Sodium in PDB 7ybg: Crystal Structure of the Sars-Cov-2 Papain-Like Protease (C111S Mutant)

All present enzymatic activity of Crystal Structure of the Sars-Cov-2 Papain-Like Protease (C111S Mutant):
3.4.19.12;

The structure of Crystal Structure of the Sars-Cov-2 Papain-Like Protease (C111S Mutant), PDB code: 7ybg was solved by R.Zeng, J.Lei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.42 / 1.90
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	80.856, 80.856, 135.938, 90, 90, 120
R / Rfree (%)	17.3 / 20.7

The structure of Crystal Structure of the Sars-Cov-2 Papain-Like Protease (C111S Mutant) also contains other interesting chemical elements:

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

The binding sites of Sodium atom in the Crystal Structure of the Sars-Cov-2 Papain-Like Protease (C111S Mutant) (pdb code 7ybg). 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 Papain-Like Protease (C111S Mutant), PDB code: 7ybg:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Sars-Cov-2 Papain-Like Protease (C111S Mutant)


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 Papain-Like Protease (C111S Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:31.5 occ:1.00 O A:HOH652 2.5 25.0 1.0 O1A A:MLA402 2.7 26.8 1.0 O A:ASN109 2.8 25.2 1.0 N A:TYR112 3.1 23.4 1.0 C1 A:MLA402 3.2 26.5 1.0 OG A:SER111 3.2 23.9 1.0 CD1 A:TYR112 3.2 22.5 1.0 O1B A:MLA402 3.3 25.4 1.0 N A:SER111 3.5 23.7 1.0 CB A:TYR112 3.6 22.1 1.0 C A:ASN109 3.7 24.8 1.0 O A:HOH683 3.7 24.7 1.0 CG A:TYR112 3.9 22.0 1.0 CA A:TYR112 3.9 23.0 1.0 C A:SER111 4.0 22.6 1.0 CA A:SER111 4.0 23.1 1.0 CB A:SER111 4.1 22.7 1.0 C A:ASN110 4.1 24.4 1.0 CE1 A:TYR112 4.3 22.9 1.0 C2 A:MLA402 4.4 26.9 1.0 N A:ASN110 4.4 24.7 1.0 CA A:ASN110 4.4 24.4 1.0 CD2 A:TYR273 4.4 21.7 1.0 O A:GLY163 4.5 22.2 1.0 CA A:ASN109 4.6 24.8 1.0 CB A:ASN109 4.7 25.4 1.0 N A:GLY163 4.7 23.3 1.0 CD2 A:LEU162 4.8 27.3 1.0 O A:ASN110 5.0 23.9 1.0 CE2 A:TYR273 5.0 21.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Sars-Cov-2 Papain-Like Protease (C111S Mutant)


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 Papain-Like Protease (C111S Mutant) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:25.2 occ:1.00 O A:HOH816 2.3 50.1 1.0 O A:HOH719 3.0 23.3 1.0 N A:VAL159 3.1 24.1 1.0 OG A:SER85 3.4 26.9 0.5 CA A:ALA86 3.5 23.3 1.0 N A:ALA86 3.6 22.9 1.0 CA A:THR158 3.7 24.0 1.0 CG2 A:VAL159 3.7 26.6 1.0 C A:SER85 3.8 23.5 1.0 CB A:THR158 3.8 25.3 1.0 CB A:VAL159 3.8 25.6 1.0 C A:THR158 3.9 23.9 1.0 O A:SER85 3.9 21.9 1.0 CB A:ALA86 4.0 23.5 1.0 CB A:SER85 4.1 25.3 0.5 CA A:VAL159 4.1 24.7 1.0 O A:HOH548 4.1 48.1 1.0 CB A:SER85 4.1 24.8 0.5 CD2 A:HIS89 4.2 32.3 1.0 CG2 A:THR158 4.2 25.3 1.0 O A:HOH875 4.3 35.4 1.0 O A:HOH926 4.3 28.3 1.0 CA A:SER85 4.6 23.9 0.5 CA A:SER85 4.6 23.8 0.5 NE2 A:HIS89 4.6 34.1 1.0 O A:HOH675 4.7 44.1 1.0 O A:ARG82 4.8 24.8 1.0 C A:ALA86 4.9 23.5 1.0 O A:VAL159 4.9 25.5 1.0

R.Zeng, J.Lei. Crystal Structure of the Sars-Cov-2 Papain-Like Protease (C111S Mutant) To Be Published.