Detailed DSSR results for the G-quadruplex: PDB entry 8d79
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
- 8d79
- Class
- DNA
- Method
- X-ray (1.99 Å)
- Summary
- Crystal structure of a four-tetrad, parallel, and na+ stabilized tetrahymena thermophila telomeric g-quadruplex in complex with n-methyl mesoporphyrin ix
- Reference
- Beseiso D, Chen EV, Yatsunyk LA: "Biophysical and structural characterization of telomeric G-quadruplexes from Tetrahymena thermophila in complex with N-Methyl Mesoporphyrin IX."
- Abstract
- G4 notes
- 4 G-tetrads, 1 G4 helix, 1 G4 stem, 4(-P-P-P), parallel(4+0), UUUU
Base-block schematics in six views
List of 4 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.076 type=planar nts=4 GGGG A.DG2,A.DG8,A.DG14,A.DG20 2 glyco-bond=---- sugar=---- groove=---- planarity=0.066 type=planar nts=4 GGGG A.DG3,A.DG9,A.DG15,A.DG21 3 glyco-bond=---- sugar=---- groove=---- planarity=0.116 type=planar nts=4 GGGG A.DG4,A.DG10,A.DG16,A.DG22 4 glyco-bond=---- sugar=--.- groove=---- planarity=0.260 type=bowl nts=4 GGGG A.DG5,A.DG11,A.DG17,A.DG23
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=---- 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 4 glyco-bond=---- sugar=--.- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG11,A.DG17,A.DG23 step#1 pm(>>,forward) area=8.04 rise=3.19 twist=36.7 step#2 pm(>>,forward) area=16.72 rise=3.33 twist=22.1 step#3 pm(>>,forward) area=10.19 rise=3.29 twist=28.4 strand#1 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG2,A.DG3,A.DG4,A.DG5 strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG8,A.DG9,A.DG10,A.DG11 strand#3 DNA glyco-bond=---- sugar=---. nts=4 GGGG A.DG14,A.DG15,A.DG16,A.DG17 strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG20,A.DG21,A.DG22,A.DG23 |
| 3 stacking diagrams | |
 |
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 |
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, UUUU, parallel, 4(-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 4 glyco-bond=---- sugar=--.- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG11,A.DG17,A.DG23 step#1 pm(>>,forward) area=8.04 rise=3.19 twist=36.7 step#2 pm(>>,forward) area=16.72 rise=3.33 twist=22.1 step#3 pm(>>,forward) area=10.19 rise=3.29 twist=28.4 strand#1 U DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG2,A.DG3,A.DG4,A.DG5 strand#2 U DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG8,A.DG9,A.DG10,A.DG11 strand#3 U DNA glyco-bond=---- sugar=---. nts=4 GGGG A.DG14,A.DG15,A.DG16,A.DG17 strand#4 U DNA glyco-bond=---- sugar=---- nts=4 GGGG A.DG20,A.DG21,A.DG22,A.DG23 loop#1 type=propeller strands=[#1,#2] nts=2 TT A.DT6,A.DT7 loop#2 type=propeller strands=[#2,#3] nts=2 TT A.DT12,A.DT13 loop#3 type=propeller strands=[#3,#4] nts=2 TT A.DT18,A.DT19 |