Zinc in PDB 8uuf: Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN11941

All present enzymatic activity of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN11941:
3.4.19.12;

The structure of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN11941, PDB code: 8uuf was solved by A.Ansari, B.Tan, F.X.Riuz, E.Arnold, J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.08 / 2.84
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	114.285, 114.285, 219.48, 90, 90, 90
R / Rfree (%)	20.9 / 23.4

The structure of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN11941 also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Zinc atom in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN11941 (pdb code 8uuf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN11941, PDB code: 8uuf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN11941


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN11941 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:45.6 occ:1.00 CL A:CL410 2.2 55.8 1.0 ND1 A:HIS73 2.3 33.4 1.0 CL A:CL409 2.3 56.8 1.0 CG A:HIS73 3.2 47.8 1.0 CE1 A:HIS73 3.3 44.3 1.0 CB A:HIS73 3.3 38.0 1.0 CB A:ASN128 4.1 34.1 1.0 CD2 A:HIS73 4.3 51.6 1.0 NE2 A:HIS73 4.4 49.8 1.0 CA A:HIS73 4.7 44.4 1.0 CG A:PRO129 4.7 44.0 1.0 O A:HIS73 4.8 46.0 1.0 CD A:PRO129 4.8 41.1 1.0 ND2 A:ASN128 4.9 52.8 1.0 N A:PRO129 4.9 46.4 1.0 CG A:ASN128 4.9 43.6 1.0

Zinc binding site 2 out of 4 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN11941


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN11941 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:91.7 occ:1.00 OD2 A:ASP108 2.2 56.1 1.0 O A:HOH549 2.6 71.4 1.0 ND1 A:HIS89 2.6 63.6 1.0 O A:HOH572 2.8 47.2 1.0 CG A:ASP108 3.0 57.7 1.0 OD1 A:ASP108 3.1 87.5 1.0 CE1 A:HIS89 3.3 93.6 1.0 CG A:HIS89 3.8 76.2 1.0 CB A:HIS89 4.2 70.2 1.0 CB A:ASP108 4.5 52.0 1.0 NE2 A:HIS89 4.5 75.6 1.0 NZ A:LYS92 4.6 76.6 1.0 CG1 A:VAL159 4.6 50.9 1.0 CD2 A:HIS89 4.8 78.0 1.0 CA A:HIS89 4.9 59.4 1.0 NE1 A:TRP93 4.9 57.6 1.0

Zinc binding site 3 out of 4 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN11941


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN11941 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:130.8 occ:1.00 SG A:CYS226 2.3 128.8 1.0 SG A:CYS189 2.3 119.9 1.0 SG A:CYS224 2.3 128.3 1.0 SG A:CYS192 2.3 80.6 1.0 CB A:CYS192 3.3 113.5 1.0 CB A:CYS224 3.4 118.7 1.0 CB A:CYS189 3.4 114.6 1.0 CB A:CYS226 3.4 124.2 1.0 N A:CYS192 3.7 116.1 1.0 N A:CYS226 3.9 127.0 1.0 CA A:CYS192 4.1 109.1 1.0 CB A:THR191 4.3 117.7 1.0 CA A:CYS226 4.3 124.9 1.0 O A:HOH589 4.3 75.2 1.0 N A:THR225 4.6 126.4 1.0 CA A:CYS224 4.7 117.5 1.0 C A:THR191 4.7 115.7 1.0 O A:LYS228 4.7 133.5 1.0 OG1 A:THR191 4.7 113.1 1.0 C A:CYS224 4.8 122.5 1.0 CA A:CYS189 4.8 99.9 1.0 CA A:THR191 4.9 108.7 1.0 N A:THR191 4.9 114.0 1.0

Zinc binding site 4 out of 4 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN11941


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN11941 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:149.5 occ:1.00 SG A:CYS111 2.1 66.8 1.0 ND1 A:HIS272 2.3 98.8 1.0 NE1 A:TRP106 3.1 80.5 1.0 CE1 A:HIS272 3.2 101.0 1.0 CG A:HIS272 3.3 94.0 1.0 CB A:CYS111 3.4 70.2 1.0 CB A:HIS272 3.8 72.5 1.0 CE2 A:TRP106 3.8 117.3 1.0 OD1 A:ASN109 3.9 83.0 1.0 CA A:HIS272 3.9 73.1 1.0 CD1 A:TRP106 4.0 104.2 1.0 O A:GLY271 4.1 94.4 1.0 CZ2 A:TRP106 4.1 116.2 1.0 O A:HOH583 4.2 54.7 1.0 NE2 A:HIS272 4.3 80.7 1.0 N A:CYS111 4.3 51.6 1.0 CA A:ASN109 4.3 66.1 1.0 CD2 A:HIS272 4.4 85.7 1.0 CA A:CYS111 4.5 52.6 1.0 CB A:ASN109 4.7 62.2 1.0 C A:ASN109 4.7 65.9 1.0 CG A:ASN109 4.7 71.1 1.0 N A:TYR273 4.8 84.8 1.0 C A:GLY271 4.8 71.5 1.0 N A:HIS272 4.8 69.7 1.0 C A:HIS272 4.9 79.6 1.0 O A:HOH592 5.0 86.6 1.0 O A:ASN109 5.0 61.6 1.0 CD2 A:TRP106 5.0 116.5 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