Sodium in PDB 7grv: Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-18

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-18:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-18, PDB code: 7grv 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)	56.82 / 1.92
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.76, 100.04, 104.28, 90, 90, 90
R / Rfree (%)	19.3 / 23.6

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-18 also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-18 (pdb code 7grv). 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-18, PDB code: 7grv:
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-18


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-18 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:32.7 occ:1.00 O A:HOH514 2.3 31.7 1.0 O A:PHE223 2.4 28.6 1.0 OD1 A:ASP263 2.6 35.0 1.0 OD1 A:ASN221 2.6 29.0 1.0 O A:ASN221 2.7 25.5 1.0 O A:ASP263 3.1 30.0 1.0 C A:PHE223 3.4 28.6 1.0 N A:PHE223 3.4 22.4 1.0 C A:ASN221 3.5 28.2 1.0 CG A:ASP263 3.7 39.2 1.0 CG A:ASN221 3.7 27.6 1.0 C A:ASP263 3.7 34.2 1.0 CA A:PHE223 3.9 25.6 1.0 N A:ASN221 4.0 35.7 1.0 CB A:ALA266 4.0 30.9 1.0 CA A:ASP263 4.0 40.5 1.0 C A:ARG222 4.1 22.7 1.0 CA A:ASN221 4.2 26.2 1.0 N A:ARG222 4.3 25.8 1.0 OG A:SER267 4.4 28.9 1.0 CB A:ASP263 4.4 38.5 1.0 OD2 A:ASP263 4.5 41.2 1.0 CB A:ASN221 4.5 23.9 1.0 CA A:ARG222 4.6 24.1 1.0 N A:THR224 4.6 27.4 1.0 CB A:PHE223 4.6 22.4 1.0 N A:SER267 4.6 30.1 1.0 ND2 A:ASN221 4.6 29.1 1.0 O A:ARG222 4.7 25.5 1.0 N A:MET264 4.8 34.1 1.0 CA A:THR224 4.9 27.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-18


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-18 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:49.2 occ:1.00 O A:HOH630 2.3 40.6 1.0 N A:GLY71 2.8 52.9 1.0 O A:GLY120 3.2 34.5 1.0 O A:MET17 3.4 27.0 1.0 CA A:GLY71 3.5 53.9 1.0 O A:DMS402 3.5 62.3 1.0 O A:GLN69 3.6 33.0 1.0 CA A:VAL18 3.8 30.4 1.0 C A:ALA70 3.8 47.6 1.0 C A:GLY120 3.9 32.7 1.0 CA A:ALA70 4.0 43.0 1.0 CA A:GLY120 4.1 28.6 1.0 N A:GLN19 4.2 29.9 1.0 C A:MET17 4.2 27.3 1.0 C A:VAL18 4.3 31.3 1.0 C A:GLN69 4.4 43.9 1.0 N A:VAL18 4.4 29.4 1.0 C A:GLY71 4.6 52.5 1.0 N A:ALA70 4.7 34.9 1.0 O A:GLY71 4.7 57.5 1.0 CB A:VAL18 4.7 31.0 1.0 O A:ASN119 4.8 37.6 1.0 N A:SER121 4.9 31.8 1.0 S A:DMS402 4.9 60.1 1.0 O A:ALA70 4.9 48.2 1.0 CG1 A:VAL18 4.9 25.4 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