DSSR-enabled G4 identification/annotation: PDB entry 9o70
Summary information and primary citation
- PDB-id
- 9o70
- Class
- DNA
- Method
- X-ray (2.02 Å)
- Summary
- Motif1-motif2, two domain left-handed parallel g-quadruplex
- Reference
- Xing ER, Yatsunyk LA: "Structure of a left-right-handed G-quadruplex from the promoter of the NSD1 gene."
- Abstract
- G4 notes
- 4 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0, 2(+P+P+P), negative twist
Cartoon-block schematics in six views (download the tarball)
List of 4 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.063 type=planar O+ nts=4 GGGG 1:A.DG1,1:A.DG4,1:A.DG7,1:A.DG10 2 glyco-bond=---- sugar=---- groove=---- planarity=0.140 type=planar O+ nts=4 GGGG 1:A.DG3,1:A.DG6,1:A.DG9,1:A.DG12 3 glyco-bond=---- sugar=---- groove=---- planarity=0.160 type=other O+ nts=4 GGGG 1:A.DG15,1:A.DG18,1:A.DG21,1:A.DG24 4 glyco-bond=---- sugar=---. groove=---- planarity=0.089 type=planar O+ nts=4 GGGG 1:A.DG16,1:A.DG19,1:A.DG22,1:A.DG26
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-tetrads, INTRA-molecular, with 1 stem
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1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG3,1:A.DG6,1:A.DG9,1:A.DG12 2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG4,1:A.DG7,1:A.DG10,1:A.DG1 3 glyco-bond=---- sugar=---. groove=---- Major-->WC O+ nts=4 GGGG 1:A.DG22,1:A.DG19,1:A.DG16,1:A.DG26 4 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG 1:A.DG21,1:A.DG18,1:A.DG15,1:A.DG24 step#1 mp(<<,backward) area=11.36 rise=3.25 twist=-26.9 step#2 mm(<>,outward) area=29.38 rise=3.27 twist=-10.8 step#3 pm(>>,forward) area=12.74 rise=3.31 twist=-26.2 strand#1 DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:A.DG3,1:A.DG4,1:A.DG22,1:A.DG21 strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:A.DG6,1:A.DG7,1:A.DG19,1:A.DG18 strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:A.DG9,1:A.DG10,1:A.DG16,1:A.DG15 strand#4 DNA glyco-bond=---- sugar=--.- nts=4 GGGG 1:A.DG12,1:A.DG1,1:A.DG26,1:A.DG24 |
| 3 stacking diagrams | |
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG3,1:A.DG6,1:A.DG9,1:A.DG12 |
|
2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG4,1:A.DG7,1:A.DG10,1:A.DG1 |
|
3 glyco-bond=---- sugar=---. groove=---- Major-->WC O+ nts=4 GGGG 1:A.DG22,1:A.DG19,1:A.DG16,1:A.DG26 |
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, 2 G-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, WARNING, 4+0, 2(+P+P+P), WARNING
|
1 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG 1:A.DG15,1:A.DG24,1:A.DG21,1:A.DG18 2 glyco-bond=---- sugar=-.-- groove=---- Major-->WC O+ nts=4 GGGG 1:A.DG16,1:A.DG26,1:A.DG22,1:A.DG19 step#1 mp(<<,backward) area=12.74 rise=3.31 twist=-26.2 strand#1 U DNA glyco-bond=-- sugar=-- nts=2 GG 1:A.DG15,1:A.DG16 strand#2* U DNA glyco-bond=-- sugar=-. nts=2 GG 1:A.DG24,1:A.DG26 bulged-nts=1 T 1:A.DT25 strand#3 U DNA glyco-bond=-- sugar=-- nts=2 GG 1:A.DG21,1:A.DG22 strand#4 U DNA glyco-bond=-- sugar=-- nts=2 GG 1:A.DG18,1:A.DG19 loop#1 type=propeller strands=[#1,#4] nts=1 T 1:A.DT17 loop#2 type=propeller strands=[#4,#3] nts=1 T 1:A.DT20 loop#3 type=propeller strands=[#3,#2] nts=1 T 1:A.DT23 |
List of 2 non-stem G4-loops (including the two closing Gs)
1 type=V-shaped helix=#1 nts=4 GTGG 1:A.DG1,1:A.DT2,1:A.DG3,1:A.DG4 2* type=V-shaped helix=#1 nts=4 GGTG 1:A.DG9,1:A.DG10,1:A.DT11,1:A.DG12