Sodium in PDB 7rc0: X-Ray Structure of Sars-Cov-2 Main Protease Covalently Modified By Compound Grl-091-20

All present enzymatic activity of X-Ray Structure of Sars-Cov-2 Main Protease Covalently Modified By Compound Grl-091-20:
3.4.22.69;

The structure of X-Ray Structure of Sars-Cov-2 Main Protease Covalently Modified By Compound Grl-091-20, PDB code: 7rc0 was solved by A.D.Mesecar, B.A.Anson, A.K.Ghosh, Center For Structural Genomics Ofinfectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.70 / 1.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	97.197, 82.43, 54.283, 90, 117.21, 90
R / Rfree (%)	12.6 / 17.4

The binding sites of Sodium atom in the X-Ray Structure of Sars-Cov-2 Main Protease Covalently Modified By Compound Grl-091-20 (pdb code 7rc0). 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 X-Ray Structure of Sars-Cov-2 Main Protease Covalently Modified By Compound Grl-091-20, PDB code: 7rc0:

Sodium binding site 1 out of 1 in the X-Ray Structure of Sars-Cov-2 Main Protease Covalently Modified By Compound Grl-091-20


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of Sars-Cov-2 Main Protease Covalently Modified By Compound Grl-091-20 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:39.3 occ:1.00 O A:HOH503 1.8 41.8 1.0 OD1 A:ASP263 2.2 28.4 0.2 O A:ASP263 2.5 31.6 0.2 OD1 A:ASN221 2.6 27.2 1.0 O A:ASP263 2.6 23.9 0.8 O A:PHE223 2.7 34.1 1.0 O A:ASN221 2.8 28.7 1.0 O A:HOH514 2.9 45.8 1.0 CG A:ASP263 3.4 28.6 0.2 O A:HOH504 3.4 45.9 1.0 OG A:SER267 3.4 45.7 1.0 C A:ASP263 3.5 26.8 0.8 C A:ASP263 3.5 27.5 0.2 CG A:ASN221 3.5 30.2 1.0 C A:ASN221 3.6 27.4 1.0 CA A:ASP263 3.8 26.4 0.8 CB A:ALA266 3.8 30.6 1.0 N A:ASN221 3.8 27.5 1.0 C A:PHE223 3.8 30.9 1.0 CB A:ASP263 3.8 28.0 0.8 CA A:ASP263 3.9 29.6 0.2 N A:PHE223 3.9 34.2 1.0 N A:SER267 3.9 23.2 1.0 CA A:ASN221 4.1 30.2 1.0 CB A:ASP263 4.2 30.7 0.2 OD2 A:ASP263 4.2 32.7 0.2 ND2 A:ASN221 4.3 34.0 1.0 CA A:PHE223 4.4 35.4 1.0 C A:ALA266 4.4 26.2 1.0 CB A:ASN221 4.4 30.8 1.0 N A:ARG222 4.4 29.4 1.0 C A:ARG222 4.5 33.8 1.0 CB A:SER267 4.6 29.7 1.0 CA A:ALA266 4.6 28.7 1.0 N A:MET264 4.6 24.0 1.0 CA A:SER267 4.6 24.3 1.0 CG A:ASP263 4.7 35.5 0.8 CA A:ARG222 4.8 33.8 1.0 N A:THR224 4.9 36.1 1.0 CB A:PHE223 4.9 38.3 1.0 N A:ALA266 4.9 23.2 1.0 C A:LEU220 4.9 25.5 1.0

A.K.Ghosh, J.Raghavaiah, D.Shahabi, M.Yadav, B.J.Anson, E.K.Lendy, S.I.Hattori, N.Higashi-Kuwata, H.Mitsuya, A.D.Mesecar. Indole Chloropyridinyl Ester-Derived Sars-Cov-2 3CLPRO Inhibitors: Enzyme Inhibition, Antiviral Efficacy, Structure-Activity Relationship, and X-Ray Structural Studies. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 34528437
DOI: 10.1021/ACS.JMEDCHEM.1C01214