Sodium in PDB 8ddl: Sars-Cov-2 Main Protease (Mpro) H163A Mutant Apo Structure

The structure of Sars-Cov-2 Main Protease (Mpro) H163A Mutant Apo Structure, PDB code: 8ddl was solved by N.Tran, M.J.Mcleod, S.Kalyaanamoorthy, A.Ganesan, T.Holyoak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.54 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.832, 101.463, 102.337, 90, 90, 90
R / Rfree (%)	16.8 / 20.7

The binding sites of Sodium atom in the Sars-Cov-2 Main Protease (Mpro) H163A Mutant Apo Structure (pdb code 8ddl). 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 Sars-Cov-2 Main Protease (Mpro) H163A Mutant Apo Structure, PDB code: 8ddl:

Sodium binding site 1 out of 1 in the Sars-Cov-2 Main Protease (Mpro) H163A Mutant Apo Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Sars-Cov-2 Main Protease (Mpro) H163A Mutant Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:33.5 occ:1.00 OD1 A:ASP263 2.1 50.8 1.0 OD1 A:ASN221 2.2 31.5 1.0 O A:PHE223 2.4 31.1 1.0 O A:HOH604 2.4 33.5 1.0 O A:ASN221 2.7 32.9 1.0 O A:ASP263 2.8 25.9 1.0 CG A:ASN221 3.3 31.5 1.0 C A:ASN221 3.4 31.2 1.0 CG A:ASP263 3.4 42.6 1.0 N A:PHE223 3.4 31.8 1.0 C A:PHE223 3.4 34.5 1.0 C A:ASP263 3.6 30.2 1.0 OG A:SER267 3.6 37.9 1.0 CB A:ALA266 3.8 30.8 1.0 N A:ASN221 3.8 26.7 1.0 CA A:PHE223 3.9 37.9 1.0 O A:HOH645 3.9 38.9 1.0 CA A:ASN221 4.0 30.9 1.0 CA A:ASP263 4.0 34.1 1.0 N A:SER267 4.1 23.6 1.0 C A:ARG222 4.1 35.2 1.0 ND2 A:ASN221 4.1 35.5 1.0 N A:ARG222 4.2 31.0 1.0 CB A:ASN221 4.2 34.0 1.0 OD2 A:ASP263 4.2 45.2 1.0 CB A:ASP263 4.3 32.8 1.0 CB A:PHE223 4.5 31.5 1.0 C A:ALA266 4.5 28.4 1.0 CA A:ARG222 4.6 32.2 0.2 CA A:ARG222 4.6 32.1 0.8 N A:THR224 4.6 32.8 1.0 CA A:ALA266 4.7 34.3 1.0 CB A:SER267 4.7 27.4 1.0 N A:MET264 4.7 24.1 1.0 CA A:SER267 4.7 24.2 1.0 O A:ARG222 4.8 31.1 1.0 N A:ALA266 5.0 27.9 1.0

N.Tran, S.Dasari, S.Barwell, M.J.Mcleod, S.Kalyaanamoorthy, T.Holyoak, A.Ganesan. Revealing An Oxidized Conformation of the Sars-Cov-2 Main Protease: Detailing the Peculiar Features of the H163A Mutant Crystal Structure To Be Published.