Sodium in PDB 7gs0: Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-23

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-23:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-23, PDB code: 7gs0 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)	55.81 / 1.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.53, 99.15, 103.22, 90, 90, 90
R / Rfree (%)	19 / 22.1

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-23 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-23 (pdb code 7gs0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-23, PDB code: 7gs0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-23


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-23 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:41.2 occ:1.00 O A:GLY120 2.3 24.9 1.0 O A:HOH606 2.4 30.6 1.0 O A:MET17 2.7 17.9 1.0 O A:DMS403 3.0 36.2 1.0 C A:GLY120 3.5 28.4 1.0 C A:MET17 3.7 22.5 1.0 S A:DMS403 3.8 56.4 1.0 CA A:SER121 4.2 25.8 1.0 N A:SER121 4.3 21.6 1.0 CB A:MET17 4.3 18.2 1.0 N A:GLY71 4.4 32.1 1.0 CA A:GLY120 4.4 22.3 1.0 CA A:MET17 4.5 21.8 1.0 N A:VAL18 4.5 19.5 1.0 CA A:VAL18 4.6 23.2 1.0 CB A:SER121 4.7 33.3 1.0 O A:GLU14 4.7 21.7 1.0 CD A:PRO122 4.9 31.6 1.0 CA A:GLY71 4.9 33.5 1.0 N A:MET17 5.0 20.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-23


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-23 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na404 b:28.2 occ:1.00 OD1 B:ASP263 2.2 31.5 1.0 O B:PHE223 2.3 24.1 1.0 OD1 B:ASN221 2.3 22.6 1.0 O B:HOH524 2.4 26.3 1.0 O B:ASN221 2.6 25.1 1.0 O B:ASP263 2.9 23.3 1.0 C B:ASN221 3.3 22.6 1.0 C B:PHE223 3.4 28.3 1.0 CG B:ASP263 3.4 38.1 1.0 N B:PHE223 3.4 20.0 1.0 CG B:ASN221 3.4 21.9 1.0 C B:ASP263 3.6 33.3 1.0 N B:ASN221 3.8 25.4 1.0 CA B:ASP263 3.9 29.1 1.0 CA B:PHE223 3.9 20.9 1.0 CB B:ALA266 3.9 26.1 1.0 CA B:ASN221 4.0 23.2 1.0 C B:ARG222 4.0 22.1 1.0 O B:HOH567 4.1 35.8 1.0 N B:ARG222 4.2 21.5 1.0 CB B:ASP263 4.2 28.8 1.0 CB B:ASN221 4.3 20.6 1.0 OD2 B:ASP263 4.3 44.6 1.0 OG B:SER267 4.3 23.5 1.0 N B:SER267 4.3 26.8 1.0 ND2 B:ASN221 4.3 24.8 1.0 CA B:ARG222 4.5 21.1 0.5 N B:THR224 4.5 26.5 1.0 CA B:ARG222 4.5 21.1 0.5 CB B:PHE223 4.6 19.1 1.0 O B:ARG222 4.7 24.9 1.0 N B:MET264 4.8 28.0 1.0 C B:ALA266 4.8 25.9 1.0 CA B:ALA266 4.8 22.8 1.0 CA B:THR224 4.9 24.8 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