Chlorine in PDB 9pfh: Crystal Structure of Sars-Cov-2 Mpro Mutant P132H with C5A

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Mpro Mutant P132H with C5A:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 Mpro Mutant P132H with C5A, PDB code: 9pfh was solved by C.Kenward, W.A.Mosimann, L.J.Worrall, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.34 / 2.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.537, 98.678, 102.435, 90, 90, 90
R / Rfree (%)	22.3 / 28.3

The binding sites of Chlorine atom in the Crystal Structure of Sars-Cov-2 Mpro Mutant P132H with C5A (pdb code 9pfh). 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 Sars-Cov-2 Mpro Mutant P132H with C5A, PDB code: 9pfh:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Sars-Cov-2 Mpro Mutant P132H with C5A


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 Mutant P132H with C5A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:74.5 occ:1.00 CL1 A:WZK401 0.0 74.5 1.0 C12 A:WZK401 1.7 55.4 1.0 C13 A:WZK401 2.6 51.2 1.0 C11 A:WZK401 2.8 53.1 1.0 CA A:ASP187 3.4 37.0 1.0 CB A:ASP187 3.5 33.1 1.0 CD2 A:HIS41 3.7 37.9 1.0 C A:ASP187 3.9 39.2 1.0 C10 A:WZK401 4.0 51.2 1.0 CB A:HIS164 4.0 30.6 1.0 CE A:MET49 4.0 44.5 1.0 CB A:MET165 4.0 42.5 1.0 O A:HIS164 4.1 38.1 1.0 CG A:MET165 4.1 42.1 1.0 S1 A:WZK401 4.2 58.2 1.0 SD A:MET165 4.2 44.4 1.0 CG A:HIS41 4.2 41.7 1.0 NE2 A:HIS41 4.2 38.8 1.0 C A:HIS164 4.3 37.0 1.0 CZ A:PHE181 4.4 32.6 1.0 N A:ARG188 4.4 39.7 1.0 O A:ASP187 4.5 41.2 1.0 N A:ASP187 4.6 38.1 1.0 O A:VAL186 4.6 36.1 1.0 CB A:HIS41 4.7 40.0 1.0 ND1 A:HIS164 4.7 31.0 1.0 CA A:HIS164 4.7 33.9 1.0 N A:MET165 4.7 36.9 1.0 CG A:HIS164 4.8 28.5 1.0 CA A:MET165 4.8 39.0 1.0 ND1 A:HIS41 4.8 41.7 1.0 CE1 A:HIS41 4.8 40.6 1.0 CG A:ASP187 5.0 37.6 1.0 CE1 A:PHE181 5.0 32.6 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Sars-Cov-2 Mpro Mutant P132H with C5A


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 Mutant P132H with C5A within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:68.8 occ:1.00 CL1 B:WZK401 0.0 68.8 1.0 C12 B:WZK401 1.7 62.5 1.0 C13 B:WZK401 2.6 61.1 1.0 C11 B:WZK401 2.8 61.6 1.0 CA B:ASP187 3.4 52.1 1.0 CB B:ASP187 3.5 54.2 1.0 CB B:HIS164 3.6 45.4 1.0 ND1 B:HIS41 3.7 56.0 1.0 CB B:MET165 3.8 49.8 1.0 C B:ASP187 4.0 56.4 1.0 C10 B:WZK401 4.0 60.1 1.0 S1 B:WZK401 4.2 57.4 1.0 C B:HIS164 4.2 46.2 1.0 CE1 B:HIS41 4.2 52.8 1.0 O B:HIS164 4.3 50.2 1.0 O B:ASP187 4.3 55.9 1.0 N B:MET165 4.4 45.2 1.0 CE B:MET165 4.5 48.4 1.0 CA B:MET165 4.5 48.2 1.0 CA B:HIS164 4.6 45.8 1.0 CG B:MET165 4.6 46.4 1.0 N B:ARG188 4.6 59.9 1.0 CG B:HIS41 4.6 56.9 1.0 CZ B:PHE181 4.6 41.3 1.0 CG B:HIS164 4.6 42.6 1.0 N B:ASP187 4.7 47.0 1.0 O B:VAL186 4.7 49.5 1.0 SD B:MET165 4.7 45.8 1.0 ND1 B:HIS164 4.7 42.2 1.0 CG B:ASP187 4.9 53.8 1.0 CE B:MET49 5.0 65.7 1.0

N.M.Deschenes, J.Perez-Vargas, Z.Zhong, M.Thomas, C.Kenward, W.A.Mosimann, L.J.Worrall, N.Waglechner, A.X.Li, F.Maguire, P.Aftanas, J.R.Smith, J.Lim, R.N.Young, A.Cherkasov, L.Farooqi, A.Moinuddin, L.Siddiqi, I.Malik, M.Lefebvre, M.Paetzel, N.C.J.Strynadka, F.Jean, A.Mcgeer, R.A.Kozak. Functional and Structural Characterization of Treatment-Emergent Nirmatrelvir Resistance Mutations at Low Frequencies in the Main Protease (Mpro) Reveals A Unique Evolutionary Route For Sars-Cov-2 to Gain Resistance. J Infect Dis 2025.
ISSN: ESSN 1537-6613
PubMed: 40459233
DOI: 10.1093/INFDIS/JIAF294