Sodium in PDB 8r12: Structure of Compound 8 Bound to Sars-Cov-2 Main Protease

All present enzymatic activity of Structure of Compound 8 Bound to Sars-Cov-2 Main Protease:
3.4.22.69;

The structure of Structure of Compound 8 Bound to Sars-Cov-2 Main Protease, PDB code: 8r12 was solved by A.Mac Sweeney, J.Hazemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.18 / 1.59
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.01, 100.34, 104.55, 90, 90, 90
R / Rfree (%)	21 / 23.8

The structure of Structure of Compound 8 Bound to Sars-Cov-2 Main Protease also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Structure of Compound 8 Bound to Sars-Cov-2 Main Protease (pdb code 8r12). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of Compound 8 Bound to Sars-Cov-2 Main Protease, PDB code: 8r12:

Sodium binding site 1 out of 1 in the Structure of Compound 8 Bound to Sars-Cov-2 Main Protease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Compound 8 Bound to Sars-Cov-2 Main Protease within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:30.8 occ:1.00 OD1 B:ASP263 2.2 38.0 1.0 OD1 B:ASN221 2.3 22.6 1.0 O B:PHE223 2.3 21.0 1.0 O B:HOH524 2.5 23.8 1.0 O B:ASN221 2.7 22.1 1.0 O B:ASP263 3.0 27.2 1.0 C B:ASN221 3.4 21.9 1.0 C B:PHE223 3.4 22.1 1.0 CG B:ASN221 3.4 23.1 1.0 CG B:ASP263 3.4 37.4 1.0 N B:PHE223 3.4 19.3 1.0 C B:ASP263 3.8 27.4 1.0 N B:ASN221 3.9 23.9 1.0 CA B:PHE223 3.9 20.6 1.0 CA B:ASP263 3.9 29.2 1.0 CB B:ALA266 4.0 26.7 1.0 CA B:ASN221 4.0 22.6 1.0 C B:ARG222 4.1 20.0 1.0 CB B:ASP263 4.2 31.9 1.0 N B:ARG222 4.2 20.8 1.0 CB B:ASN221 4.3 22.5 1.0 ND2 B:ASN221 4.3 23.5 1.0 OG B:SER267 4.4 26.3 1.0 OD2 B:ASP263 4.4 39.7 1.0 CA B:ARG222 4.5 19.9 1.0 N B:THR224 4.6 23.9 1.0 N B:SER267 4.6 24.6 1.0 CB B:PHE223 4.6 20.4 1.0 O B:ARG222 4.8 20.3 1.0 C B:ALA266 4.9 25.4 1.0 CA B:ALA266 4.9 26.3 1.0 N B:MET264 5.0 26.5 1.0 CA B:THR224 5.0 25.7 1.0

A.Mac Sweeney, J.Hazemann. Identification of Sars-Cov-2 Mpro Inhibitors Through Deep Reinforcement Learning For De Novo Drug Design and Computational Chemistry Approaches To Be Published.