Detailed DSSR results for the G-quadruplex: PDB entry 6f4z
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
- 6f4z
- Class
- DNA
- Method
- NMR
- Summary
- 2'f-arag modified quadruplex with flipped g-tract and central tetrad
- Reference
- Dickerhoff J, Weisz K (2018): "Fluorine-Mediated Editing of a G-Quadruplex Folding Pathway." Chembiochem, 19, 927-930. doi: 10.1002/cbic.201800099.
- Abstract
- A (3+1)-hybrid-type G-quadruplex was substituted within its central tetrad by a single 2'-fluoro-modified guanosine. Driven by the anti-favoring nucleoside analogue, a novel quadruplex fold with inversion of a single G-tract and conversion of a propeller loop into a lateral loop emerges. In addition, scalar couplings across hydrogen bonds demonstrate the formation of intra- and inter-residual Fâ â â H8-C8 pseudo-hydrogen bonds within the modified quadruplexes. Alternative folding can be rationalized by the impact of fluorine on intermediate species on the basis of a kinetic partitioning mechanism. Apparently, chemical or other environmental perturbations are able to redirect folding of a quadruplex, possibly modulating its regulatory role in physiological processes.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, 3(+LnD-Lw), basket(2+2), UUDD
Base-block schematics in six views
List of 3 G-tetrads
1 glyco-bond=ss-- sugar=---- groove=-w-n planarity=0.276 type=other nts=4 GGGG A.DG1,A.DG14,A.DG22,A.DG8 2 glyco-bond=--ss sugar=---- groove=-w-n planarity=0.202 type=other nts=4 GgGG A.DG2,A.GFL15,A.DG21,A.DG7 3 glyco-bond=--ss sugar=---- groove=-w-n planarity=0.265 type=other nts=4 GGGG A.DG3,A.DG16,A.DG20,A.DG6
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, INTRA-molecular, with 1 stem
 |
1 glyco-bond=ss-- sugar=---- groove=-w-n Major-->WC nts=4 GGGG A.DG1,A.DG14,A.DG22,A.DG8 2 glyco-bond=--ss sugar=---- groove=-w-n WC-->Major nts=4 GgGG A.DG2,A.GFL15,A.DG21,A.DG7 3 glyco-bond=--ss sugar=---- groove=-w-n WC-->Major nts=4 GGGG A.DG3,A.DG16,A.DG20,A.DG6 step#1 mm(<>,outward) area=15.75 rise=3.57 twist=14.6 step#2 pm(>>,forward) area=11.22 rise=3.44 twist=29.1 strand#1 DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG1,A.DG2,A.DG3 strand#2 DNA glyco-bond=s-- sugar=--- nts=3 GgG A.DG14,A.GFL15,A.DG16 strand#3 DNA glyco-bond=-ss sugar=--- nts=3 GGG A.DG22,A.DG21,A.DG20 strand#4 DNA glyco-bond=-ss sugar=--- nts=3 GGG A.DG8,A.DG7,A.DG6 |
| 2 stacking diagrams | |
 |
1 glyco-bond=ss-- sugar=---- groove=-w-n Major-->WC nts=4 GGGG A.DG1,A.DG14,A.DG22,A.DG8 |
 |
2 glyco-bond=--ss sugar=---- groove=-w-n WC-->Major nts=4 GgGG A.DG2,A.GFL15,A.DG21,A.DG7 |
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, 3 loops, INTRA-molecular, UUDD, anti-parallel, 3(+LnD-Lw), basket(2+2)
 |
1 glyco-bond=ss-- sugar=---- groove=-w-n Major-->WC nts=4 GGGG A.DG1,A.DG14,A.DG22,A.DG8 2 glyco-bond=--ss sugar=---- groove=-w-n WC-->Major nts=4 GgGG A.DG2,A.GFL15,A.DG21,A.DG7 3 glyco-bond=--ss sugar=---- groove=-w-n WC-->Major nts=4 GGGG A.DG3,A.DG16,A.DG20,A.DG6 step#1 mm(<>,outward) area=15.75 rise=3.57 twist=14.6 step#2 pm(>>,forward) area=11.22 rise=3.44 twist=29.1 strand#1 U DNA glyco-bond=s-- sugar=--- nts=3 GGG A.DG1,A.DG2,A.DG3 strand#2 U DNA glyco-bond=s-- sugar=--- nts=3 GgG A.DG14,A.GFL15,A.DG16 strand#3 D DNA glyco-bond=-ss sugar=--- nts=3 GGG A.DG22,A.DG21,A.DG20 strand#4 D DNA glyco-bond=-ss sugar=--- nts=3 GGG A.DG8,A.DG7,A.DG6 loop#1 type=lateral strands=[#1,#4] nts=2 AT A.DA4,A.DT5 loop#2 type=diagonal strands=[#4,#2] nts=5 ACACA A.DA9,A.DC10,A.DA11,A.DC12,A.DA13 loop#3 type=lateral strands=[#2,#3] nts=3 GAC A.DG17,A.DA18,A.DC19 |