Sodium in PDB 7z3u: Crystal Structure of Sars-Cov-2 Main Protease After Incubation with Sulfo-Calpeptin

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease After Incubation with Sulfo-Calpeptin:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 Main Protease After Incubation with Sulfo-Calpeptin, PDB code: 7z3u was solved by P.Y.A.Reinke, S.Falke, J.Lieske, W.Ewert, J.Loboda, A.Rahmani Mashhour, M.Hauser, K.Karnicar, A.Usenik, N.Lindic, M.Lach, H.Boehler, T.Beck, R.Cox, H.N.Chapman, W.Hinrichs, D.Turk, S.Guenther, A.Meents, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.22 / 1.72
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.692, 99.598, 103.261, 90, 90, 90
R / Rfree (%)	18.7 / 21.6

The structure of Crystal Structure of Sars-Cov-2 Main Protease After Incubation with Sulfo-Calpeptin also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Sars-Cov-2 Main Protease After Incubation with Sulfo-Calpeptin (pdb code 7z3u). 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 After Incubation with Sulfo-Calpeptin, PDB code: 7z3u:
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 After Incubation with Sulfo-Calpeptin


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 After Incubation with Sulfo-Calpeptin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:44.3 occ:1.00 OD1 A:ASP263 2.2 47.2 1.0 OD1 A:ASN221 2.2 41.2 1.0 O A:PHE223 2.3 35.7 1.0 O A:HOH509 2.5 37.3 1.0 O A:ASP263 2.8 35.9 1.0 O A:ASN221 2.8 37.6 1.0 HB1 A:ALA266 2.9 50.7 1.0 H A:PHE223 2.9 40.5 1.0 HG A:SER267 3.2 47.0 1.0 H A:ASN221 3.2 50.5 1.0 CG A:ASN221 3.3 42.2 1.0 CG A:ASP263 3.4 53.9 1.0 N A:PHE223 3.4 33.6 1.0 C A:PHE223 3.4 36.5 1.0 HA A:ASP263 3.4 49.0 1.0 C A:ASN221 3.4 37.3 1.0 C A:ASP263 3.6 38.2 1.0 CB A:ALA266 3.8 42.1 1.0 H A:SER267 3.9 43.7 1.0 CA A:ASP263 3.9 40.8 1.0 CA A:PHE223 3.9 38.6 1.0 N A:ASN221 3.9 42.0 1.0 HD22 A:ASN221 3.9 50.0 1.0 HB2 A:ALA266 4.0 50.7 1.0 OG A:SER267 4.0 39.1 1.0 HB2 A:PHE223 4.0 45.9 1.0 ND2 A:ASN221 4.0 41.6 1.0 O A:HOH581 4.1 47.9 1.0 CA A:ASN221 4.1 39.1 1.0 C A:ARG222 4.1 34.8 1.0 CB A:ASP263 4.2 36.2 1.0 N A:ARG222 4.2 35.9 1.0 CB A:ASN221 4.2 37.5 1.0 OD2 A:ASP263 4.3 54.1 1.0 N A:SER267 4.3 36.4 1.0 HA A:THR224 4.3 44.2 1.0 HB3 A:ALA266 4.4 50.7 1.0 CB A:PHE223 4.5 38.2 1.0 N A:THR224 4.5 38.3 1.0 CA A:ARG222 4.6 35.8 1.0 H A:ALA266 4.7 46.8 1.0 HA A:ARG222 4.7 43.0 1.0 N A:MET264 4.7 39.8 1.0 HA A:MET264 4.7 42.1 1.0 C A:ALA266 4.7 38.4 1.0 HB2 A:ASN221 4.7 45.1 1.0 CA A:ALA266 4.7 40.6 1.0 HA A:PHE223 4.8 46.5 1.0 HB2 A:ASP263 4.8 43.6 1.0 HD21 A:ASN221 4.8 50.0 1.0 O A:ARG222 4.8 36.1 1.0 HB3 A:ASP263 4.8 43.6 1.0 HA A:LEU220 4.8 44.9 1.0 H A:ARG222 4.8 43.1 1.0 HA A:SER267 4.9 46.7 1.0 CB A:SER267 4.9 37.3 1.0 CA A:THR224 4.9 36.8 1.0 HB3 A:ASN221 5.0 45.1 1.0 CA A:SER267 5.0 38.9 1.0 HA A:ASN221 5.0 47.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Sars-Cov-2 Main Protease After Incubation with Sulfo-Calpeptin


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 After Incubation with Sulfo-Calpeptin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:65.0 occ:1.00 O A:HOH633 2.4 48.6 1.0 O A:HOH541 2.4 50.3 1.0 O A:MET17 2.6 30.1 1.0 O A:HOH627 2.9 57.1 1.0 H A:GLY71 2.9 57.9 1.0 O A:GLY120 2.9 40.9 1.0 HA A:VAL18 3.4 34.6 1.0 C A:MET17 3.6 29.4 1.0 N A:GLY71 3.7 48.1 1.0 HA A:ALA70 3.9 53.4 1.0 HA2 A:GLY71 3.9 64.5 1.0 HB2 A:MET17 4.0 37.7 1.0 C A:GLY120 4.0 40.3 1.0 HD3 A:PRO122 4.1 51.5 1.0 CA A:VAL18 4.2 28.8 1.0 HA A:SER121 4.3 43.7 1.0 CA A:GLY71 4.3 53.7 1.0 N A:VAL18 4.3 29.6 1.0 HA3 A:GLY120 4.4 51.1 1.0 HG13 A:VAL18 4.4 38.4 1.0 C A:ALA70 4.6 44.7 1.0 CB A:MET17 4.6 31.4 1.0 CA A:MET17 4.6 26.2 1.0 HB3 A:MET17 4.6 37.7 1.0 HA3 A:GLY71 4.7 64.5 1.0 CA A:ALA70 4.7 44.4 1.0 O A:HOH661 4.7 49.4 1.0 O A:HOH631 4.8 52.4 1.0 CA A:GLY120 4.8 42.5 1.0 H A:MET17 4.8 34.7 1.0 HD2 A:PRO122 4.9 51.5 1.0 CD A:PRO122 4.9 42.9 1.0 HA2 A:GLY120 5.0 51.1 1.0 O A:GLU14 5.0 28.3 1.0 N A:SER121 5.0 38.8 1.0 HG11 A:VAL18 5.0 38.4 1.0

P.Y.A.Reinke, S.Falke, J.Lieske, W.Ewert, J.Loboda, A.Rahmani Mashhour, M.Hauser, K.Karnicar, A.Usenik, N.Lindic, M.Lach, H.Boehler, T.Beck, R.Cox, H.N.Chapman, W.Hinrichs, D.Turk, S.Guenther, A.Meents. Sulfonated Calpeptin Is A Promising Drug Candidate Against Sars-Cov-2 Infections To Be Published.