DSSR-derived G-quadruplex features in PDB entry 1jrn
- X-ray (2.0 Å)
- Orthorhombic form of oxytricha telomeric DNA at 2.0a
- Haider, S., Parkinson, G.N., Neidle, S.: (2002) "Crystal structure of the potassium form of an Oxytricha nova G-quadruplex." J.Mol.Biol., 320, 189-200.
- The crystal structures of the potassium-containing quadruplex formed from the Oxytricha nova sequence d(GGGGTTTTGGGG) are reported, in two space groups, the orthorhombic P2(1)2(1)2(1) and the trigonal P3(2)21, which diffract to 2.0 A and 1.49 A, respectively. The orthorhombic form contains two independent quadruplexes in the asymmetric unit, and the trigonal form contains one. All three of these quadruplexes adopt an identical fold, with two strands forming an antiparallel diagonal arrangement. This is identical with that observed previously in NMR studies of the native sodium and potassium forms, and a crystallographic analysis of it complexed with an O. nova protein. The present analysis demonstrates that the native structure is the same in solution and in the crystalline state and, moreover, that the nature of the counter-ion does not affect the overall fold of this quadruplex. The analysis corrects an earlier crystallographic study of this quadruplex. The conformation of the tetra-thymine loop is described in detail, which involves the third thymine base folding back to interact with the first thymine base. The water networks in the grooves and loops are described and, in particular, the ability of water molecules to form a continuous spine of hydration in the narrow groove is detailed. Each quadruplex has five potassium ions organised in a linear channel, with square antiprismatic coordination to each ion from oxygen atoms.
- G4 notes
- 8 G-tetrads, 2 G4 helices, 2 G4 stems · (2+2), UDDU
1 glyco-bond=s--s groove=w-n- planarity=0.262 type=other nts=4 GGGG A.DG1001,B.DG2004,A.DG1012,B.DG2009 2 glyco-bond=-ss- groove=w-n- planarity=0.187 type=other nts=4 GGGG A.DG1002,B.DG2003,A.DG1011,B.DG2010 3 glyco-bond=s--s groove=w-n- planarity=0.189 type=other nts=4 GGGG A.DG1003,B.DG2002,A.DG1010,B.DG2011 4 glyco-bond=-ss- groove=w-n- planarity=0.274 type=bowl nts=4 GGGG A.DG1004,B.DG2001,A.DG1009,B.DG2012 5 glyco-bond=s--s groove=w-n- planarity=0.289 type=other nts=4 GGGG C.DG3001,D.DG4004,C.DG3012,D.DG4009 6 glyco-bond=-ss- groove=w-n- planarity=0.246 type=other nts=4 GGGG C.DG3002,D.DG4003,C.DG3011,D.DG4010 7 glyco-bond=s--s groove=w-n- planarity=0.161 type=other nts=4 GGGG C.DG3003,D.DG4002,C.DG3010,D.DG4011 8 glyco-bond=-ss- groove=w-n- planarity=0.261 type=other nts=4 GGGG C.DG3004,D.DG4001,C.DG3009,D.DG4012
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
Helix#2, 4 G-tetrad layers, inter-molecular, with 1 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.