Detailed DSSR results for the G-quadruplex: PDB entry 7zur
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
- 7zur
- Class
- DNA
- Method
- X-ray (1.6 Å)
- Summary
- Four carbons pendant pyridine derivative of the natural alkaloid berberine as human telomeric g-quadruplex binder
- Reference
- Bazzicalupi C, Bonardi A, Biver T, Ferraroni M, Papi F, Savastano M, Lombardi P, Gratteri P (2022): "Probing the Efficiency of 13-Pyridylalkyl Berberine Derivatives to Human Telomeric G-Quadruplexes Binding: Spectroscopic, Solid State and In Silico Analysis." Int J Mol Sci, 23. doi: 10.3390/ijms232214061.
- Abstract
- The interaction between the series of berberine derivatives
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, parallel(4+0), UUUU
Base-block schematics in six views
List of 3 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.128 type=planar nts=4 GGGG 1:A.DG3,1:A.DG9,2:A.DG3,2:A.DG9 2 glyco-bond=---- sugar=---- groove=---- planarity=0.149 type=planar nts=4 GGGG 1:A.DG4,1:A.DG10,2:A.DG4,2:A.DG10 3 glyco-bond=---- sugar=---- groove=---- planarity=0.300 type=bowl nts=4 GGGG 1:A.DG5,1:A.DG11,2:A.DG5,2:A.DG11
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, 3 G-tetrad layers, inter-molecular, with 1 stem
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG3,1:A.DG9,2:A.DG3,2:A.DG9 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG4,1:A.DG10,2:A.DG4,2:A.DG10 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG5,1:A.DG11,2:A.DG5,2:A.DG11 step#1 pm(>>,forward) area=10.30 rise=3.36 twist=29.6 step#2 pm(>>,forward) area=13.31 rise=3.38 twist=26.1 strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG 1:A.DG3,1:A.DG4,1:A.DG5 strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG 1:A.DG9,1:A.DG10,1:A.DG11 strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG 2:A.DG3,2:A.DG4,2:A.DG5 strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG 2:A.DG9,2:A.DG10,2:A.DG11 |
| 2 stacking diagrams | |
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG3,1:A.DG9,2:A.DG3,2:A.DG9 |
 |
2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG4,1:A.DG10,2:A.DG4,2:A.DG10 |
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, 3 G-tetrad layers, 2 loops, inter-molecular, UUUU, parallel, parallel(4+0)
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG3,1:A.DG9,2:A.DG3,2:A.DG9 2 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG4,1:A.DG10,2:A.DG4,2:A.DG10 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG 1:A.DG5,1:A.DG11,2:A.DG5,2:A.DG11 step#1 pm(>>,forward) area=10.30 rise=3.36 twist=29.6 step#2 pm(>>,forward) area=13.31 rise=3.38 twist=26.1 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG 1:A.DG3,1:A.DG4,1:A.DG5 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG 1:A.DG9,1:A.DG10,1:A.DG11 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG 2:A.DG3,2:A.DG4,2:A.DG5 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG 2:A.DG9,2:A.DG10,2:A.DG11 loop#1 type=propeller strands=[#1,#2] nts=3 TTA 1:A.DT6,1:A.DT7,1:A.DA8 loop#2 type=propeller strands=[#3,#4] nts=3 TTA 2:A.DT6,2:A.DT7,2:A.DA8 |