DSSR-enabled G4 identification/annotation: PDB entry 5ov2
Summary information and primary citation
- PDB-id
- 5ov2
- Class
- DNA
- Method
- NMR
- Summary
- 2'f-ana-g modified quadruplex with a flipped tetrad
- Reference
- Dickerhoff J, Weisz K (2017): "Nonconventional C-HF Hydrogen Bonds Support a Tetrad Flip in Modified G-Quadruplexes." J Phys Chem Lett, 8, 5148-5152. doi: 10.1021/acs.jpclett.7b02428.
- Abstract
- A G-quadruplex adopting a (3 + 1)-hybrid structure was substituted at its 5'-tetrad by 2'-deoxy-2'-fluoro-arabinoguanosine (<sub>F</sub>araG) analogs. Incorporation of anti-favoring <sub>F</sub>araG at syn-positions of the 5'-outer tetrad induced a reversal of the tetrad polarity without noticeably compromising the quadruplex stability. This conformational change is shown to be promoted by nonconventional C-H···F hydrogen bonds acting within the anti-<sub>F</sub>araG residues.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, UUUD, hybrid2, 3+1, 3(-PD+Lw)
Cartoon-block schematics in six views (download the tarball)
List of 3 G-tetrads
1 glyco-bond=---s sugar=---- groove=--wn planarity=0.372 type=other N+ nts=4 gggG X.GFL1,X.GFL6,X.GFL20,X.DG16 2 glyco-bond=---s sugar=---- groove=--wn planarity=0.393 type=other N+ nts=4 GGGG X.DG2,X.DG7,X.DG21,X.DG15 3 glyco-bond=---s sugar=---- groove=--wn planarity=0.279 type=saddle N+ nts=4 GGGG X.DG3,X.DG8,X.DG22,X.DG14
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-tetrads, INTRA-molecular, with 1 stem
|
1 glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 gggG X.GFL1,X.GFL6,X.GFL20,X.DG16 2 glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGG X.DG2,X.DG7,X.DG21,X.DG15 3 glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGG X.DG3,X.DG8,X.DG22,X.DG14 step#1 pm(>>,forward) area=15.84 rise=3.46 twist=24.0 step#2 pm(>>,forward) area=13.68 rise=3.47 twist=27.3 strand#1 DNA glyco-bond=--- sugar=--- nts=3 gGG X.GFL1,X.DG2,X.DG3 strand#2 DNA glyco-bond=--- sugar=--- nts=3 gGG X.GFL6,X.DG7,X.DG8 strand#3 DNA glyco-bond=--- sugar=--- nts=3 gGG X.GFL20,X.DG21,X.DG22 strand#4 DNA glyco-bond=sss sugar=--- nts=3 GGG X.DG16,X.DG15,X.DG14 |
| 2 stacking diagrams | |
|
1 glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 gggG X.GFL1,X.GFL6,X.GFL20,X.DG16 |
|
2 glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGG X.DG2,X.DG7,X.DG21,X.DG15 |
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-tetrads, 3 loops, INTRA-molecular, UUUD, hybrid2, 3+1, 3(-PD+Lw)
|
1 glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 gggG X.GFL1,X.GFL6,X.GFL20,X.DG16 2 glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGG X.DG2,X.DG7,X.DG21,X.DG15 3 glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGG X.DG3,X.DG8,X.DG22,X.DG14 step#1 pm(>>,forward) area=15.84 rise=3.46 twist=24.0 step#2 pm(>>,forward) area=13.68 rise=3.47 twist=27.3 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 gGG X.GFL1,X.DG2,X.DG3 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 gGG X.GFL6,X.DG7,X.DG8 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 gGG X.GFL20,X.DG21,X.DG22 strand#4 D DNA glyco-bond=sss sugar=--- nts=3 GGG X.DG16,X.DG15,X.DG14 loop#1 type=propeller strands=[#1,#2] nts=2 AT X.DA4,X.DT5 loop#2 type=diagonal strands=[#2,#4] nts=5 ACACA X.DA9,X.DC10,X.DA11,X.DC12,X.DA13 loop#3 type=lateral strands=[#4,#3] nts=3 GAC X.DG17,X.DA18,X.DC19 |