Zinc in PDB 8iho: Crystal Structures of Sars-Cov-2 Papain-Like Protease in Complex with Covalent Inhibitors

All present enzymatic activity of Crystal Structures of Sars-Cov-2 Papain-Like Protease in Complex with Covalent Inhibitors:
3.4.19.12;

The structure of Crystal Structures of Sars-Cov-2 Papain-Like Protease in Complex with Covalent Inhibitors, PDB code: 8iho was solved by Q.Wang, H.Hu, M.Li, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.00 / 2.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	118.629, 137.35, 59.571, 90, 90, 90
R / Rfree (%)	25.4 / 30.5

The binding sites of Zinc atom in the Crystal Structures of Sars-Cov-2 Papain-Like Protease in Complex with Covalent Inhibitors (pdb code 8iho). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structures of Sars-Cov-2 Papain-Like Protease in Complex with Covalent Inhibitors, PDB code: 8iho:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structures of Sars-Cov-2 Papain-Like Protease in Complex with Covalent Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structures of Sars-Cov-2 Papain-Like Protease in Complex with Covalent Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:107.0 occ:1.00 SG A:CYS226 2.4 100.2 1.0 SG A:CYS224 2.7 98.7 1.0 CB A:CYS224 2.7 80.4 1.0 CB A:CYS192 2.7 95.0 1.0 SG A:CYS192 2.8 108.5 1.0 SG A:CYS189 2.8 84.4 1.0 CB A:CYS189 2.8 82.4 1.0 CB A:CYS226 3.0 88.2 1.0 N A:CYS192 3.5 92.4 1.0 CA A:CYS192 3.7 92.0 1.0 N A:CYS226 3.7 85.8 1.0 CA A:CYS226 3.9 86.2 1.0 CA A:CYS224 4.1 78.4 1.0 CA A:CYS189 4.3 80.3 1.0 C A:CYS224 4.4 78.9 1.0 C A:THR191 4.5 94.2 1.0 N A:THR225 4.6 77.2 1.0 C A:THR225 4.9 83.0 1.0 C A:CYS189 4.9 82.4 1.0 C A:CYS192 4.9 87.4 1.0 O A:CYS224 5.0 83.0 1.0 N A:CYS224 5.0 75.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structures of Sars-Cov-2 Papain-Like Protease in Complex with Covalent Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structures of Sars-Cov-2 Papain-Like Protease in Complex with Covalent Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:122.9 occ:1.00 SG C:CYS226 2.4 97.1 1.0 SG C:CYS224 2.5 98.6 1.0 SG C:CYS192 2.5 102.3 1.0 SG C:CYS189 2.6 105.9 1.0 CB C:CYS226 2.8 99.1 1.0 CB C:CYS224 2.9 90.7 1.0 CB C:CYS189 3.0 96.6 1.0 CB C:CYS192 3.2 97.1 1.0 N C:CYS226 3.4 95.0 1.0 CA C:CYS226 3.7 98.2 1.0 N C:THR225 4.1 101.1 1.0 CA C:CYS224 4.2 87.1 1.0 N C:CYS192 4.2 90.4 1.0 C C:CYS224 4.3 89.9 1.0 CA C:CYS192 4.3 93.1 1.0 OG1 C:THR191 4.4 95.0 1.0 CA C:CYS189 4.5 93.1 1.0 C C:THR225 4.5 93.2 1.0 C C:CYS226 4.8 93.9 1.0 CA C:THR225 4.9 97.0 1.0 C C:THR191 4.9 92.8 1.0

Q.Wang, G.Chen, J.He, J.Li, M.Xiong, H.Su, M.Li, H.Hu, Y.Xu. Structure-Based Design of Potent Peptidomimetic Inhibitors Covalently Targeting Sars-Cov-2 Papain-Like Protease. Int J Mol Sci V. 24 2023.
ISSN: ESSN 1422-0067
PubMed: 37239980
DOI: 10.3390/IJMS24108633