Sodium in PDB 5ndi: The Structure of the E.Coli Guanidine II Riboswitch P1 Stem-Loop

The structure of The Structure of the E.Coli Guanidine II Riboswitch P1 Stem-Loop, PDB code: 5ndi 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)	40.34 / 2.57
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.476, 48.185, 153.066, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 23.8

The structure of The Structure of the E.Coli Guanidine II Riboswitch P1 Stem-Loop also contains other interesting chemical elements:

Bromine

(Br)

4 atoms

The binding sites of Sodium atom in the The Structure of the E.Coli Guanidine II Riboswitch P1 Stem-Loop (pdb code 5ndi). 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 E.Coli Guanidine II Riboswitch P1 Stem-Loop, PDB code: 5ndi:

Sodium binding site 1 out of 1 in the The Structure of the E.Coli Guanidine II Riboswitch P1 Stem-Loop


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 E.Coli Guanidine II Riboswitch P1 Stem-Loop within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:55.6 occ:1.00 H22 B:G8 2.7 73.8 1.0 H62 A:A9 3.2 84.2 1.0 N2 B:G8 3.5 61.5 1.0 H1' B:C14 3.9 80.1 1.0 N3 B:G8 3.9 61.7 1.0 N6 A:A9 4.0 70.2 1.0 H21 B:G8 4.1 73.8 1.0 N7 A:A9 4.1 75.2 1.0 C2 B:G8 4.2 59.1 1.0 O2' B:G8 4.3 65.3 1.0 H61 A:A9 4.4 84.2 1.0 O2 B:C14 4.5 64.7 1.0 H1' B:G8 4.5 75.4 1.0 HO2' B:G8 4.6 78.4 1.0 C6 A:A9 4.8 69.8 1.0 H2' B:G8 4.8 77.7 1.0 C5 A:A9 4.8 70.2 1.0 C1' B:C14 4.8 66.7 1.0 O2' B:C14 4.9 71.9 1.0 C2' B:G8 5.0 64.8 1.0

L.Huang, J.Wang, D.M.J.Lilley. The Structure of the Guanidine-II Riboswitch. Cell Chem Biol V. 24 695 2017.
ISSN: ESSN 2451-9456
PubMed: 28529131
DOI: 10.1016/J.CHEMBIOL.2017.05.014