DSSR-enabled G4 identification/annotation: PDB entry 9mxo
Summary information and primary citation
- PDB-id
- 9mxo
- Class
- DNA
- Method
- X-ray (1.68 Å)
- Summary
- Motif2-motif1 left-handed parallel g-quadruplex in h3 spacegroup
- Reference
- Hendrickson AD, Xing ER, Yatsunyk LA: "Preservation of left-handed fold and interaction with N-methylmesoporphyrin IX by two-block sequences with left-hand folding potential."
- 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=0.223 type=other O+ nts=4 GGGG 1:A.DG1,1:A.DG4,1:A.DG7,1:A.DG10 2 glyco-bond=---- sugar=---- groove=---- planarity=0.075 type=planar O+ nts=4 GGGG 1:A.DG2,1:A.DG5,1:A.DG8,1:A.DG12 3 glyco-bond=---- sugar=---- groove=---- planarity=0.118 type=planar O+ nts=4 GGGG 1:A.DG15,1:A.DG18,1:A.DG21,1:A.DG24 4 glyco-bond=---- sugar=---- groove=---- planarity=0.186 type=other O+ nts=4 GGGG 1:A.DG17,1:A.DG20,1:A.DG23,1: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.DG1,1:A.DG4,1:A.DG7,1:A.DG10 2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG2,1:A.DG5,1:A.DG8,1:A.DG12 3 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG 1:A.DG24,1:A.DG21,1:A.DG18,1:A.DG15 4 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG 1:A.DG23,1:A.DG20,1:A.DG17,1:A.DG26 step#1 mp(<<,backward) area=11.84 rise=3.30 twist=-26.9 step#2 mm(<>,outward) area=29.75 rise=3.32 twist=-11.5 step#3 pm(>>,forward) area=11.75 rise=3.29 twist=-25.9 strand#1 DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:A.DG1,1:A.DG2,1:A.DG24,1:A.DG23 strand#2 DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:A.DG4,1:A.DG5,1:A.DG21,1:A.DG20 strand#3 DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:A.DG7,1:A.DG8,1:A.DG18,1:A.DG17 strand#4 DNA glyco-bond=---- sugar=---- nts=4 GGGG 1:A.DG10,1:A.DG12,1:A.DG15,1:A.DG26 |
| 3 stacking diagrams | |
|
1 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG1,1:A.DG4,1:A.DG7,1:A.DG10 |
|
2 glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG 1:A.DG2,1:A.DG5,1:A.DG8,1:A.DG12 |
|
3 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG 1:A.DG24,1:A.DG21,1:A.DG18,1:A.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, 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.DG1,1:A.DG10,1:A.DG7,1:A.DG4 2 glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG 1:A.DG2,1:A.DG12,1:A.DG8,1:A.DG5 step#1 mp(<<,backward) area=11.84 rise=3.30 twist=-26.9 strand#1 U DNA glyco-bond=-- sugar=-- nts=2 GG 1:A.DG1,1:A.DG2 strand#2* U DNA glyco-bond=-- sugar=-- nts=2 GG 1:A.DG10,1:A.DG12 bulged-nts=1 T 1:A.DT11 strand#3 U DNA glyco-bond=-- sugar=-- nts=2 GG 1:A.DG7,1:A.DG8 strand#4 U DNA glyco-bond=-- sugar=-- nts=2 GG 1:A.DG4,1:A.DG5 loop#1 type=propeller strands=[#1,#4] nts=1 T 1:A.DT3 loop#2 type=propeller strands=[#4,#3] nts=1 T 1:A.DT6 loop#3 type=propeller strands=[#3,#2] nts=1 T 1:A.DT9 |
List of 2 non-stem G4-loops (including the two closing Gs)
1 type=V-shaped helix=#1 nts=4 GTGG 1:A.DG15,1:A.DT16,1:A.DG17,1:A.DG18 2* type=V-shaped helix=#1 nts=4 GGTG 1:A.DG23,1:A.DG24,1:A.DT25,1:A.DG26