Zinc 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
Sodium	(Na)	2 atoms

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

Zinc 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 Zinc with other atoms in the Zn 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 B:Zn4401 b:64.0 occ:1.00 NE2 B:HIS4336 2.1 94.1 1.0 SG B:CYS4327 2.3 59.5 1.0 SG B:CYS4343 2.3 72.0 1.0 SG B:CYS4330 2.3 65.5 1.0 CD2 B:HIS4336 3.1 81.9 1.0 CE1 B:HIS4336 3.1 86.7 1.0 CB B:CYS4327 3.2 61.8 1.0 CB B:CYS4343 3.3 82.0 1.0 CB B:CYS4330 3.5 65.5 1.0 N B:CYS4330 3.6 66.5 1.0 CA B:CYS4330 4.0 63.9 1.0 ND1 B:HIS4336 4.2 92.0 1.0 CG B:HIS4336 4.2 92.3 1.0 CB B:TYR4329 4.4 78.5 1.0 CA B:CYS4343 4.5 87.6 1.0 C B:TYR4329 4.5 69.8 1.0 CA B:CYS4327 4.6 61.5 1.0 CB B:LYS4346 4.7 58.5 0.5 CB B:LYS4346 4.7 56.9 0.5 CA B:TYR4329 4.8 73.5 1.0 N B:LYS4346 4.8 54.5 0.5 O B:HOH4541 4.8 76.5 1.0 N B:LYS4346 4.8 55.0 0.5 O B:CYS4327 4.9 59.2 1.0 C B:CYS4327 5.0 61.1 1.0 N B:TYR4329 5.0 67.1 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn4402 b:91.6 occ:1.00 SG B:CYS4370 2.3 91.0 1.0 SG B:CYS4381 2.3 77.6 1.0 SG B:CYS4383 2.4 116.7 1.0 SG B:CYS4373 2.4 97.5 1.0 CB B:CYS4370 3.3 93.1 1.0 CB B:CYS4373 3.4 98.3 1.0 CB B:CYS4383 3.4 121.1 1.0 CB B:CYS4381 3.5 87.8 1.0 N B:CYS4373 3.6 98.5 1.0 CA B:CYS4381 4.0 90.3 1.0 CA B:CYS4373 4.1 96.8 1.0 N B:CYS4383 4.1 110.4 1.0 CB B:VAL4372 4.2 109.8 1.0 CA B:CYS4383 4.4 124.8 1.0 N B:SER4382 4.4 99.1 1.0 C B:CYS4381 4.6 94.0 1.0 C B:VAL4372 4.7 101.0 1.0 CG1 B:VAL4372 4.7 109.3 1.0 CA B:CYS4370 4.8 91.7 1.0 CA B:VAL4372 4.8 106.0 1.0 C B:CYS4373 4.9 86.7 1.0 N B:VAL4372 4.9 103.0 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