Detailed DSSR results for the G-quadruplex: PDB entry 8g2n
Created and maintained by Xiang-Jun Lu <xiangjun@x3dna.org>
Citation: Please cite the NAR'20 DSSR-PyMOL schematics paper and/or the NAR'15 DSSR method paper.
Summary information
- PDB id
- 8g2n
- Class
- DNA
- Method
- X-ray (1.33 Å)
- Summary
- Crystal structure of tetrahymena thermophila g-rich DNA with novel ligand pydh2
- Reference
- Martin KN, Yatsunyk LA: "Crystal structure of Tetrahymena thermophila G-rich DNA with novel ligand PyDH2."
- Abstract
- G4 notes
- 4 G-tetrads, 1 G4 helix, 1 G4 stem, 4(+Ln+Lw+Ln), chair(2+2), UDUD
Base-block schematics in six views
List of 4 G-tetrads
1 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.543 type=other nts=4 GGGG A.DG4,A.DG25,A.DG16,A.DG13 2 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.529 type=other nts=4 GGGG A.DG5,A.DG24,A.DG17,A.DG12 3 glyco-bond=s-s- sugar=---- groove=wnwn planarity=0.447 type=other nts=4 GGGG A.DG6,A.DG23,A.DG18,A.DG11 4 glyco-bond=-s-s sugar=---- groove=wnwn planarity=0.522 type=bowl-2 nts=4 GGGG A.DG7,A.DG22,A.DG19,A.DG10
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 1 stem
 |
1 glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG4,A.DG25,A.DG16,A.DG13 2 glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG5,A.DG24,A.DG17,A.DG12 3 glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG6,A.DG23,A.DG18,A.DG11 4 glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG7,A.DG22,A.DG19,A.DG10 step#1 mm(<>,outward) area=15.70 rise=3.49 twist=15.6 step#2 pp(><,inward) area=0.00 rise=6.67 twist=20.5 step#3 mm(<>,outward) area=18.80 rise=3.51 twist=12.2 strand#1 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG A.DG4,A.DG5,A.DG6,A.DG7 strand#2 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG A.DG25,A.DG24,A.DG23,A.DG22 strand#3 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG A.DG16,A.DG17,A.DG18,A.DG19 strand#4 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG A.DG13,A.DG12,A.DG11,A.DG10 |
| 3 stacking diagrams | |
 |
1 glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG4,A.DG25,A.DG16,A.DG13 |
 |
2 glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG5,A.DG24,A.DG17,A.DG12 |
 |
3 glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG6,A.DG23,A.DG18,A.DG11 |
List of 1 G4-stem
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, 4 G-tetrad layers, 3 loops, INTRA-molecular, UDUD, anti-parallel, 4(+Ln+Lw+Ln), chair(2+2)
 |
1 glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG4,A.DG25,A.DG16,A.DG13 2 glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG5,A.DG24,A.DG17,A.DG12 3 glyco-bond=s-s- sugar=---- groove=wnwn Major-->WC nts=4 GGGG A.DG6,A.DG23,A.DG18,A.DG11 4 glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major nts=4 GGGG A.DG7,A.DG22,A.DG19,A.DG10 step#1 mm(<>,outward) area=15.70 rise=3.49 twist=15.6 step#2 pp(><,inward) area=0.00 rise=6.67 twist=20.5 step#3 mm(<>,outward) area=18.80 rise=3.51 twist=12.2 strand#1 U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG A.DG4,A.DG5,A.DG6,A.DG7 strand#2 D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG A.DG25,A.DG24,A.DG23,A.DG22 strand#3 U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG A.DG16,A.DG17,A.DG18,A.DG19 strand#4 D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG A.DG13,A.DG12,A.DG11,A.DG10 loop#1 type=lateral strands=[#1,#4] nts=2 TT A.DT8,A.DT9 loop#2 type=lateral strands=[#4,#3] nts=2 TT A.DT14,A.DT15 loop#3 type=lateral strands=[#3,#2] nts=2 TT A.DT20,A.DT21 |