Sodium in PDB 7p51: Crystal Structure of the Sars-Cov-2 Main Protease Complexed with Fragment F01

All present enzymatic activity of Crystal Structure of the Sars-Cov-2 Main Protease Complexed with Fragment F01:
3.4.22.69;

The structure of Crystal Structure of the Sars-Cov-2 Main Protease Complexed with Fragment F01, PDB code: 7p51 was solved by X.Hanoulle, D.Moschidi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.44 / 1.47
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.17, 53.56, 44.88, 90, 101.24, 90
R / Rfree (%)	18.1 / 21.6

The structure of Crystal Structure of the Sars-Cov-2 Main Protease Complexed with Fragment F01 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the Sars-Cov-2 Main Protease Complexed with Fragment F01 (pdb code 7p51). 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 the Sars-Cov-2 Main Protease Complexed with Fragment F01, PDB code: 7p51:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Sars-Cov-2 Main Protease Complexed with Fragment F01


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 the Sars-Cov-2 Main Protease Complexed with Fragment F01 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:25.9 occ:1.00 H A:GLY174 2.1 12.9 1.0 HA A:ALA173 2.5 14.2 1.0 HB2 A:TYR182 2.6 16.0 1.0 O A:PHE134 2.8 25.6 1.0 O A:TYR182 2.8 18.8 1.0 N A:GLY174 3.0 12.9 1.0 HD2 A:PHE185 3.1 17.8 1.0 O A:GLY174 3.2 13.1 1.0 CA A:ALA173 3.2 14.2 1.0 HB1 A:ALA173 3.3 15.4 1.0 HB2 A:ALA173 3.4 15.4 1.0 CB A:ALA173 3.5 15.4 1.0 CB A:TYR182 3.5 16.0 1.0 HD2 A:PHE181 3.5 16.4 1.0 C A:ALA173 3.6 13.4 1.0 H A:TYR182 3.7 14.9 1.0 C A:TYR182 3.7 15.8 1.0 HB3 A:TYR182 3.7 16.0 1.0 HE1 A:TYR161 3.8 17.0 1.0 HE2 A:PHE185 3.8 18.9 1.0 HA A:THR135 3.8 18.0 1.0 CD2 A:PHE185 3.8 17.8 1.0 CA A:TYR182 4.0 15.0 1.0 HB3 A:PHE134 4.0 18.1 1.0 C A:PHE134 4.0 19.8 1.0 C A:GLY174 4.0 12.7 1.0 CA A:GLY174 4.1 12.5 1.0 N A:TYR182 4.1 14.9 1.0 CE2 A:PHE185 4.2 18.9 1.0 HD2 A:TYR182 4.3 14.6 1.0 O A:HIS172 4.4 16.1 1.0 HH A:TYR161 4.4 13.9 0.0 CD2 A:PHE181 4.5 16.4 1.0 HB3 A:ALA173 4.5 15.4 1.0 N A:ALA173 4.5 14.3 1.0 HE1 A:MET130 4.5 25.0 1.0 HA3 A:GLY174 4.6 12.5 1.0 CG A:TYR182 4.6 15.7 1.0 HB2 A:PHE185 4.6 17.6 1.0 CA A:THR135 4.7 18.0 1.0 CE1 A:TYR161 4.7 17.0 1.0 HA2 A:GLY174 4.7 12.5 1.0 HB3 A:PHE181 4.7 15.2 1.0 HE2 A:PHE181 4.8 18.8 1.0 N A:THR135 4.8 17.5 1.0 HA3 A:GLY183 4.8 16.8 1.0 CB A:PHE134 4.8 18.1 1.0 N A:GLY183 4.8 16.7 1.0 CD2 A:TYR182 4.9 14.6 1.0 O A:ALA173 4.9 13.4 1.0 C A:HIS172 4.9 15.6 1.0 CG A:PHE185 4.9 18.8 1.0 HA A:TYR182 4.9 15.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Sars-Cov-2 Main Protease Complexed with Fragment F01


