Sodium in PDB 9f7p: Sars-Cov-2 Papain-Like Protease (Plpro) C112S Mutant

All present enzymatic activity of Sars-Cov-2 Papain-Like Protease (Plpro) C112S Mutant:
3.4.19.12;

The structure of Sars-Cov-2 Papain-Like Protease (Plpro) C112S Mutant, PDB code: 9f7p was solved by A.Camara-Artigas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.69 / 1.70
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.076, 81.076, 135.173, 90, 90, 120
R / Rfree (%)	16.5 / 18

The structure of Sars-Cov-2 Papain-Like Protease (Plpro) C112S Mutant also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Zinc	(Zn)	1 atom

The binding sites of Sodium atom in the Sars-Cov-2 Papain-Like Protease (Plpro) C112S Mutant (pdb code 9f7p). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Sars-Cov-2 Papain-Like Protease (Plpro) C112S Mutant, PDB code: 9f7p:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Sars-Cov-2 Papain-Like Protease (Plpro) C112S Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Sars-Cov-2 Papain-Like Protease (Plpro) C112S Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:43.8 occ:1.00 O A:HOH701 2.1 40.7 1.0 O A:ILE124 2.3 32.4 1.0 O A:LEU121 2.5 29.2 1.0 O A:HOH583 2.5 39.3 1.0 O A:HOH742 2.5 40.4 1.0 O A:HOH749 2.6 41.7 1.0 HH A:TYR137 2.7 42.5 1.0 OH A:TYR137 3.4 35.4 1.0 HA A:GLN122 3.5 37.4 1.0 H A:ILE124 3.5 38.3 1.0 C A:ILE124 3.5 31.0 1.0 H A:LEU126 3.5 40.2 1.0 C A:LEU121 3.6 30.9 1.0 HE2 A:TYR137 3.7 44.1 1.0 HA A:GLU125 3.7 38.6 1.0 N A:ILE124 4.1 31.9 1.0 O A:HOH804 4.1 49.5 1.0 N A:LEU126 4.1 33.5 1.0 CA A:GLN122 4.1 31.1 1.0 O A:HOH774 4.2 46.5 1.0 HG13 A:ILE124 4.2 38.8 1.0 HB3 A:LEU126 4.2 39.2 1.0 C A:GLN122 4.3 32.8 1.0 CE2 A:TYR137 4.4 36.8 1.0 CZ A:TYR137 4.4 34.1 1.0 N A:GLN122 4.4 32.5 1.0 O A:LEU126 4.4 37.2 1.0 N A:GLU125 4.4 33.2 1.0 CA A:GLU125 4.4 32.2 1.0 CA A:ILE124 4.4 31.5 1.0 HB3 A:LEU121 4.5 31.1 1.0 N A:GLN123 4.5 29.5 1.0 H A:GLN123 4.6 35.4 1.0 HA A:LEU121 4.6 34.6 1.0 HG12 A:ILE124 4.7 38.8 1.0 O A:GLN122 4.7 32.7 1.0 CA A:LEU121 4.7 28.8 1.0 C A:GLU125 4.7 35.8 1.0 HD2 A:ARG141 4.8 48.4 1.0 CG1 A:ILE124 4.8 32.3 1.0 O A:HOH760 4.9 50.3 1.0 O A:HOH747 4.9 42.9 1.0 CB A:LEU126 4.9 32.6 1.0 C A:GLN123 5.0 31.5 1.0 CA A:LEU126 5.0 34.6 1.0

Sodium binding site 2 out of 2 in the Sars-Cov-2 Papain-Like Protease (Plpro) C112S Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Sars-Cov-2 Papain-Like Protease (Plpro) C112S Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:40.1 occ:1.00 O A:HOH567 2.3 35.7 1.0 O A:HOH666 2.3 39.0 1.0 O A:HOH708 2.5 38.4 1.0 O A:HOH547 2.5 37.1 1.0 O A:ALA177 2.5 31.2 1.0 HD22 A:ASN129 3.0 52.7 1.0 HD21 A:ASN129 3.4 52.7 1.0 ND2 A:ASN129 3.5 43.9 1.0 H A:LEU179 3.6 39.8 1.0 HA A:ASN178 3.6 41.0 1.0 C A:ALA177 3.7 33.5 1.0 O A:GLN175 3.9 34.4 1.0 H A:ALA177 4.0 37.9 1.0 O A:HOH779 4.1 49.1 1.0 O A:HOH720 4.1 38.7 1.0 O A:HOH623 4.3 43.7 1.0 N A:ALA177 4.4 31.6 1.0 N A:LEU179 4.4 33.1 1.0 O A:PHE174 4.4 33.9 1.0 CA A:ASN178 4.5 34.2 1.0 HA A:GLN175 4.5 42.7 1.0 C A:GLN175 4.5 34.7 1.0 OD1 A:ASP180 4.6 38.2 1.0 N A:ASN178 4.6 32.9 1.0 HB2 A:LEU179 4.7 38.9 1.0 CA A:ALA177 4.7 29.3 1.0 CG A:ASN129 4.8 41.9 1.0 HA A:HIS176 5.0 41.1 1.0 C A:ASN178 5.0 35.6 1.0

A.Camara-Artigas, A.Camara-Artigas. N/A N/A.