Chlorine in PDB 8cz7: Crystal Structure of Sars-Cov-2 Mpro with Compound C2

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Mpro with Compound C2:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 Mpro with Compound C2, PDB code: 8cz7 was solved by L.J.Worrall, J.Lee, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.64 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	62.574, 67.47, 93.099, 74.95, 80.03, 66.73
R / Rfree (%)	24.2 / 27.1

The binding sites of Chlorine atom in the Crystal Structure of Sars-Cov-2 Mpro with Compound C2 (pdb code 8cz7). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Sars-Cov-2 Mpro with Compound C2, PDB code: 8cz7:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Sars-Cov-2 Mpro with Compound C2


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 Sars-Cov-2 Mpro with Compound C2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:69.3 occ:1.00 CL01 A:P7L401 0.0 69.3 1.0 C18 A:P7L401 1.8 47.1 1.0 C09 A:P7L401 2.8 41.4 1.0 C12 A:P7L401 2.8 43.7 1.0 CB A:ASP187 3.3 17.9 1.0 ND1 A:HIS41 3.3 18.1 1.0 CA A:ASP187 3.4 18.3 1.0 O A:HIS164 3.7 16.3 1.0 CE1 A:HIS41 3.8 18.8 1.0 CB A:HIS164 3.8 14.6 1.0 CB A:MET165 3.9 24.5 1.0 C19 A:P7L401 4.0 36.1 1.0 C A:HIS164 4.1 15.1 1.0 C A:ASP187 4.2 17.6 1.0 CZ A:PHE181 4.3 14.9 1.0 S01 A:P7L401 4.3 40.8 1.0 CE A:MET165 4.3 41.2 1.0 CE A:MET49 4.4 41.2 1.0 CG A:HIS41 4.5 16.9 1.0 O A:HOH554 4.5 21.0 1.0 ND1 A:HIS164 4.5 14.9 1.0 CA A:HIS164 4.5 14.0 1.0 N A:ASP187 4.5 18.4 1.0 N A:MET165 4.7 17.5 1.0 CG A:HIS164 4.7 15.0 1.0 O A:VAL186 4.7 16.3 1.0 N A:ARG188 4.7 18.3 1.0 CG A:MET165 4.7 30.3 1.0 SD A:MET165 4.7 41.6 1.0 CA A:MET165 4.7 20.4 1.0 CG A:ASP187 4.8 18.5 1.0 O A:ASP187 4.9 16.7 1.0 CB A:HIS41 4.9 16.4 1.0 NE2 A:HIS41 5.0 18.7 1.0 C A:VAL186 5.0 18.7 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Sars-Cov-2 Mpro with Compound C2


