Sodium in PDB 7grx: Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-20

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-20:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-20, PDB code: 7grx 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)	56.08 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.87, 99.57, 103.83, 90, 90, 90
R / Rfree (%)	18.7 / 21.9

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-20 also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Fluorine	(F)	4 atoms

The binding sites of Sodium atom in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-20 (pdb code 7grx). 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-20, PDB code: 7grx:
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-20


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-20 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:42.0 occ:1.00 O A:GLY120 2.3 23.7 1.0 O A:HOH626 2.4 35.8 1.0 O A:MET17 2.4 19.9 1.0 O A:DMS401 2.6 38.9 1.0 O A:DMS402 3.0 40.0 1.0 NE2 B:GLN306 3.4 46.3 1.0 C A:MET17 3.4 18.8 1.0 C A:GLY120 3.5 23.5 1.0 S A:DMS402 3.6 58.0 1.0 S A:DMS401 3.6 55.8 1.0 CG B:GLN306 3.8 51.2 1.0 CD B:GLN306 4.1 61.3 1.0 CB A:MET17 4.1 20.8 1.0 O B:HOH701 4.2 47.1 1.0 CA A:MET17 4.3 14.8 1.0 N A:VAL18 4.3 16.4 1.0 CA A:GLY120 4.4 17.1 1.0 CA A:VAL18 4.4 19.7 1.0 N A:GLY71 4.4 30.0 1.0 N A:SER121 4.4 19.2 1.0 C2 A:DMS401 4.4 64.5 1.0 CA A:SER121 4.5 19.9 1.0 O A:GLU14 4.6 18.8 1.0 N A:MET17 4.7 15.2 1.0 CD A:PRO122 4.7 30.9 1.0 C2 A:DMS402 4.8 37.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-20


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-20 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:26.2 occ:1.00 OD1 B:ASP263 2.2 27.0 1.0 O B:PHE223 2.2 18.6 1.0 OD1 B:ASN221 2.3 20.1 1.0 O B:HOH539 2.5 19.4 1.0 O B:ASP263 2.8 21.7 1.0 O B:ASN221 2.9 18.7 1.0 CG B:ASP263 3.3 38.5 1.0 C B:PHE223 3.3 21.8 1.0 CG B:ASN221 3.4 18.4 1.0 N B:PHE223 3.5 17.8 1.0 C B:ASN221 3.6 17.6 1.0 C B:ASP263 3.6 27.1 1.0 CB B:ALA266 3.7 25.2 1.0 CA B:ASP263 3.9 32.9 1.0 CA B:PHE223 3.9 16.0 1.0 N B:ASN221 4.0 21.4 1.0 OD2 B:ASP263 4.1 35.9 1.0 ND2 B:ASN221 4.2 21.2 1.0 CA B:ASN221 4.2 20.4 1.0 CB B:ASP263 4.2 27.8 1.0 C B:ARG222 4.2 20.2 1.0 OG B:SER267 4.3 21.7 1.0 N B:SER267 4.3 22.0 1.0 N B:ARG222 4.4 19.7 1.0 CB B:ASN221 4.4 18.1 1.0 N B:THR224 4.5 19.7 1.0 O B:HOH660 4.5 38.7 1.0 CB B:PHE223 4.5 16.7 1.0 C B:ALA266 4.6 19.8 1.0 CA B:ALA266 4.7 24.9 1.0 N B:MET264 4.7 22.9 1.0 CA B:ARG222 4.7 22.7 1.0 CA B:THR224 4.8 22.5 1.0 O B:ARG222 4.9 19.8 1.0 N B:ALA266 5.0 24.1 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