Chlorine 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:

Zinc	(Zn)	2 atoms
Sodium	(Na)	1 atom
Fluorine	(F)	3 atoms

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

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl7102 b:93.7 occ:1.00 CL2 A:XDU7102 0.0 93.7 1.0 C10 A:XDU7102 1.8 89.3 1.0 C9 A:XDU7102 2.7 82.7 1.0 C5 A:XDU7102 2.9 80.8 1.0 C3 A:XDU7102 3.0 73.8 1.0 C4 A:XDU7102 3.3 85.0 1.0 OG A:SER6896 3.6 73.8 1.0 CE1 A:PHE6868 3.8 58.4 1.0 CG2 A:VAL6916 3.9 63.7 1.0 CD1 A:PHE6868 3.9 56.4 1.0 CA A:CYS6913 3.9 74.4 1.0 N A:CYS6913 4.0 66.5 1.0 C8 A:XDU7102 4.0 89.9 1.0 C6 A:XDU7102 4.1 80.5 1.0 C2 A:XDU7102 4.1 69.2 1.0 O A:HOH7329 4.2 50.4 1.0 CB A:CYS6913 4.3 85.7 1.0 C11 A:XDU7102 4.3 63.4 1.0 C A:ASP6912 4.4 70.0 1.0 C7 A:XDU7102 4.6 91.1 1.0 CB A:SER6896 4.6 54.9 1.0 O A:GLY6911 4.6 64.3 1.0 CZ A:PHE6868 4.8 56.8 1.0 O A:ASP6912 4.8 68.8 1.0 CG A:PHE6868 4.9 50.1 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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 A:Cl7102 b:80.5 occ:1.00 CL1 A:XDU7102 0.0 80.5 1.0 C8 A:XDU7102 1.8 89.9 1.0 C9 A:XDU7102 2.8 82.7 1.0 C7 A:XDU7102 2.8 91.1 1.0 CG A:MET6929 3.2 68.1 1.0 CB A:MET6929 3.3 50.1 1.0 CD1 A:PHE6947 3.8 48.3 1.0 CB A:PHE6947 3.9 52.0 1.0 CD1 A:ILE6951 3.9 55.9 1.0 CG1 A:ILE6951 4.0 52.1 1.0 CB A:PHE6868 4.0 44.6 1.0 SD A:MET6929 4.0 88.9 1.0 CG A:PHE6947 4.0 51.9 1.0 C10 A:XDU7102 4.0 89.3 1.0 C6 A:XDU7102 4.1 80.5 1.0 CG A:PHE6868 4.4 50.1 1.0 OG A:SER6927 4.4 41.3 1.0 O A:HOH7329 4.5 50.4 1.0 C5 A:XDU7102 4.6 80.8 1.0 CE1 A:PHE6947 4.6 48.8 1.0 O A:PHE6947 4.7 52.3 1.0 CD2 A:PHE6868 4.8 54.4 1.0 CA A:MET6929 4.8 42.1 1.0 CD1 A:PHE6868 4.9 56.4 1.0 CA A:PHE6947 5.0 51.3 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