Chlorine in PDB 8cz4: Crystal Structure of Sars-Cov-2 Mpro with Compound C3

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Mpro with Compound C3:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 Mpro with Compound C3, PDB code: 8cz4 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)	46.71 / 2.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	62.81, 67.817, 94.614, 74.59, 79.39, 66.39
R / Rfree (%)	21.6 / 24.4

The binding sites of Chlorine atom in the Crystal Structure of Sars-Cov-2 Mpro with Compound C3 (pdb code 8cz4). 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 C3, PDB code: 8cz4:
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 C3


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 C3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:110.4 occ:1.00 CL01 A:P6R401 0.0 110.4 1.0 C18 A:P6R401 1.8 113.2 1.0 C12 A:P6R401 2.8 122.8 1.0 C09 A:P6R401 2.8 116.1 1.0 CB A:ASP187 3.3 42.5 1.0 CA A:ASP187 3.3 43.2 1.0 ND1 A:HIS41 3.7 53.9 1.0 CB A:HIS164 3.7 42.1 1.0 CB A:MET165 3.8 57.0 1.0 O A:HIS164 3.8 46.1 1.0 C19 A:P6R401 4.0 117.0 1.0 CZ A:PHE181 4.1 42.4 1.0 C A:HIS164 4.1 46.5 1.0 C A:ASP187 4.2 44.6 1.0 CE1 A:HIS41 4.2 51.1 1.0 S01 A:P6R401 4.3 128.2 1.0 SD A:MET165 4.3 78.0 1.0 CE A:MET165 4.3 73.5 1.0 O A:VAL186 4.3 42.0 1.0 CG A:MET165 4.3 64.0 1.0 N A:ASP187 4.4 43.9 1.0 O A:HOH567 4.4 39.8 1.0 CA A:HIS164 4.5 43.4 1.0 CE A:MET49 4.5 73.5 1.0 ND1 A:HIS164 4.5 46.0 1.0 N A:MET165 4.6 48.9 1.0 CG A:HIS164 4.6 43.4 1.0 N A:ARG188 4.7 46.3 1.0 CA A:MET165 4.7 52.2 1.0 O A:ASP187 4.7 50.2 1.0 CG A:HIS41 4.7 49.7 1.0 C A:VAL186 4.7 44.1 1.0 CG A:ASP187 4.8 43.6 1.0 CE1 A:PHE181 4.8 41.1 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Sars-Cov-2 Mpro with Compound C3


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 C3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:136.6 occ:1.00 CL01 B:P6R401 0.0 136.6 1.0 C18 B:P6R401 1.8 125.6 1.0 C09 B:P6R401 2.8 129.1 1.0 C12 B:P6R401 2.8 123.4 1.0 CB B:ASP187 3.3 50.5 1.0 CA B:ASP187 3.4 47.2 1.0 ND1 B:HIS41 3.5 54.1 1.0 O B:HIS164 3.7 45.6 1.0 SD B:MET165 3.8 72.3 1.0 CB B:HIS164 3.8 43.9 1.0 CG B:MET165 3.9 59.9 1.0 CB B:MET165 4.0 55.4 1.0 CE1 B:HIS41 4.0 54.2 1.0 C19 B:P6R401 4.0 128.9 1.0 C B:HIS164 4.1 45.3 1.0 C B:ASP187 4.2 48.5 1.0 O B:HOH547 4.2 40.3 1.0 S01 B:P6R401 4.3 118.0 1.0 CZ B:PHE181 4.3 48.1 1.0 CE B:MET49 4.4 83.3 1.0 CG B:HIS41 4.4 51.2 1.0 CA B:HIS164 4.5 43.9 1.0 N B:ASP187 4.5 49.6 1.0 O B:VAL186 4.5 46.6 1.0 ND1 B:HIS164 4.5 46.6 1.0 N B:ARG188 4.7 48.0 1.0 CG B:HIS164 4.7 45.5 1.0 N B:MET165 4.7 46.8 1.0 CG B:ASP187 4.7 52.6 1.0 O B:ASP187 4.7 50.2 1.0 CA B:MET165 4.8 51.0 1.0 CB B:HIS41 4.8 50.2 1.0 CE1 B:PHE181 4.9 45.4 1.0 C B:VAL186 4.9 48.6 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Sars-Cov-2 Mpro with Compound C3


