Sodium in PDB 9f7s: Sars-Cov-2 Papain-Like Protease (Plpro) C112S-K191D-K229R Mutant

All present enzymatic activity of Sars-Cov-2 Papain-Like Protease (Plpro) C112S-K191D-K229R Mutant:
3.4.19.12;

The structure of Sars-Cov-2 Papain-Like Protease (Plpro) C112S-K191D-K229R Mutant, PDB code: 9f7s 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)	19.79 / 1.80
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.819, 81.819, 135.647, 90, 90, 120
R / Rfree (%)	16 / 18.4

The structure of Sars-Cov-2 Papain-Like Protease (Plpro) C112S-K191D-K229R Mutant also contains other interesting chemical elements:

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

The binding sites of Sodium atom in the Sars-Cov-2 Papain-Like Protease (Plpro) C112S-K191D-K229R Mutant (pdb code 9f7s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Sars-Cov-2 Papain-Like Protease (Plpro) C112S-K191D-K229R Mutant, PDB code: 9f7s:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Sars-Cov-2 Papain-Like Protease (Plpro) C112S-K191D-K229R 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-K191D-K229R Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:35.5 occ:1.00 O A:HOH645 2.1 32.3 1.0 O A:ILE124 2.2 24.9 1.0 O A:LEU121 2.4 21.3 1.0 O A:HOH741 2.5 34.7 1.0 O A:HOH540 2.5 30.4 1.0 O A:HOH712 2.6 32.1 1.0 H A:LEU126 3.4 28.1 1.0 C A:ILE124 3.4 24.1 1.0 OH A:TYR137 3.4 29.2 1.0 H A:ILE124 3.5 27.2 1.0 HA A:GLN122 3.6 27.3 1.0 C A:LEU121 3.6 21.9 1.0 HA A:GLU125 3.8 27.8 1.0 HE2 A:TYR137 3.8 31.0 1.0 HH A:TYR137 3.9 35.0 1.0 HG13 A:ILE124 4.0 28.3 1.0 N A:LEU126 4.0 23.4 1.0 N A:ILE124 4.1 22.6 1.0 HB3 A:LEU126 4.1 29.6 1.0 O A:HOH826 4.2 47.4 1.0 CA A:GLN122 4.2 22.8 1.0 O A:HOH777 4.3 36.5 1.0 N A:GLU125 4.3 22.3 1.0 O A:LEU126 4.3 27.2 1.0 C A:GLN122 4.3 24.5 1.0 CA A:ILE124 4.4 23.5 1.0 N A:GLN122 4.4 20.4 1.0 CZ A:TYR137 4.4 25.5 1.0 CA A:GLU125 4.4 23.1 1.0 CE2 A:TYR137 4.4 25.8 1.0 HB3 A:LEU121 4.5 23.0 1.0 N A:GLN123 4.6 20.5 1.0 HA A:LEU121 4.6 20.4 1.0 HG12 A:ILE124 4.6 28.3 1.0 H A:GLN123 4.6 24.6 1.0 C A:GLU125 4.7 28.7 1.0 CA A:LEU121 4.7 17.0 1.0 CG1 A:ILE124 4.7 23.6 1.0 O A:GLN122 4.7 24.3 1.0 CB A:LEU126 4.8 24.7 1.0 CA A:LEU126 4.9 24.9 1.0 O A:HOH788 4.9 48.5 1.0 O A:HOH755 4.9 39.3 1.0 HB2 A:LEU126 4.9 29.6 1.0 C A:GLN123 5.0 21.7 1.0

Sodium binding site 2 out of 3 in the Sars-Cov-2 Papain-Like Protease (Plpro) C112S-K191D-K229R 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-K191D-K229R Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:31.2 occ:1.00 O A:HOH666 2.3 32.2 1.0 O A:HOH519 2.4 31.8 1.0 O A:HOH602 2.5 31.0 1.0 O A:ALA177 2.5 23.2 1.0 O A:HOH732 2.6 30.2 1.0 HD22 A:ASN129 3.1 47.2 1.0 H A:LEU179 3.5 27.1 1.0 HA A:ASN178 3.5 27.6 1.0 HD21 A:ASN129 3.5 47.2 1.0 ND2 A:ASN129 3.6 39.3 1.0 C A:ALA177 3.7 26.5 1.0 H A:ALA177 3.9 29.2 1.0 O A:HOH717 4.0 32.3 1.0 O A:GLN175 4.0 26.6 1.0 O A:HOH792 4.1 37.6 1.0 O A:HOH569 4.2 38.1 1.0 N A:LEU179 4.3 22.6 1.0 O A:PHE174 4.3 22.6 1.0 CA A:ASN178 4.3 23.0 1.0 OD1 A:ASP180 4.3 38.5 1.0 N A:ALA177 4.4 24.3 1.0 HB2 A:LEU179 4.5 28.9 1.0 N A:ASN178 4.5 23.3 1.0 C A:GLN175 4.6 26.7 1.0 HA A:GLN175 4.7 29.1 1.0 CA A:ALA177 4.7 19.8 1.0 C A:ASN178 4.9 26.6 1.0 CG A:ASN129 4.9 34.9 1.0 CG A:ASP180 5.0 34.1 1.0

Sodium binding site 3 out of 3 in the Sars-Cov-2 Papain-Like Protease (Plpro) C112S-K191D-K229R Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Sars-Cov-2 Papain-Like Protease (Plpro) C112S-K191D-K229R Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:45.6 occ:1.00 O A:HOH768 2.4 42.3 1.0 O A:HOH637 2.4 33.3 1.0 O A:HOH868 2.5 48.5 1.0 OG A:SER86 2.5 37.7 1.0 O A:HOH635 2.6 24.1 1.0 O A:HOH779 2.7 31.1 1.0 HB2 A:SER86 3.4 39.4 1.0 CB A:SER86 3.4 32.9 1.0 HA A:SER86 3.6 27.3 1.0 HE2 A:HIS90 3.8 33.5 1.0 O A:HOH767 3.8 40.8 1.0 O A:HOH553 4.0 28.9 1.0 CA A:SER86 4.0 22.8 1.0 O A:HOH769 4.1 35.0 1.0 HB3 A:SER86 4.3 39.4 1.0 O A:SER86 4.3 21.6 1.0 O A:HOH511 4.4 39.5 1.0 O A:HOH678 4.5 35.0 1.0 C A:SER86 4.5 23.6 1.0 NE2 A:HIS90 4.5 27.9 1.0 HD2 A:HIS90 4.7 31.1 1.0 O A:HOH618 4.8 43.0 1.0

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