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 the Sars-Cov-2 Main Protease Complexed with Fragment F01 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:24.4 occ:1.00 HD1 A:HIS164 2.1 14.7 0.0 H A:HIS41 2.4 16.5 1.0 HD2 A:HIS41 2.5 18.8 1.0 HG2 A:ARG40 2.9 17.0 1.0 OD2 A:ASP187 2.9 19.9 1.0 ND1 A:HIS164 2.9 14.7 1.0 HB3 A:HIS41 2.9 17.9 1.0 CD2 A:HIS41 3.1 18.8 1.0 H A:ARG40 3.1 13.8 1.0 HB3 A:PRO39 3.1 14.3 1.0 N A:HIS41 3.1 16.5 1.0 HB2 A:ASP187 3.2 16.6 1.0 HB3 A:ASP187 3.3 16.6 1.0 HE1 A:HIS164 3.3 13.5 1.0 HG3 A:ARG40 3.4 17.0 1.0 N A:ARG40 3.4 13.8 1.0 CE1 A:HIS164 3.5 13.5 1.0 CG A:HIS41 3.5 18.3 1.0 CB A:HIS41 3.5 17.9 1.0 CG A:ARG40 3.6 17.0 1.0 CB A:ASP187 3.6 16.6 1.0 O A:CYS85 3.6 16.6 1.0 HB3 A:CYS85 3.6 14.9 1.0 CG A:ASP187 3.7 16.7 1.0 CB A:PRO39 3.8 14.3 1.0 HA A:PRO39 3.9 14.2 1.0 CA A:HIS41 3.9 18.4 1.0 C A:PRO39 3.9 13.7 1.0 HB2 A:PRO39 3.9 14.3 1.0 C A:ARG40 4.0 17.6 1.0 HE A:ARG40 4.0 16.9 1.0 HB3 A:HIS164 4.1 13.6 1.0 CA A:PRO39 4.1 14.2 1.0 CG A:HIS164 4.1 13.6 1.0 CA A:ARG40 4.1 15.1 1.0 NE2 A:HIS41 4.2 21.6 1.0 HH A:TYR54 4.2 17.2 0.0 CB A:ARG40 4.4 16.5 1.0 HA A:HIS41 4.4 18.4 1.0 HB2 A:HIS41 4.4 17.9 1.0 OH A:TYR54 4.4 17.2 1.0 HE2 A:HIS41 4.5 21.6 0.0 CB A:CYS85 4.6 14.9 1.0 CB A:HIS164 4.6 13.6 1.0 C A:CYS85 4.7 16.6 1.0 NE A:ARG40 4.7 16.9 1.0 CD A:ARG40 4.7 16.7 1.0 NE2 A:HIS164 4.7 14.9 1.0 ND1 A:HIS41 4.7 20.0 1.0 O A:PRO39 4.8 16.4 1.0 HB3 A:ARG40 4.8 16.5 1.0 HE1 A:PHE181 4.9 17.3 1.0 HZ A:PHE181 4.9 17.9 1.0 HE1 A:TYR54 4.9 18.4 1.0 CZ A:TYR54 4.9 18.0 1.0 OD1 A:ASP187 4.9 18.3 1.0 HA A:CYS85 4.9 15.7 1.0

F.X.Cantrelle, E.Boll, L.Brier, D.Moschidi, S.Belouzard, V.Landry, F.Leroux, F.Dewitte, I.Landrieu, J.Dubuisson, B.Deprez, J.Charton, X.Hanoulle. uc(Nmr) Spectroscopy of the Main Protease of Sars-Cov-2 and Fragment-Based Screening Identify Three Protein Hotspots and An Antiviral Fragment. Angew.Chem.Int.Ed.Engl. 2021.
ISSN: ESSN 1521-3773
PubMed: 34570415
DOI: 10.1002/ANIE.202109965