Sodium in PDB 8f4y: Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10

The structure of Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10, PDB code: 8f4y 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)	29.62 / 2.13
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	171.04, 171.04, 52.029, 90, 90, 120
R / Rfree (%)	15.7 / 18

The structure of Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10 also contains other interesting chemical elements:

Chlorine	(Cl)	8 atoms
Fluorine	(F)	12 atoms
Zinc	(Zn)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10 (pdb code 8f4y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10, PDB code: 8f4y:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10


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 Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na7101 b:53.1 occ:1.00 O A:HOH7408 2.4 60.4 1.0 O A:LEU6887 2.4 39.4 1.0 O A:GLN6885 2.4 37.7 1.0 O B:HOH4529 2.4 59.8 1.0 O A:ARG6884 2.4 39.9 1.0 C A:GLN6885 3.0 37.5 1.0 C A:ARG6884 3.5 37.9 1.0 O A:HOH7318 3.5 41.2 1.0 CA A:GLN6885 3.5 40.2 1.0 C A:LEU6887 3.6 36.8 1.0 N A:LEU6887 3.9 36.2 1.0 N A:TRP6886 3.9 36.4 1.0 N A:GLN6885 3.9 39.2 1.0 C A:TRP6886 4.1 35.4 1.0 OG1 B:THR4311 4.2 58.8 1.0 CA A:LEU6887 4.3 38.0 1.0 N A:THR6889 4.4 45.1 1.0 OG1 A:THR6889 4.5 52.6 1.0 O A:TRP6886 4.5 34.9 1.0 C A:PRO6888 4.5 41.2 1.0 CA A:TRP6886 4.5 37.0 1.0 N A:PRO6888 4.6 37.0 1.0 CB B:THR4311 4.7 51.2 1.0 O B:VAL4310 4.7 47.3 1.0 CA A:PRO6888 4.7 40.4 1.0 CA A:ARG6884 4.8 38.1 1.0 O A:PRO6888 4.9 40.4 1.0 CA A:THR6889 4.9 48.8 1.0 CB A:GLN6885 4.9 39.9 1.0 O A:HOH7220 5.0 44.6 1.0 O A:HOH7433 5.0 51.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Sars-Cov-2 2'-O-Methyltransferase in Complex with Compound 5A Covalently Bound to NSP16 and NSP10 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na4403 b:86.6 occ:1.00 O B:THR4364 2.4 86.2 1.0 O B:ASN4367 2.4 98.0 1.0 O B:LEU4365 2.4 102.7 1.0 C B:LEU4365 3.2 95.3 1.0 C B:THR4364 3.5 79.4 1.0 CA B:LEU4365 3.6 90.7 1.0 C B:ASN4367 3.6 92.4 1.0 N B:LEU4365 4.0 82.2 1.0 N B:ASN4367 4.2 96.3 1.0 CG2 B:THR4368 4.3 94.0 1.0 N B:LYS4366 4.3 96.9 1.0 C B:LYS4366 4.4 101.6 1.0 N B:THR4368 4.5 90.8 1.0 CA B:ASN4367 4.5 96.4 1.0 CA B:THR4368 4.6 89.9 1.0 CA B:THR4364 4.8 75.6 1.0 O B:LYS4366 4.9 108.5 1.0 CA B:LYS4366 4.9 101.2 1.0 CB B:LEU4365 5.0 89.3 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