Sodium in PDB 7grm: Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-9

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-9:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-9, PDB code: 7grm 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)	56.65 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.61, 99.63, 103.81, 90, 90, 90
R / Rfree (%)	20.1 / 23.1

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-9 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-9 (pdb code 7grm). 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-9, PDB code: 7grm:
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-9


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-9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:51.2 occ:1.00 O A:GLU14 3.1 19.5 1.0 O A:GLY120 3.2 23.4 1.0 CD A:PRO122 3.4 29.1 1.0 O A:MET17 3.4 20.3 1.0 O A:DMS402 3.7 62.5 1.0 CB A:MET17 3.8 18.8 1.0 CG A:PRO122 3.8 30.7 1.0 S A:DMS402 4.0 62.0 1.0 C A:MET17 4.2 20.7 1.0 C A:GLU14 4.2 18.9 1.0 CA A:MET17 4.4 16.5 1.0 C A:GLY120 4.4 23.8 1.0 CA A:SER121 4.4 19.7 1.0 O A:HOH571 4.4 38.0 1.0 N A:MET17 4.5 17.5 1.0 N A:PRO122 4.6 23.0 1.0 CG A:MET17 4.8 19.0 1.0 CA A:GLU14 4.8 16.3 1.0 O A:HOH694 4.9 42.6 1.0 N A:SER121 4.9 21.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-9


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-9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:44.5 occ:1.00 OD1 B:ASN221 2.0 24.3 1.0 OD1 B:ASP263 2.4 31.3 1.0 O B:HOH525 2.4 24.0 1.0 O B:PHE223 2.5 24.3 1.0 O B:ASN221 2.6 21.4 1.0 O B:ASP263 3.0 25.6 1.0 CG B:ASN221 3.0 23.4 1.0 C B:ASN221 3.2 22.1 1.0 N B:PHE223 3.4 22.5 1.0 C B:PHE223 3.5 24.7 1.0 CG B:ASP263 3.6 39.0 1.0 N B:ASN221 3.7 25.6 1.0 CA B:ASN221 3.8 23.1 1.0 CB B:ALA266 3.8 24.6 1.0 C B:ASP263 3.8 28.4 1.0 CA B:PHE223 3.9 21.5 1.0 ND2 B:ASN221 3.9 24.2 1.0 CB B:ASN221 4.0 20.9 1.0 N B:ARG222 4.0 20.6 1.0 C B:ARG222 4.0 20.0 1.0 OG B:SER267 4.1 24.9 1.0 CA B:ASP263 4.1 32.6 1.0 N B:SER267 4.3 26.6 1.0 CB B:ASP263 4.4 33.4 1.0 CB B:PHE223 4.4 20.4 1.0 CA B:ARG222 4.5 21.3 1.0 OD2 B:ASP263 4.5 40.0 1.0 N B:THR224 4.6 24.3 1.0 C B:ALA266 4.7 25.1 1.0 CA B:ALA266 4.8 28.1 1.0 O B:ARG222 4.8 20.9 1.0 C B:LEU220 4.9 27.8 1.0 CA B:SER267 5.0 23.8 1.0 N B:MET264 5.0 25.9 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