Sodium in PDB 7gro: Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-11

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-11:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-11, PDB code: 7gro 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)	56.68 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.62, 99.49, 103.93, 90, 90, 90
R / Rfree (%)	19.2 / 23.2

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-11 also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Fluorine	(F)	3 atoms

The binding sites of Sodium atom in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-11 (pdb code 7gro). 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-11, PDB code: 7gro:
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-11


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-11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:25.6 occ:1.00 O A:PHE223 2.2 21.4 1.0 OD1 A:ASP263 2.2 27.2 1.0 OD1 A:ASN221 2.3 18.2 1.0 O A:HOH528 2.4 21.1 1.0 O A:ASP263 2.8 20.9 1.0 O A:ASN221 2.9 16.9 1.0 C A:PHE223 3.3 22.4 1.0 CG A:ASN221 3.4 19.5 1.0 N A:PHE223 3.5 17.9 1.0 CG A:ASP263 3.5 36.0 1.0 C A:ASN221 3.5 16.1 1.0 C A:ASP263 3.6 25.4 1.0 CB A:ALA266 3.7 24.8 1.0 CA A:PHE223 3.9 17.8 1.0 CA A:ASP263 3.9 33.6 1.0 N A:ASN221 4.0 26.2 1.0 CA A:ASN221 4.1 20.5 1.0 C A:ARG222 4.2 19.2 1.0 N A:SER267 4.2 22.1 1.0 OG A:SER267 4.2 20.6 1.0 ND2 A:ASN221 4.2 19.1 1.0 N A:ARG222 4.3 20.0 1.0 OD2 A:ASP263 4.3 32.9 1.0 CB A:ASP263 4.3 31.4 1.0 CB A:ASN221 4.3 17.1 1.0 N A:THR224 4.4 22.9 1.0 CB A:PHE223 4.5 16.2 1.0 C A:ALA266 4.6 22.1 1.0 CA A:ALA266 4.6 28.0 1.0 CA A:ARG222 4.7 18.2 1.0 N A:MET264 4.8 21.2 1.0 CA A:THR224 4.8 22.8 1.0 O A:ARG222 4.8 18.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-11


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-11 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na510 b:51.9 occ:1.00 O B:MET17 2.5 18.8 1.0 O B:HOH778 2.5 34.0 1.0 O B:GLY120 2.6 24.5 1.0 OE1 A:GLN306 3.0 65.0 1.0 C B:MET17 3.5 23.4 1.0 NE2 A:GLN306 3.7 51.2 1.0 CD A:GLN306 3.8 51.3 1.0 C B:GLY120 3.8 22.8 1.0 N B:GLY71 4.0 29.7 1.0 N B:VAL18 4.4 16.7 1.0 CA B:VAL18 4.4 17.1 1.0 CB B:MET17 4.4 18.6 1.0 O A:HOH733 4.4 45.4 1.0 CA B:MET17 4.4 12.1 1.0 CA B:GLY120 4.6 19.4 1.0 CA B:SER121 4.6 18.4 1.0 N B:SER121 4.7 19.3 1.0 O B:GLU14 4.7 17.3 1.0 CA B:GLY71 4.7 37.0 1.0 N B:MET17 4.8 14.5 1.0 CA B:ALA70 5.0 26.8 1.0 C B:ALA70 5.0 37.2 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