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 Sars-Cov-2 Mpro with Compound C2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:83.8 occ:1.00 CL01 B:P7L401 0.0 83.8 1.0 C18 B:P7L401 1.8 59.8 1.0 C09 B:P7L401 2.7 56.9 1.0 C12 B:P7L401 2.8 58.5 1.0 ND1 B:HIS41 3.4 24.3 1.0 SD B:MET165 3.5 40.2 1.0 CB B:ASP187 3.5 21.8 1.0 CA B:ASP187 3.5 23.1 1.0 O B:HIS164 3.5 18.9 1.0 CG B:MET165 3.6 30.2 1.0 CB B:MET165 3.8 25.9 1.0 CB B:HIS164 3.8 16.6 1.0 CE1 B:HIS41 3.8 23.7 1.0 C19 B:P7L401 4.0 49.7 1.0 C B:HIS164 4.0 18.2 1.0 C B:ASP187 4.2 22.0 1.0 S01 B:P7L401 4.3 55.4 1.0 CZ B:PHE181 4.4 22.1 1.0 CE B:MET49 4.4 42.9 1.0 CA B:HIS164 4.5 16.8 1.0 O B:HOH555 4.5 18.5 1.0 ND1 B:HIS164 4.5 16.4 1.0 CG B:HIS41 4.6 22.9 1.0 N B:MET165 4.6 20.1 1.0 N B:ARG188 4.6 23.6 1.0 CA B:MET165 4.6 23.4 1.0 N B:ASP187 4.6 24.0 1.0 CG B:HIS164 4.7 16.0 1.0 O B:VAL186 4.7 23.0 1.0 O B:ASP187 4.9 24.3 1.0 CG B:ASP187 5.0 21.7 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Sars-Cov-2 Mpro with Compound C2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Sars-Cov-2 Mpro with Compound C2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl401 b:50.0 occ:1.00 CL01 C:P7L401 0.0 50.0 1.0 C18 C:P7L401 1.9 37.4 1.0 C09 C:P7L401 2.8 35.0 1.0 C12 C:P7L401 2.9 35.2 1.0 CB C:ASP187 3.2 21.7 1.0 CA C:ASP187 3.4 21.9 1.0 ND1 C:HIS41 3.5 25.7 1.0 CE C:MET165 3.8 35.3 1.0 CB C:HIS164 3.8 19.7 1.0 CE1 C:HIS41 3.9 24.3 1.0 CB C:MET165 3.9 25.1 1.0 CZ C:PHE181 3.9 19.7 1.0 C19 C:P7L401 4.0 32.9 1.0 O C:HIS164 4.1 18.8 1.0 ND1 C:HIS164 4.3 22.0 1.0 C C:HIS164 4.3 19.5 1.0 O C:VAL186 4.3 22.5 1.0 O C:HOH545 4.3 24.6 1.0 S01 C:P7L401 4.3 36.6 1.0 C C:ASP187 4.3 23.5 1.0 N C:ASP187 4.4 21.5 1.0 CE C:MET49 4.5 31.9 1.0 CG C:HIS164 4.6 20.1 1.0 CA C:HIS164 4.6 19.3 1.0 CG C:ASP187 4.7 21.4 1.0 CE1 C:PHE181 4.7 18.9 1.0 C C:VAL186 4.7 21.6 1.0 N C:MET165 4.7 19.4 1.0 CG C:HIS41 4.7 24.8 1.0 CA C:MET165 4.8 21.1 1.0 O C:ASP187 4.8 25.4 1.0 CE2 C:PHE181 4.9 17.7 1.0 CG C:MET165 4.9 30.6 1.0 SD C:MET165 4.9 39.6 1.0 N C:ARG188 5.0 25.1 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Sars-Cov-2 Mpro with Compound C2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Sars-Cov-2 Mpro with Compound C2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl401 b:49.7 occ:1.00 CL01 D:P7L401 0.0 49.7 1.0 C18 D:P7L401 1.9 40.9 1.0 C09 D:P7L401 2.8 36.6 1.0 C12 D:P7L401 2.9 39.5 1.0 CB D:ASP187 3.2 21.4 1.0 CA D:ASP187 3.2 21.8 1.0 CE D:MET165 3.3 37.5 1.0 ND1 D:HIS41 3.7 23.9 1.0 CZ D:PHE181 3.8 17.4 1.0 CB D:MET165 3.9 25.5 1.0 CB D:HIS164 4.0 15.9 1.0 C19 D:P7L401 4.0 35.0 1.0 O D:VAL186 4.1 18.1 1.0 C D:ASP187 4.2 24.1 1.0 O D:HIS164 4.2 20.5 1.0 N D:ASP187 4.2 19.4 1.0 CE1 D:HIS41 4.2 24.1 1.0 CE D:MET49 4.3 41.1 1.0 S01 D:P7L401 4.3 35.5 1.0 C D:HIS164 4.4 18.6 1.0 ND1 D:HIS164 4.5 15.2 1.0 C D:VAL186 4.5 19.2 1.0 O D:HOH525 4.6 14.2 1.0 CE1 D:PHE181 4.6 17.3 1.0 CG D:ASP187 4.7 20.9 1.0 SD D:MET165 4.7 37.6 1.0 CG D:HIS164 4.7 14.6 1.0 CE2 D:PHE181 4.7 17.1 1.0 N D:ARG188 4.7 25.5 1.0 CG D:MET165 4.7 29.4 1.0 CA D:HIS164 4.7 16.9 1.0 N D:MET165 4.8 20.3 1.0 CA D:MET165 4.8 22.2 1.0 O D:ASP187 4.8 27.2 1.0 CG D:HIS41 4.9 23.6 1.0

J.Perez-Vargas, L.J.Worrall, A.D.Olmstead, A.T.Ton, J.Lee, I.Villanueva, C.A.H.Thompson, S.Dudek, S.Ennis, J.R.Smith, T.Shapira, J.De Guzman, S.Gang, F.Ban, M.Vuckovic, M.Bielecki, S.Kovacic, C.Kenward, C.Y.Hong, D.G.Gordon, P.N.Levett, M.Krajden, R.Leduc, P.L.Boudreault, M.Niikura, M.Paetzel, R.N.Young, A.Cherkasov, N.C.J.Strynadka, F.Jean. A Novel Class of Broad-Spectrum Active-Site-Directed 3C-Like Protease Inhibitors with Nanomolar Antiviral Activity Against Highly Immune-Evasive Sars-Cov-2 Omicron Subvariants. Emerg Microbes Infect V. 12 46594 2023.
ISSN: ESSN 2222-1751
PubMed: 37555275
DOI: 10.1080/22221751.2023.2246594