Chlorine in PDB 8uug: Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12303

All present enzymatic activity of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12303:
3.4.19.12;

The structure of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12303, PDB code: 8uug was solved by A.Ansari, B.Tan, F.X.Ruiz, E.Arnold, J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.05 / 2.74
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	114.2, 114.2, 218.557, 90, 90, 90
R / Rfree (%)	20 / 23.3

The structure of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12303 also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Zinc	(Zn)	5 atoms

The binding sites of Chlorine atom in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12303 (pdb code 8uug). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12303, PDB code: 8uug:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12303


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12303 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl409 b:70.4 occ:1.00 N A:LYS306 3.2 61.4 1.0 OG1 A:THR259 3.5 48.3 1.0 CA A:PHE258 3.6 49.4 1.0 C A:PHE258 3.7 46.0 1.0 N A:THR259 3.7 44.9 1.0 CA A:TYR305 3.9 44.0 1.0 CB A:LYS306 3.9 48.6 1.0 N A:PHE258 4.0 52.6 1.0 C A:TYR305 4.0 49.8 1.0 CA A:LYS306 4.1 48.9 1.0 O A:HOH617 4.2 53.6 1.0 CG A:LYS306 4.2 57.8 1.0 CB A:TYR305 4.3 45.6 1.0 O A:THR257 4.3 50.9 1.0 O A:PHE258 4.3 46.5 1.0 C A:THR257 4.3 54.1 1.0 CD2 A:TYR305 4.5 55.2 1.0 CA A:THR259 4.5 42.2 1.0 CB A:THR259 4.6 42.5 1.0 O A:LYS306 4.6 58.0 1.0 O A:PHE304 4.8 44.9 1.0 CG A:TYR305 4.8 57.8 1.0 C A:LYS306 4.9 49.5 1.0 CB A:PHE258 5.0 49.7 1.0

Chlorine binding site 2 out of 4 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12303


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12303 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl410 b:89.2 occ:1.00 CZ A:TYR268 4.2 66.4 1.0 CE2 A:TYR268 4.3 66.3 1.0 CE1 A:TYR268 4.3 68.3 1.0 F11 A:XXW401 4.4 99.3 1.0 CD2 A:TYR268 4.5 69.2 1.0 C7 A:XXW401 4.5 55.3 1.0 CD1 A:TYR268 4.6 65.8 1.0 OH A:TYR268 4.6 63.0 1.0 CG A:TYR268 4.7 68.8 1.0 C14 A:XXW401 4.8 50.7 1.0

Chlorine binding site 3 out of 4 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12303


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12303 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl411 b:48.4 occ:1.00 ZN A:ZN404 2.2 42.6 1.0 O A:HOH522 3.6 56.9 1.0 CL A:CL412 3.7 46.9 1.0 CD A:PRO129 3.7 42.5 1.0 CG A:PRO129 3.7 34.6 1.0 CD2 A:HIS175 3.7 52.9 1.0 CB A:ASN128 3.8 45.7 1.0 CA A:HIS175 3.9 40.1 1.0 ND1 A:HIS73 3.9 37.9 1.0 CG A:HIS175 4.1 54.6 1.0 CB A:HIS73 4.1 39.0 1.0 CB A:HIS175 4.1 45.1 1.0 O A:HOH608 4.1 50.5 1.0 ND2 A:ASN128 4.3 46.4 1.0 O A:HIS175 4.4 45.1 1.0 CG A:HIS73 4.4 40.6 1.0 C A:HIS175 4.5 48.0 1.0 N A:PRO129 4.5 43.0 1.0 O A:GLN174 4.5 47.2 1.0 CG A:ASN128 4.6 48.4 1.0 NE2 A:HIS175 4.7 60.7 1.0 CA A:ASN128 4.9 43.6 1.0 C A:ASN128 4.9 42.6 1.0 CE1 A:HIS73 5.0 41.9 1.0 CB A:PRO129 5.0 38.5 1.0

Chlorine binding site 4 out of 4 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12303


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12303 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl412 b:46.9 occ:1.00 ZN A:ZN404 2.2 42.6 1.0 ND1 A:HIS73 3.6 37.9 1.0 CL A:CL411 3.7 48.4 1.0 CB A:HIS73 3.8 39.0 1.0 O A:HOH654 3.8 55.1 1.0 O A:HIS73 4.1 45.0 1.0 CG A:HIS73 4.1 40.6 1.0 CZ A:PHE69 4.3 44.1 1.0 O A:HOH608 4.4 50.5 1.0 CE1 A:PHE69 4.6 39.1 1.0 CA A:HIS73 4.7 42.2 1.0 CE1 A:HIS73 4.7 41.9 1.0 C A:HIS73 4.7 43.5 1.0

B.Tan, X.Zhang, A.Ansari, P.Jadhav, H.Tan, K.Li, A.Chopra, A.Ford, X.Chi, F.X.Ruiz, E.Arnold, X.Deng, J.Wang. Design of A Sars-Cov-2 Papain-Like Protease Inhibitor with Antiviral Efficacy in A Mouse Model Science V. 383 1434 2024.
ISSN: ESSN 1095-9203
DOI: 10.1126/SCIENCE.ADM9724