DSSR-enabled G4 identification/annotation: PDB entry 8zw3
Summary information and primary citation
- PDB-id
- 8zw3
- Class
- DNA
- Method
- NMR
- Summary
- Solution structure of tmprss2 promoter g-quadruplex
- Reference
- Tang ZY, Li SR, Bian YT, Chen ZY, Wang YY, Zhang YQ, Li YP, Liu YS, Yang MH, Kong LY, Wang KB: "NMR Solution Structure of the Major TMPRSS2 Promoter G-Quadruplex and Its Complex with Berberine."
- Abstract
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, UUUU, parallel, 4+0, 3(-P-P-P)
Cartoon-block schematics in six views (download the tarball)
List of 3 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.222 type=other O+ nts=4 GGGG X.DG4,X.DG8,X.DG14,X.DG18 2 glyco-bond=---- sugar=---- groove=---- planarity=0.355 type=bowl-2 O+ nts=4 GGGG X.DG5,X.DG9,X.DG15,X.DG19 3 glyco-bond=---- sugar=---- groove=---- planarity=0.428 type=bowl O+ nts=4 GGGG X.DG6,X.DG10,X.DG16,X.DG20
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=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG4,X.DG8,X.DG14,X.DG18 2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG5,X.DG9,X.DG15,X.DG19 3 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG6,X.DG10,X.DG16,X.DG20 step#1 pm(>>,forward) area=14.46 rise=3.40 twist=24.2 step#2 pm(>>,forward) area=12.03 rise=3.42 twist=27.6 strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG4,X.DG5,X.DG6 strand#2 DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG8,X.DG9,X.DG10 strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG14,X.DG15,X.DG16 strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG18,X.DG19,X.DG20 |
| 2 stacking diagrams | |
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG4,X.DG8,X.DG14,X.DG18 |
|
2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG5,X.DG9,X.DG15,X.DG19 |
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, UUUU, parallel, 4+0, 3(-P-P-P)
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG4,X.DG8,X.DG14,X.DG18 2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG5,X.DG9,X.DG15,X.DG19 3 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG X.DG6,X.DG10,X.DG16,X.DG20 step#1 pm(>>,forward) area=14.46 rise=3.40 twist=24.2 step#2 pm(>>,forward) area=12.03 rise=3.42 twist=27.6 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG4,X.DG5,X.DG6 strand#2 U DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG8,X.DG9,X.DG10 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG14,X.DG15,X.DG16 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG X.DG18,X.DG19,X.DG20 loop#1 type=propeller strands=[#1,#2] nts=1 C X.DC7 loop#2 type=propeller strands=[#2,#3] nts=3 CGA X.DC11,X.DG12,X.DA13 loop#3 type=propeller strands=[#3,#4] nts=1 C X.DC17 |