Sodium in PDB 7phz: Crystal Structure of X77 Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 in Spacegroup P2(1)2(1)2(1).

The structure of Crystal Structure of X77 Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 in Spacegroup P2(1)2(1)2(1)., PDB code: 7phz was solved by E.Costanzi, N.Demitri, P.Storici, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.33 / 1.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.686, 100.578, 104.395, 90, 90, 90
R / Rfree (%)	16.1 / 18.2

The structure of Crystal Structure of X77 Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 in Spacegroup P2(1)2(1)2(1). also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of X77 Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 in Spacegroup P2(1)2(1)2(1). (pdb code 7phz). 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 X77 Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 in Spacegroup P2(1)2(1)2(1)., PDB code: 7phz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of X77 Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 in Spacegroup P2(1)2(1)2(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 X77 Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 in Spacegroup P2(1)2(1)2(1). within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:36.7 occ:1.00 OD1 B:ASP263 2.1 43.6 1.0 OD1 B:ASN221 2.2 28.1 1.0 O B:PHE223 2.3 26.1 1.0 O B:HOH521 2.4 31.1 1.0 O B:ASN221 2.5 30.6 1.0 HB3 B:ALA266 3.0 40.0 1.0 H B:PHE223 3.0 27.3 1.0 O B:ASP263 3.1 33.0 1.0 H B:ASN221 3.2 36.5 1.0 C B:ASN221 3.3 27.3 1.0 CG B:ASN221 3.3 29.2 1.0 CG B:ASP263 3.4 48.4 1.0 N B:PHE223 3.4 22.8 1.0 C B:PHE223 3.4 28.2 1.0 HA B:ASP263 3.5 51.3 1.0 CB B:ALA266 3.9 33.4 1.0 C B:ASP263 3.9 41.0 1.0 N B:ASN221 3.9 30.4 1.0 CA B:PHE223 3.9 25.7 1.0 HB1 B:ALA266 4.0 40.0 1.0 CA B:ASN221 4.0 28.8 1.0 C B:ARG222 4.0 23.6 1.0 CA B:ASP263 4.1 42.7 1.0 HB2 B:PHE223 4.1 30.0 1.0 HD21 B:ASN221 4.1 40.0 1.0 N B:ARG222 4.1 24.2 1.0 ND2 B:ASN221 4.2 33.3 1.0 H B:SER267 4.2 40.2 1.0 OD2 B:ASP263 4.2 54.6 1.0 CB B:ASN221 4.3 28.7 1.0 HA B:THR224 4.3 39.9 1.0 OG B:SER267 4.3 33.0 1.0 CB B:ASP263 4.3 47.1 1.0 HB2 B:ALA266 4.3 40.0 1.0 CA B:ARG222 4.5 23.7 1.0 HA B:ARG222 4.5 28.3 1.0 N B:SER267 4.5 33.5 1.0 N B:THR224 4.6 29.0 1.0 CB B:PHE223 4.6 25.0 1.0 HG B:SER267 4.6 39.6 1.0 O B:ARG222 4.7 24.5 1.0 HB2 B:ASN221 4.8 34.5 1.0 HA B:PHE223 4.8 30.8 1.0 H B:ARG222 4.8 29.0 1.0 C B:ALA266 4.8 38.4 1.0 HA B:LEU220 4.9 34.4 1.0 CA B:ALA266 4.9 34.9 1.0 H B:ALA266 4.9 39.0 1.0 HG23 B:ILE259 4.9 42.1 0.6 HA B:ASN221 4.9 34.6 1.0 HB2 B:ASP263 4.9 56.5 1.0 HB3 B:ASP263 4.9 56.5 1.0 CA B:THR224 4.9 33.2 1.0 HB3 B:ASN221 5.0 34.5 1.0 HD22 B:ASN221 5.0 40.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of X77 Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 in Spacegroup P2(1)2(1)2(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 X77 Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 in Spacegroup P2(1)2(1)2(1). within 5.0Å range: probe atom residue distance (Å) B Occ B:Na407 b:44.4 occ:1.00 HH B:TYR101 1.7 33.6 1.0 OD2 B:ASP33 2.2 42.2 1.0 HB2 B:ASP33 2.4 39.9 1.0 OH B:TYR101 2.5 28.0 1.0 O B:HOH547 2.6 32.1 1.0 HE1 B:TYR101 3.0 31.3 1.0 CG B:ASP33 3.0 41.5 1.0 CB B:ASP33 3.1 33.2 1.0 CZ B:TYR101 3.4 26.7 1.0 CE1 B:TYR101 3.6 26.0 1.0 HB3 B:ASP33 3.7 39.9 1.0 HB3 B:LEU32 3.8 26.8 1.0 O B:LEU32 3.9 24.6 1.0 O B:HOH515 4.0 43.1 1.0 C B:LEU32 4.1 25.5 1.0 HB2 B:LEU32 4.1 26.8 1.0 N B:ASP33 4.2 29.0 1.0 OD1 B:ASP33 4.2 42.1 1.0 CA B:ASP33 4.3 29.9 1.0 HG21 B:THR98 4.3 34.9 1.0 CB B:LEU32 4.4 22.3 1.0 H B:ASP33 4.5 34.9 1.0 CE2 B:TYR101 4.7 25.6 1.0 OH B:TYR37 4.9 29.7 1.0 CA B:LEU32 4.9 24.7 1.0 CD1 B:TYR101 4.9 26.0 1.0 HA B:ASP33 4.9 35.9 1.0 H B:ASP34 5.0 35.9 1.0

E.Costanzi, N.Demitri, P.Storici. Crystal Structure of X77 Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 in Spacegroup P2(1)2(1)2(1). To Be Published.