Sodium in PDB 8f4s: Crystal Structure of the Sars-Cov-2 2'-O-Methyltransferase with Compound 5A Bound to the Cryptic Pocket of NSP16

The structure of Crystal Structure of the Sars-Cov-2 2'-O-Methyltransferase with Compound 5A Bound to the Cryptic Pocket of NSP16, PDB code: 8f4s was solved by G.Minasov, L.Shuvalova, J.S.Brunzelle, M.Rosas-Lemus, O.Kiryukhina, K.J.F.Satchell, Center For Structural Biology Of Infectious Diseases(Csbid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.59 / 2.15
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	170.847, 170.847, 51.881, 90, 90, 120
R / Rfree (%)	16.6 / 19.1

The structure of Crystal Structure of the Sars-Cov-2 2'-O-Methyltransferase with Compound 5A Bound to the Cryptic Pocket of NSP16 also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Zinc	(Zn)	2 atoms
Fluorine	(F)	3 atoms

The binding sites of Sodium atom in the Crystal Structure of the Sars-Cov-2 2'-O-Methyltransferase with Compound 5A Bound to the Cryptic Pocket of NSP16 (pdb code 8f4s). 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 Crystal Structure of the Sars-Cov-2 2'-O-Methyltransferase with Compound 5A Bound to the Cryptic Pocket of NSP16, PDB code: 8f4s:

Sodium binding site 1 out of 1 in the Crystal Structure of the Sars-Cov-2 2'-O-Methyltransferase with Compound 5A Bound to the Cryptic Pocket of NSP16


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Sars-Cov-2 2'-O-Methyltransferase with Compound 5A Bound to the Cryptic Pocket of NSP16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na7101 b:58.8 occ:1.00 O A:HOH7351 2.4 67.8 1.0 O A:LEU6887 2.4 43.7 1.0 O A:HOH7322 2.4 65.7 1.0 O A:GLN6885 2.4 43.0 1.0 O A:ARG6884 2.4 46.0 1.0 C A:GLN6885 3.0 42.2 1.0 CA A:GLN6885 3.5 41.8 1.0 C A:ARG6884 3.5 43.2 1.0 C A:LEU6887 3.6 38.4 1.0 O A:HOH7306 3.6 45.9 1.0 N A:TRP6886 3.9 40.7 1.0 N A:LEU6887 3.9 38.5 1.0 N A:GLN6885 3.9 42.5 1.0 C A:TRP6886 4.0 38.0 1.0 OG1 B:THR4311 4.2 69.4 1.0 CA A:LEU6887 4.3 40.3 1.0 O A:TRP6886 4.4 39.2 1.0 CA A:TRP6886 4.4 39.3 1.0 N A:THR6889 4.5 51.0 1.0 C A:PRO6888 4.5 47.1 1.0 OG1 A:THR6889 4.6 60.8 1.0 N A:PRO6888 4.6 41.9 1.0 CB B:THR4311 4.7 59.8 1.0 CA A:PRO6888 4.7 46.0 1.0 O A:HOH7259 4.8 51.0 1.0 O B:VAL4310 4.8 53.1 1.0 CA A:ARG6884 4.8 41.9 1.0 O A:PRO6888 4.9 46.5 1.0 CB A:GLN6885 4.9 41.1 1.0

N.L.Inniss, J.Kozic, F.Li, M.Rosas-Lemus, G.Minasov, J.Rybacek, Y.Zhu, R.Pohl, L.Shuvalova, L.Rulisek, J.S.Brunzelle, L.Bednarova, M.Stefek, J.M.Kormanik, E.Andris, J.Sebestik, A.S.M.Li, P.J.Brown, U.Schmitz, K.Saikatendu, E.Chang, R.Nencka, M.Vedadi, K.J.F.Satchell. Discovery of A Druggable, Cryptic Pocket in Sars-Cov-2 NSP16 Using Allosteric Inhibitors. Acs Infect Dis. 2023.
ISSN: ESSN 2373-8227
PubMed: 37728236
DOI: 10.1021/ACSINFECDIS.3C00203