Detailed DSSR results for the G-quadruplex: PDB entry 2akg
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
- 2akg
- Class
- DNA
- Method
- NMR
- Summary
- Thallium form of the g-quadruplex from oxytricha nova, d(g4t4g4)2
- Reference
- Gill ML, Strobel SA, Loria JP (2005): "(205)Tl NMR methods for the characterization of monovalent cation binding to nucleic acids." J.Am.Chem.Soc., 127, 16723-16732. doi: 10.1021/ja055358f.
- Abstract
- Monovalent cations play an important role in many biological functions. The guanine rich sequence, d(G4T4G4), requires monovalent cations for formation of the G-quadruplex, d(G4T4G4)2. This requirement can be satisfied by thallium (Tl+), a potassium (K+) surrogate. To verify that the structure of d(G4T4G4)2 in the presence of Tl+ is similar to the K+-form of the G-quadruplex, the solution structure of the Tl+-form of d(G4T4G4)2 was determined. The 10 lowest energy structures have an all atom RMSD of 0.76 +/- 0.16 A. Comparison of this structure to the identical G-quadruplex formed in the presence of K+ validates the isomorphous nature of Tl+ and K+. Using a 1H-205Tl spin-echo difference experiment we show that, in the Tl+-form of d(G4T4G4)2, small scalar couplings (<1 Hz) exist between 205Tl and protons in the G-quadruplex. These data comprise the first 1H-205Tl scalar couplings observed in a biological system and have the potential to provide important constraints for structure determination. These experiments can be applied to any system in which the substituted Tl+ cations are in slow exchange with the bulk ions in solution.
- G4 notes
- 4 G-tetrads, 1 G4 helix, 1 G4 stem, (2+2), UDDU
Base-block schematics in six views
List of 4 G-tetrads
1 glyco-bond=s--s sugar=.-.. groove=w-n- planarity=0.339 type=other nts=4 GGGG A.DG1,B.DG16,A.DG12,B.DG21 2 glyco-bond=-ss- sugar=-.-- groove=w-n- planarity=0.098 type=planar nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22 3 glyco-bond=s--s sugar=.--- groove=w-n- planarity=0.094 type=planar nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23 4 glyco-bond=-ss- sugar=-... groove=w-n- planarity=0.335 type=other nts=4 GGGG A.DG4,B.DG13,A.DG9,B.DG24
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-tetrad layers, inter-molecular, with 1 stem
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1 glyco-bond=s--s sugar=.-.. groove=w-n- Major-->WC nts=4 GGGG A.DG1,B.DG16,A.DG12,B.DG21 2 glyco-bond=-ss- sugar=-.-- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22 3 glyco-bond=s--s sugar=.--- groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23 4 glyco-bond=-ss- sugar=-... groove=w-n- WC-->Major nts=4 GGGG A.DG4,B.DG13,A.DG9,B.DG24 step#1 mm(<>,outward) area=14.15 rise=3.30 twist=17.5 step#2 pp(><,inward) area=22.03 rise=2.80 twist=40.6 step#3 mm(<>,outward) area=14.15 rise=3.30 twist=17.5 strand#1 DNA glyco-bond=s-s- sugar=.-.- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4 strand#2 DNA glyco-bond=-s-s sugar=-.-. nts=4 GGGG B.DG16,B.DG15,B.DG14,B.DG13 strand#3 DNA glyco-bond=-s-s sugar=.--. nts=4 GGGG A.DG12,A.DG11,A.DG10,A.DG9 strand#4 DNA glyco-bond=s-s- sugar=.--. nts=4 GGGG B.DG21,B.DG22,B.DG23,B.DG24 |
| 3 stacking diagrams | |
 |
1 glyco-bond=s--s sugar=.-.. groove=w-n- Major-->WC nts=4 GGGG A.DG1,B.DG16,A.DG12,B.DG21 |
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2 glyco-bond=-ss- sugar=-.-- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22 |
 |
3 glyco-bond=s--s sugar=.--- groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23 |
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, 4 G-tetrad layers, 2 loops, inter-molecular, UDDU, anti-parallel, (2+2)
 |
1 glyco-bond=s--s sugar=.-.. groove=w-n- Major-->WC nts=4 GGGG A.DG1,B.DG16,A.DG12,B.DG21 2 glyco-bond=-ss- sugar=-.-- groove=w-n- WC-->Major nts=4 GGGG A.DG2,B.DG15,A.DG11,B.DG22 3 glyco-bond=s--s sugar=.--- groove=w-n- Major-->WC nts=4 GGGG A.DG3,B.DG14,A.DG10,B.DG23 4 glyco-bond=-ss- sugar=-... groove=w-n- WC-->Major nts=4 GGGG A.DG4,B.DG13,A.DG9,B.DG24 step#1 mm(<>,outward) area=14.15 rise=3.30 twist=17.5 step#2 pp(><,inward) area=22.03 rise=2.80 twist=40.6 step#3 mm(<>,outward) area=14.15 rise=3.30 twist=17.5 strand#1 U DNA glyco-bond=s-s- sugar=.-.- nts=4 GGGG A.DG1,A.DG2,A.DG3,A.DG4 strand#2 D DNA glyco-bond=-s-s sugar=-.-. nts=4 GGGG B.DG16,B.DG15,B.DG14,B.DG13 strand#3 D DNA glyco-bond=-s-s sugar=.--. nts=4 GGGG A.DG12,A.DG11,A.DG10,A.DG9 strand#4 U DNA glyco-bond=s-s- sugar=.--. nts=4 GGGG B.DG21,B.DG22,B.DG23,B.DG24 loop#1 type=diagonal strands=[#1,#3] nts=4 TTTT A.DT5,A.DT6,A.DT7,A.DT8 loop#2 type=diagonal strands=[#2,#4] nts=4 TTTT B.DT17,B.DT18,B.DT19,B.DT20 |