Sodium in PDB 5ny8: The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Aminoguanidine

The structure of The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Aminoguanidine, PDB code: 5ny8 was solved by L.Huang, J.Wang, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.96 / 2.04
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	83.390, 83.390, 66.330, 90.00, 90.00, 120.00
R / Rfree (%)	18.9 / 22.5

The structure of The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Aminoguanidine also contains other interesting chemical elements:

Magnesium	(Mg)	3 atoms
Bromine	(Br)	2 atoms

The binding sites of Sodium atom in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Aminoguanidine (pdb code 5ny8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Aminoguanidine, PDB code: 5ny8:

Sodium binding site 1 out of 1 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Aminoguanidine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Aminoguanidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:87.6 occ:1.00 O6 A:G12 2.8 50.0 1.0 N7 A:G12 3.0 51.0 1.0 N1 A:U11 3.2 47.1 1.0 O4' A:U11 3.2 48.4 1.0 C6 A:U11 3.3 45.5 1.0 C2 A:U11 3.5 53.7 1.0 C6 A:G12 3.5 51.5 1.0 C1' A:U11 3.6 50.3 1.0 C5 A:G12 3.6 45.7 1.0 H6 A:U11 3.6 54.6 1.0 H41 A:C13 3.7 61.1 1.0 H1' A:U11 3.7 60.4 1.0 C5 A:U11 3.7 48.9 1.0 N3 A:U11 3.8 60.8 1.0 O2 A:U11 4.0 50.7 1.0 C4 A:U11 4.0 49.4 1.0 N4 A:C13 4.1 50.9 1.0 H42 A:C41 4.2 54.1 1.0 H5 A:U11 4.2 58.6 1.0 C8 A:G12 4.2 53.1 1.0 H42 A:C13 4.2 61.1 1.0 H3 A:U11 4.3 72.9 1.0 H8 A:G12 4.6 63.7 1.0 C4' A:U11 4.6 48.8 1.0 O6 A:G40 4.7 41.1 1.0 H5' A:U11 4.8 64.0 1.0 H4' A:U11 4.8 58.6 1.0 N1 A:G12 4.9 44.9 1.0 O4 A:U11 4.9 46.2 1.0 OP1 A:U11 4.9 60.5 1.0 N4 A:C41 4.9 45.1 1.0 C4 A:G12 4.9 49.6 1.0

L.Huang, J.Wang, T.J.Wilson, D.M.J.Lilley. Structure of the Guanidine III Riboswitch. Cell Chem Biol V. 24 1407 2017.
ISSN: ESSN 2451-9456
PubMed: 28988949
DOI: 10.1016/J.CHEMBIOL.2017.08.021