Zinc in PDB 8eua: Structure of Sars-COV2 Plpro Bound to A Covalent Inhibitor

All present enzymatic activity of Structure of Sars-COV2 Plpro Bound to A Covalent Inhibitor:
3.4.19.12;

The structure of Structure of Sars-COV2 Plpro Bound to A Covalent Inhibitor, PDB code: 8eua was solved by I.I.Mathews, S.Pokhrel, S.Wakatsuki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.05 / 3.10
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	112.33, 112.33, 217.33, 90, 90, 90
R / Rfree (%)	19.1 / 25.3

The binding sites of Zinc atom in the Structure of Sars-COV2 Plpro Bound to A Covalent Inhibitor (pdb code 8eua). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of Sars-COV2 Plpro Bound to A Covalent Inhibitor, PDB code: 8eua:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of Sars-COV2 Plpro Bound to A Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Sars-COV2 Plpro Bound to A Covalent Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:163.4 occ:1.00 SG A:CYS224 2.3 140.9 1.0 SG A:CYS192 2.3 132.5 1.0 SG A:CYS226 2.4 193.6 1.0 SG A:CYS189 2.4 116.9 1.0 CB A:CYS189 3.0 176.2 1.0 CB A:CYS224 3.1 144.4 1.0 CB A:CYS192 3.2 174.9 1.0 N A:CYS226 3.5 167.4 1.0 CB A:CYS226 3.6 141.3 1.0 N A:CYS192 4.0 170.8 1.0 N A:GLY227 4.0 135.9 1.0 CA A:CYS192 4.1 177.9 1.0 N A:THR225 4.1 99.9 1.0 CA A:CYS226 4.1 145.4 1.0 OG1 A:THR225 4.1 133.6 1.0 C A:CYS224 4.1 110.8 1.0 CA A:CYS224 4.3 127.6 1.0 C A:THR225 4.3 168.3 1.0 CB A:ALA230 4.5 151.7 1.0 N A:LYS228 4.5 210.8 1.0 O A:CYS224 4.5 122.5 1.0 CA A:CYS189 4.6 174.2 1.0 C A:CYS226 4.6 133.7 1.0 CA A:THR225 4.7 121.1 1.0 C A:LYS228 4.9 214.3 1.0 C A:GLY227 4.9 171.5 1.0 O A:LYS228 4.9 182.4 1.0 N A:GLN229 5.0 206.0 1.0

Zinc binding site 2 out of 3 in the Structure of Sars-COV2 Plpro Bound to A Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Sars-COV2 Plpro Bound to A Covalent Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:121.9 occ:1.00 SG A:CYS270 2.3 111.2 1.0 O A:HOH501 3.1 22.8 1.0 CB A:CYS270 3.3 127.0 1.0 O A:CYS270 4.3 94.0 1.0 CA A:CYS270 4.5 102.0 1.0 C A:CYS270 5.0 102.9 1.0

Zinc binding site 3 out of 3 in the Structure of Sars-COV2 Plpro Bound to A Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Sars-COV2 Plpro Bound to A Covalent Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:58.9 occ:1.00 ND1 A:HIS73 2.0 49.2 1.0 CG A:HIS73 2.9 64.1 1.0 CE1 A:HIS73 3.0 63.3 1.0 CB A:HIS73 3.3 60.3 1.0 CD2 A:HIS73 4.1 60.1 1.0 CB A:ASN128 4.1 77.1 1.0 NE2 A:HIS73 4.1 63.2 1.0 CD A:PRO129 4.4 76.6 1.0 CG A:PRO129 4.4 80.1 1.0 CA A:HIS73 4.7 61.8 1.0 N A:PRO129 4.8 64.8 1.0 O A:HIS73 4.9 75.3 1.0 ND2 A:ASN128 4.9 87.8 1.0

B.C.Sanders, S.Pokhrel, A.D.Labbe, I.I.Mathews, C.J.Cooper, R.B.Davidson, G.Phillips, K.L.Weiss, Q.Zhang, H.O'neill, M.Kaur, J.G.Schmidt, W.Reichard, S.Surendranathan, J.Parvathareddy, L.Phillips, C.Rainville, D.E.Sterner, D.Kumaran, B.Andi, G.Babnigg, N.W.Moriarty, P.D.Adams, A.Joachimiak, B.L.Hurst, S.Kumar, T.R.Butt, C.B.Jonsson, L.Ferrins, S.Wakatsuki, S.Galanie, M.S.Head, J.M.Parks. Potent and Selective Covalent Inhibition of the Papain-Like Protease From Sars-Cov-2. Nat Commun V. 14 1733 2023.
ISSN: ESSN 2041-1723
PubMed: 36977673
DOI: 10.1038/S41467-023-37254-W