-nts=2 TT A.DT13,A.DT14
  loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT4
  loop#2 type=propeller strands=[#2,#3] nts=1 T A.DT7
  loop#3 type=propeller strands=[#3,#4] nts=2 TT A.DT10,A.DT11

Download PDB file
Interactive view in 3Dmol.js

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

 1  glyco-bond=---- sugar=---. groove=---- WC-->Major nts=4 GGGG A.DG17,A.DG20,A.DG23,A.DG26
 2  glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG18,A.DG21,A.DG24,A.DG27
  step#1  pm(>>,forward)  area=7.51  rise=3.26 twist=35.1
  strand#1  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG17,A.DG18
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG20,A.DG21
  strand#3  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG23,A.DG24
  strand#4  U DNA glyco-bond=-- sugar=.- nts=2 GG A.DG26,A.DG27
  loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT19
  loop#2 type=propeller strands=[#2,#3] nts=1 T A.DT22
  loop#3 type=propeller strands=[#3,#4] nts=1 T A.DT25