Chlorine in PDB 7grj: Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-6

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-6:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-6, PDB code: 7grj was solved by C.-Y.Huang, A.Metz, M.Sharpe, A.Sweeney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.36 / 1.74
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.03, 100.96, 104.38, 90, 90, 90
R / Rfree (%)	22.3 / 26.8

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-6 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Chlorine atom in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-6 (pdb code 7grj). 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 Main Protease in Complex with Cpd-6, PDB code: 7grj:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-6


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 Main Protease in Complex with Cpd-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:33.4 occ:0.72 CL10 A:Y1L403 0.0 33.4 0.7 C09 A:Y1L403 1.7 26.6 0.7 C08 A:Y1L403 2.7 25.1 0.7 C11 A:Y1L403 2.7 24.2 0.7 CA A:ASP187 3.4 21.9 1.0 CB A:ASP187 3.5 24.7 1.0 O A:HIS164 3.5 21.1 1.0 CB A:MET165 3.6 26.0 1.0 CD2 A:HIS41 3.6 30.2 1.0 SD A:MET165 3.7 39.0 1.0 CB A:HIS164 3.7 15.8 1.0 CG A:MET165 3.9 27.1 1.0 C A:HIS164 3.9 24.7 1.0 C07 A:Y1L403 4.0 33.5 0.7 C12 A:Y1L403 4.0 38.5 0.7 CZ A:PHE181 4.0 17.3 1.0 NE2 A:HIS41 4.1 25.8 1.0 C A:ASP187 4.2 29.7 1.0 N A:MET165 4.4 18.4 1.0 O A:VAL186 4.4 32.8 1.0 CA A:HIS164 4.4 17.6 1.0 N A:ASP187 4.5 20.8 1.0 CA A:MET165 4.5 27.7 1.0 C06 A:Y1L403 4.5 41.0 0.7 ND1 A:HIS164 4.6 26.6 1.0 N A:ARG188 4.6 30.7 1.0 CG A:HIS41 4.6 27.2 1.0 CE A:MET165 4.6 42.9 1.0 CG A:HIS164 4.7 25.5 1.0 O A:HOH615 4.7 18.4 1.0 CE A:MET49 4.8 32.9 1.0 C A:VAL186 4.8 23.7 1.0 CE1 A:PHE181 4.9 14.6 1.0 CE2 A:PHE181 4.9 22.8 1.0 O A:ASP187 5.0 24.8 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-6


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 Main Protease in Complex with Cpd-6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl405 b:44.6 occ:0.82 CL10 B:Y1L405 0.0 44.6 0.8 C09 B:Y1L405 1.7 34.4 0.8 C11 B:Y1L405 2.7 30.0 0.8 C08 B:Y1L405 2.7 36.0 0.8 CB B:ASP187 3.5 29.4 1.0 CA B:ASP187 3.5 25.8 1.0 CB B:MET165 3.6 31.2 1.0 CG B:MET165 3.7 32.2 1.0 O B:HIS164 3.7 24.0 1.0 CD2 B:HIS41 3.8 36.2 1.0 CB B:HIS164 3.8 26.2 1.0 SD B:MET165 3.8 42.5 1.0 C07 B:Y1L405 4.0 42.8 0.8 C12 B:Y1L405 4.0 49.3 0.8 C B:HIS164 4.0 29.5 1.0 CZ B:PHE181 4.1 24.1 1.0 O B:VAL186 4.3 25.6 1.0 NE2 B:HIS41 4.3 27.9 1.0 CD2 B:HIS164 4.4 21.6 1.0 C B:ASP187 4.4 37.1 1.0 N B:ASP187 4.4 22.5 1.0 N B:MET165 4.5 20.8 1.0 CA B:HIS164 4.5 24.0 1.0 CG B:HIS164 4.5 24.2 1.0 C06 B:Y1L405 4.5 50.8 0.8 CA B:MET165 4.6 32.9 1.0 O B:HOH573 4.6 25.9 1.0 C B:VAL186 4.7 26.8 1.0 CG B:HIS41 4.8 33.9 1.0 N B:ARG188 4.9 42.2 1.0 CE1 B:PHE181 4.9 23.0 1.0 CG B:ASP187 4.9 28.2 1.0

C.Y.Huang, A.Metz, R.Lange, N.Artico, C.Potot, J.Hazemann, M.Muller, M.Dos Santos, A.Chambovey, D.Ritz, D.Eris, S.Meyer, G.Bourquin, M.Sharpe, A.Mac Sweeney. Fragment-Based Screening Targeting An Open Form of the Sars-Cov-2 Main Protease Binding Pocket. Acta Crystallogr D Struct V. 80 123 2024BIOL.
ISSN: ISSN 2059-7983
PubMed: 38289714
DOI: 10.1107/S2059798324000329