Sodium in PDB 7bfb: Crystal Structure of Ebselen Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.

All present enzymatic activity of Crystal Structure of Ebselen Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.:
2.7.7.48; 3.4.19.12; 3.4.22.69; 3.6.4.12; 3.6.4.13;

The structure of Crystal Structure of Ebselen Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2., PDB code: 7bfb was solved by E.Costanzi, N.Demitri, B.Giabbai, P.Storici, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.30 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.739, 100.455, 104.597, 90, 90, 90
R / Rfree (%)	18.4 / 19.9

The binding sites of Sodium atom in the Crystal Structure of Ebselen Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. (pdb code 7bfb). 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 Ebselen Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2., PDB code: 7bfb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Ebselen Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.


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 Ebselen Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:53.2 occ:1.00 OD1 A:ASP263 2.4 64.7 1.0 OD1 A:ASN221 2.5 47.8 1.0 O A:PHE223 2.6 45.9 1.0 O A:ASP263 2.7 38.1 1.0 O A:ASN221 2.7 36.0 1.0 HG A:SER267 2.8 73.3 1.0 HB3 A:ALA266 3.0 49.1 1.0 H A:ASN221 3.1 49.1 1.0 C A:ASP263 3.4 43.4 1.0 OG A:SER267 3.4 61.0 1.0 HA A:ASP263 3.4 50.9 1.0 CG A:ASP263 3.5 64.3 1.0 C A:ASN221 3.6 45.4 1.0 H A:PHE223 3.6 52.4 1.0 CG A:ASN221 3.7 48.2 1.0 H A:SER267 3.7 50.6 1.0 C A:PHE223 3.8 47.1 1.0 CA A:ASP263 3.8 42.4 1.0 N A:ASN221 3.9 41.0 1.0 HB3 A:ASP263 3.9 61.8 1.0 CB A:ASP263 4.0 51.5 1.0 N A:PHE223 4.0 43.7 1.0 CB A:ALA266 4.0 40.9 1.0 N A:SER267 4.2 42.2 1.0 CA A:ASN221 4.2 43.2 1.0 HB1 A:ALA266 4.2 49.1 1.0 HA A:MET264 4.4 52.8 1.0 CA A:PHE223 4.4 45.2 1.0 HB2 A:ALA266 4.5 49.1 1.0 N A:MET264 4.5 40.8 1.0 HD21 A:ASN221 4.5 58.9 1.0 OD2 A:ASP263 4.5 70.8 1.0 ND2 A:ASN221 4.5 49.1 1.0 N A:ARG222 4.5 44.3 1.0 HA A:THR224 4.5 55.2 1.0 CB A:ASN221 4.5 43.3 1.0 C A:ARG222 4.6 51.0 1.0 HB2 A:PHE223 4.6 62.3 1.0 CB A:SER267 4.6 43.3 1.0 H A:ALA266 4.6 40.4 1.0 HA A:ARG222 4.7 54.2 1.0 HA A:LEU220 4.7 46.6 1.0 C A:ALA266 4.8 35.9 1.0 HA A:SER267 4.8 47.7 1.0 CA A:ALA266 4.8 36.2 1.0 CA A:SER267 4.8 39.7 1.0 HB2 A:SER267 4.8 51.9 1.0 HB3 A:LEU220 4.9 48.7 1.0 CA A:ARG222 4.9 45.2 1.0 HD22 A:LEU220 4.9 56.4 1.0 N A:THR224 4.9 41.5 1.0 HB2 A:ASP263 4.9 61.8 1.0 CA A:MET264 4.9 44.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Ebselen Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.


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 Ebselen Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1006 b:58.4 occ:1.00 OD1 B:ASP263 2.1 72.5 1.0 OD1 B:ASN221 2.2 61.6 1.0 O B:PHE223 2.4 60.5 1.0 O B:ASN221 2.5 54.5 1.0 O B:HOH1106 2.6 55.9 1.0 O B:ASP263 2.8 51.3 1.0 H B:PHE223 2.9 71.3 1.0 H B:ASN221 3.1 71.0 1.0 HB3 B:ALA266 3.1 71.4 1.0 CG B:ASP263 3.2 71.8 1.0 C B:ASN221 3.3 56.6 1.0 N B:PHE223 3.4 59.4 1.0 CG B:ASN221 3.4 52.7 1.0 C B:PHE223 3.5 63.9 1.0 HA B:ASP263 3.5 77.9 1.0 C B:ASP263 3.7 57.9 1.0 N B:ASN221 3.8 59.1 1.0 OG B:SER267 3.9 60.5 1.0 CA B:PHE223 3.9 64.9 1.0 CA B:ASN221 3.9 51.6 1.0 CA B:ASP263 4.0 64.9 1.0 CB B:ALA266 4.0 59.5 1.0 OD2 B:ASP263 4.0 72.9 1.0 HB2 B:PHE223 4.1 69.8 1.0 C B:ARG222 4.1 64.5 1.0 HG B:SER267 4.1 72.7 1.0 HB1 B:ALA266 4.1 71.4 1.0 N B:ARG222 4.1 62.5 1.0 H B:SER267 4.2 70.7 1.0 CB B:ASP263 4.2 61.2 1.0 CB B:ASN221 4.2 56.9 1.0 HD21 B:ASN221 4.3 70.9 1.0 ND2 B:ASN221 4.3 59.1 1.0 HB2 B:ALA266 4.4 71.4 1.0 CA B:ARG222 4.5 65.9 1.0 HA B:ARG222 4.5 79.1 1.0 CB B:PHE223 4.6 58.2 1.0 HA B:THR224 4.6 82.6 1.0 N B:SER267 4.6 58.9 1.0 N B:THR224 4.7 61.3 1.0 HB2 B:ASN221 4.7 68.3 1.0 HA B:MET264 4.7 62.7 1.0 HB2 B:ASP263 4.7 73.4 1.0 HA B:PHE223 4.8 77.9 1.0 HA B:LEU220 4.8 60.2 1.0 H B:ARG222 4.8 75.0 1.0 N B:MET264 4.8 56.1 1.0 O B:ARG222 4.8 69.0 1.0 HA B:ASN221 4.9 61.9 1.0 HB3 B:ASP263 4.9 73.4 1.0 HG23 B:ILE259 4.9 73.9 1.0 HB3 B:ASN221 5.0 68.3 1.0

E.Costanzi, N.Demitri, B.Giabbai, P.Storici. Crystal Structure of Ebselen Covalently Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. To Be Published.