Detailed DSSR results for the G-quadruplex: PDB entry 2mgn
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
- 2mgn
- Class
- DNA
- Method
- NMR
- Summary
- Solution structure of a g-quadruplex bound to the bisquinolinium compound phen-dc3
- Reference
- Chung WJ, Heddi B, Hamon F, Teulade-Fichou MP, Phan AT (2014): "Solution Structure of a G-quadruplex Bound to the Bisquinolinium Compound Phen-DC3." Angew.Chem.Int.Ed.Engl., 53, 999-1002. doi: 10.1002/anie.201308063.
- Abstract
- Phen-DC3 is a highly promising compound that specifically targets G-quadruplexes, with potent biological effects observed in vivo. We used NMR spectroscopy to solve the structure of the complex formed between Phen-DC3 and an intramolecular G-quadruplex derived from the c-myc promoter. Structural information revealed that Phen-DC3 interacts with the quadruplex through extensive π-stacking with guanine bases of the top G-tetrad. On the basis of our structure, modifications are proposed for the development of this compound for selective targeting of a specific G-quadruplex conformation.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, 2(-P-P-P), parallel(4+0), UUUU
Base-block schematics in six views
List of 3 G-tetrads
1 glyco-bond=---- sugar=.--- groove=---- planarity=0.314 type=other nts=4 GGGG A.DG4,A.DG8,A.DG13,A.DG17 2 glyco-bond=---- sugar=.--. groove=---- planarity=0.252 type=other nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18 3 glyco-bond=-s-- sugar=-3-- groove=wn-- planarity=0.493 type=other nts=4 GGGG A.DG6,A.DG24,A.DG15,A.DG19
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=---- sugar=.--- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG13,A.DG17 2 glyco-bond=---- sugar=.--. groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18 3 glyco-bond=-s-- sugar=-3-- groove=wn-- WC-->Major nts=4 GGGG A.DG6,A.DG24,A.DG15,A.DG19 step#1 pm(>>,forward) area=14.42 rise=3.16 twist=29.6 step#2 pm(>>,forward) area=11.55 rise=3.34 twist=30.9 strand#1 DNA glyco-bond=--- sugar=..- nts=3 GGG A.DG4,A.DG5,A.DG6 strand#2 DNA glyco-bond=--s sugar=--3 nts=3 GGG A.DG8,A.DG9,A.DG24 strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG13,A.DG14,A.DG15 strand#4 DNA glyco-bond=--- sugar=-.- nts=3 GGG A.DG17,A.DG18,A.DG19 |
| 2 stacking diagrams | |
 |
1 glyco-bond=---- sugar=.--- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG13,A.DG17 |
 |
2 glyco-bond=---- sugar=.--. groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18 |
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-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)
 |
1 glyco-bond=---- sugar=.--- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG13,A.DG17 2 glyco-bond=---- sugar=.--. groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18 step#1 pm(>>,forward) area=14.42 rise=3.16 twist=29.6 strand#1 U DNA glyco-bond=-- sugar=.. nts=2 GG A.DG4,A.DG5 strand#2 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG8,A.DG9 strand#3 U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG13,A.DG14 strand#4 U DNA glyco-bond=-- sugar=-. nts=2 GG A.DG17,A.DG18 loop#1 type=propeller strands=[#1,#2] nts=2 GT A.DG6,A.DT7 loop#2 type=propeller strands=[#2,#3] nts=3 TGA A.DT10,A.DG11,A.DA12 loop#3 type=propeller strands=[#3,#4] nts=2 GT A.DG15,A.DT16 |
List of 1 non-stem G4-loop (including the two closing Gs)
1 type=diagonal helix=#1 nts=6 GGAAGG A.DG19,A.DG20,A.DA21,A.DA22,A.DG23,A.DG24