Zinc in PDB 7nt4: X-Ray Structure of SCOV2-Plpro in Complex with Small Molecule Inhibitor

All present enzymatic activity of X-Ray Structure of SCOV2-Plpro in Complex with Small Molecule Inhibitor:
3.4.19.12;

The structure of X-Ray Structure of SCOV2-Plpro in Complex with Small Molecule Inhibitor, PDB code: 7nt4 was solved by V.Napolitano, A.Mourao, M.Bostock, A.Matsuda, A.Czarna, G.M.Popowicz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.47 / 2.68
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	116.37, 116.37, 253.566, 90, 90, 120
R / Rfree (%)	19.3 / 26.4

The binding sites of Zinc atom in the X-Ray Structure of SCOV2-Plpro in Complex with Small Molecule Inhibitor (pdb code 7nt4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the X-Ray Structure of SCOV2-Plpro in Complex with Small Molecule Inhibitor, PDB code: 7nt4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the X-Ray Structure of SCOV2-Plpro in Complex with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of SCOV2-Plpro in Complex with Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn408 b:65.6 occ:1.00 SG A:CYS225 2.4 85.2 1.0 SG A:CYS227 2.4 89.8 1.0 SG A:CYS193 2.4 85.6 1.0 SG A:CYS190 2.4 77.4 1.0 CB A:CYS225 3.4 77.7 1.0 CB A:CYS193 3.4 78.4 1.0 CB A:CYS227 3.5 87.2 1.0 CB A:CYS190 3.6 69.0 1.0 N A:CYS193 4.1 73.3 1.0 CA A:CYS193 4.3 73.7 1.0 N A:CYS227 4.4 79.5 1.0 CA A:CYS227 4.5 80.7 1.0 CE A:LYS229 4.6 68.8 1.0 OG1 A:THR192 4.7 72.3 1.0 CA A:CYS225 4.8 71.3 1.0 CA A:CYS190 4.9 62.3 1.0

Zinc binding site 2 out of 2 in the X-Ray Structure of SCOV2-Plpro in Complex with Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of SCOV2-Plpro in Complex with Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn407 b:112.1 occ:1.00 SG B:CYS190 2.4 142.2 1.0 SG B:CYS227 2.4 155.4 1.0 SG B:CYS193 2.4 142.8 1.0 SG B:CYS225 2.4 161.2 1.0 CB B:CYS227 3.4 146.4 1.0 CB B:CYS193 3.4 130.1 1.0 CB B:CYS225 3.5 137.2 1.0 CB B:CYS190 3.5 125.3 1.0 N B:CYS193 3.9 121.7 1.0 O B:CYS190 3.9 111.2 1.0 N B:CYS227 4.2 130.2 1.0 CA B:CYS193 4.2 122.8 1.0 CA B:CYS227 4.3 135.1 1.0 CA B:CYS190 4.4 111.1 1.0 C B:CYS190 4.6 111.3 1.0 OG1 B:THR192 4.6 119.8 1.0 CB B:LYS229 4.6 106.9 1.0 CA B:CYS225 4.8 120.8 1.0 N B:THR226 4.9 121.6 1.0 C B:THR192 4.9 123.2 1.0 C B:CYS225 5.0 121.1 1.0

V.Napolitano, A.Dabrowska, K.Schorpp, A.Mourao, E.Barreto-Duran, M.Benedyk, P.Botwina, S.Brandner, M.Bostock, Y.Chykunova, A.Czarna, G.Dubin, T.Frohlich, M.Holscher, M.Jedrysik, A.Matsuda, K.Owczarek, M.Pachota, O.Plettenburg, J.Potempa, I.Rothenaigner, F.Schlauderer, K.Slysz, A.Szczepanski, K.Greve-Isdahl Mohn, B.Blomberg, M.Sattler, K.Hadian, G.M.Popowicz, K.Pyrc. Acriflavine, A Clinically Approved Drug, Inhibits Sars-Cov-2 and Other Betacoronaviruses. Cell Chem Biol V. 29 774 2022.
ISSN: ESSN 2451-9456
PubMed: 35021060
DOI: 10.1016/J.CHEMBIOL.2021.11.006