Zinc 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
Sodium	(Na)	1 atom
Fluorine	(F)	3 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where 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:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 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 Zinc with other atoms in the Zn 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 B:Zn4401 b:73.8 occ:1.00 NE2 B:HIS4336 2.1 104.7 1.0 SG B:CYS4327 2.3 69.1 1.0 SG B:CYS4343 2.3 75.1 1.0 SG B:CYS4330 2.3 76.7 1.0 CD2 B:HIS4336 3.1 91.6 1.0 CE1 B:HIS4336 3.2 89.9 1.0 CB B:CYS4327 3.2 70.0 1.0 CB B:CYS4343 3.4 92.9 1.0 CB B:CYS4330 3.5 71.3 1.0 N B:CYS4330 3.6 72.5 1.0 CA B:CYS4330 4.0 67.2 1.0 ND1 B:HIS4336 4.3 100.4 1.0 CG B:HIS4336 4.3 104.8 1.0 CB B:TYR4329 4.4 76.4 1.0 C B:TYR4329 4.5 69.2 1.0 CA B:CYS4343 4.6 97.7 1.0 CA B:CYS4327 4.6 72.3 1.0 CB B:LYS4346 4.8 68.8 1.0 CA B:TYR4329 4.8 72.2 1.0 O B:CYS4327 4.9 70.8 1.0 C B:CYS4327 4.9 75.0 1.0 N B:LYS4346 5.0 63.1 1.0 N B:TYR4329 5.0 66.7 1.0

Zinc binding site 2 out of 2 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 Zinc with other atoms in the Zn binding site number 2 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 B:Zn4402 b:115.2 occ:1.00 SG B:CYS4381 2.4 95.9 1.0 SG B:CYS4373 2.4 110.6 1.0 SG B:CYS4370 2.4 99.0 1.0 SG B:CYS4383 2.4 151.2 1.0 CB B:CYS4370 3.3 105.8 1.0 CB B:CYS4373 3.5 105.2 1.0 CB B:CYS4381 3.5 113.4 1.0 CB B:CYS4383 3.5 145.8 1.0 N B:CYS4373 3.8 100.0 1.0 CA B:CYS4381 4.1 115.3 1.0 N B:CYS4383 4.2 139.5 1.0 CA B:CYS4373 4.3 104.4 1.0 N B:SER4382 4.4 124.5 1.0 CA B:CYS4383 4.4 149.1 1.0 CB B:VAL4372 4.5 119.9 1.0 C B:CYS4381 4.6 116.2 1.0 CA B:CYS4370 4.8 99.8 1.0 C B:VAL4372 4.9 104.9 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