Sodium in PDB 7k16: Tamana Bat Virus XRRNA1

The structure of Tamana Bat Virus XRRNA1, PDB code: 7k16 was solved by R.A.Jones, J.S.Kieft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.55 / 2.10
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	79.100, 79.100, 40.690, 90.00, 90.00, 120.00
R / Rfree (%)	18.7 / 24.6

The structure of Tamana Bat Virus XRRNA1 also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Sodium atom in the Tamana Bat Virus XRRNA1 (pdb code 7k16). 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 Tamana Bat Virus XRRNA1, PDB code: 7k16:

Sodium binding site 1 out of 1 in the Tamana Bat Virus XRRNA1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Tamana Bat Virus XRRNA1 within 5.0Å range: probe atom residue distance (Å) B Occ P:Na106 b:54.5 occ:1.00 O P:HOH210 2.1 55.9 1.0 O P:HOH222 2.4 46.0 1.0 O P:HOH253 2.4 61.5 1.0 O P:HOH249 2.4 61.8 1.0 O P:HOH201 2.4 48.6 1.0 O P:HOH202 2.6 35.7 1.0 O2P P:5GP1 3.7 56.0 1.0 OP2 P:G2 3.7 40.6 1.0 N7 P:G2 3.9 33.6 1.0 OP1 P:C36 4.0 42.0 1.0 O P:HOH225 4.0 41.9 1.0 OP2 P:C36 4.0 40.0 1.0 H8 P:G2 4.1 39.2 1.0 C8 P:G2 4.3 32.7 1.0 O P:HOH205 4.3 38.9 1.0 H3' P:5GP1 4.4 53.0 1.0 P P:C36 4.5 38.3 1.0 O3P P:5GP1 4.6 59.3 1.0 H5 P:C3 4.6 40.1 1.0 P P:5GP1 4.6 59.6 1.0 O P:HOH246 4.6 33.6 1.0 OP1 P:A35 4.8 39.2 1.0 H5'2 P:5GP1 4.8 61.0 1.0 O5' P:5GP1 4.9 55.8 1.0 C5 P:G2 5.0 32.8 1.0

R.A.Jones, A.L.Steckelberg, Q.Vicens, M.J.Szucs, B.M.Akiyama, J.S.Kieft. Different Tertiary Interactions Create the Same Important 3-D Features in A Distinct Flavivirus Xrrna. Rna 2020.
ISSN: ESSN 1469-9001
PubMed: 33004436
DOI: 10.1261/RNA.077065.120