Sodium in PDB 7gre: Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-1

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-1:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-1, PDB code: 7gre was solved by C.-Y.Huang, A.Metz, M.Sharpe, A.M.Sweeney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.82 / 1.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.79, 99.93, 104.2, 90, 90, 90
R / Rfree (%)	20.6 / 24.9

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-1 also contains other interesting chemical elements:

Fluorine	(F)	3 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-1 (pdb code 7gre). 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-1, PDB code: 7gre:
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-1


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-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na506 b:34.3 occ:1.00 O A:GLY120 2.2 19.7 1.0 O A:DMS502 2.5 29.0 1.0 O A:MET17 2.5 15.2 1.0 O A:HOH702 2.7 29.2 1.0 O A:DMS503 2.9 30.6 1.0 NE2 B:GLN306 3.3 47.6 1.0 C A:GLY120 3.4 18.8 1.0 C A:MET17 3.4 17.0 1.0 S A:DMS502 3.6 56.8 1.0 S A:DMS503 3.8 42.7 1.0 CG B:GLN306 3.8 45.6 1.0 C2 A:DMS502 3.9 39.4 1.0 CD B:GLN306 4.0 50.0 1.0 CB A:MET17 4.2 15.7 1.0 N A:VAL18 4.3 13.3 1.0 CA A:GLY120 4.3 16.6 1.0 N A:SER121 4.3 16.1 1.0 CA A:MET17 4.3 12.9 1.0 CA A:SER121 4.3 18.0 1.0 N A:GLY71 4.4 29.4 1.0 CA A:VAL18 4.4 17.4 1.0 O A:GLU14 4.7 14.3 1.0 N A:MET17 4.7 15.8 1.0 C2 A:DMS503 4.7 29.6 1.0 CD A:PRO122 4.9 26.4 1.0 CB A:SER121 4.9 27.4 1.0 CA A:GLY71 5.0 32.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-1


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-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na405 b:23.2 occ:1.00 OD1 B:ASP263 2.1 26.6 1.0 O B:HOH542 2.2 19.3 1.0 O B:PHE223 2.3 17.8 1.0 OD1 B:ASN221 2.4 19.4 1.0 O B:ASN221 2.7 17.0 1.0 O B:ASP263 2.9 18.4 1.0 CG B:ASP263 3.3 29.7 1.0 C B:PHE223 3.4 18.4 1.0 C B:ASN221 3.4 17.0 1.0 CG B:ASN221 3.5 17.2 1.0 N B:PHE223 3.5 14.6 1.0 C B:ASP263 3.7 23.1 1.0 N B:ASN221 3.9 22.6 1.0 CB B:ALA266 4.0 22.4 1.0 CA B:PHE223 4.0 15.6 1.0 CA B:ASP263 4.0 29.3 1.0 C B:ARG222 4.1 16.1 1.0 CA B:ASN221 4.1 15.4 1.0 OD2 B:ASP263 4.2 31.0 1.0 N B:ARG222 4.2 16.7 1.0 CB B:ASP263 4.2 27.2 1.0 OG B:SER267 4.3 21.0 1.0 ND2 B:ASN221 4.3 17.5 1.0 CB B:ASN221 4.3 15.2 1.0 N B:SER267 4.5 18.0 1.0 N B:THR224 4.5 16.4 1.0 CA B:ARG222 4.5 17.4 1.0 CB B:PHE223 4.6 15.4 1.0 O B:ARG222 4.7 18.5 1.0 N B:MET264 4.8 21.0 1.0 O B:HOH691 4.9 32.6 1.0 C B:ALA266 4.9 17.9 1.0 CA B:THR224 4.9 22.1 1.0 CA B:ALA266 4.9 20.4 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