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 C3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl401 b:105.9 occ:1.00 CL01 C:P6R401 0.0 105.9 1.0 C18 C:P6R401 1.8 105.8 1.0 C09 C:P6R401 2.8 107.0 1.0 C12 C:P6R401 2.8 108.7 1.0 CB C:ASP187 3.2 51.4 1.0 CA C:ASP187 3.3 50.2 1.0 ND1 C:HIS41 3.6 52.6 1.0 CB C:MET165 3.8 61.0 1.0 CB C:HIS164 3.8 47.2 1.0 O C:HIS164 4.0 51.3 1.0 C19 C:P6R401 4.0 111.3 1.0 CE1 C:HIS41 4.0 56.3 1.0 CE C:MET165 4.1 64.5 1.0 C C:ASP187 4.1 56.6 1.0 CE C:MET49 4.2 81.4 1.0 C C:HIS164 4.2 51.1 1.0 CZ C:PHE181 4.2 41.6 1.0 S01 C:P6R401 4.3 116.0 1.0 CG C:MET165 4.3 63.5 1.0 O C:VAL186 4.3 44.1 1.0 O C:HOH525 4.4 44.7 1.0 N C:ASP187 4.4 48.5 1.0 SD C:MET165 4.4 67.7 1.0 CA C:HIS164 4.6 47.6 1.0 ND1 C:HIS164 4.6 47.7 1.0 N C:MET165 4.6 52.7 1.0 N C:ARG188 4.7 62.7 1.0 CG C:HIS41 4.7 52.7 1.0 CG C:ASP187 4.7 52.1 1.0 CA C:MET165 4.7 56.3 1.0 O C:ASP187 4.7 57.9 1.0 CG C:HIS164 4.7 47.9 1.0 C C:VAL186 4.8 47.8 1.0 CE1 C:PHE181 4.9 41.8 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Sars-Cov-2 Mpro with Compound C3


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 C3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl401 b:107.2 occ:1.00 CL01 D:P6R401 0.0 107.2 1.0 C18 D:P6R401 1.8 103.3 1.0 C09 D:P6R401 2.8 102.5 1.0 C12 D:P6R401 2.8 105.4 1.0 CA D:ASP187 3.4 45.7 1.0 CB D:ASP187 3.4 46.1 1.0 ND1 D:HIS41 3.7 50.3 1.0 CB D:MET165 3.7 54.2 1.0 CE D:MET165 3.9 67.2 1.0 CB D:HIS164 3.9 39.9 1.0 O D:HIS164 3.9 51.2 1.0 C19 D:P6R401 4.0 97.5 1.0 CE D:MET49 4.1 85.0 1.0 CZ D:PHE181 4.1 34.6 1.0 CE1 D:HIS41 4.2 52.6 1.0 O D:VAL186 4.2 39.8 1.0 C D:HIS164 4.2 46.3 1.0 CG D:MET165 4.2 59.8 1.0 C D:ASP187 4.2 49.4 1.0 S01 D:P6R401 4.3 101.3 1.0 N D:ASP187 4.4 42.0 1.0 SD D:MET165 4.4 72.1 1.0 O D:HOH519 4.5 38.1 1.0 CA D:HIS164 4.6 43.1 1.0 N D:MET165 4.7 46.9 1.0 C D:VAL186 4.7 41.3 1.0 N D:ARG188 4.7 56.7 1.0 ND1 D:HIS164 4.7 39.6 1.0 CA D:MET165 4.7 51.4 1.0 CG D:HIS164 4.8 37.8 1.0 CE1 D:PHE181 4.8 34.3 1.0 CG D:HIS41 4.9 51.1 1.0 CG D:ASP187 4.9 46.3 1.0 O D:ASP187 4.9 50.1 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