Zinc in PDB 7dk1: Crystal Structure of Zinc Bound Sars-Cov-2 Main Protease

All present enzymatic activity of Crystal Structure of Zinc Bound Sars-Cov-2 Main Protease:
3.4.22.69;

The structure of Crystal Structure of Zinc Bound Sars-Cov-2 Main Protease, PDB code: 7dk1 was solved by K.S.Sonkar, L.Panchariya, S.Kuila, W.A.Khan, A.Arockiasamy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.32 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.62, 102.2, 102.35, 90, 90, 90
R / Rfree (%)	19 / 20.9

The structure of Crystal Structure of Zinc Bound Sars-Cov-2 Main Protease also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Zinc Bound Sars-Cov-2 Main Protease (pdb code 7dk1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Zinc Bound Sars-Cov-2 Main Protease, PDB code: 7dk1:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Zinc Bound Sars-Cov-2 Main Protease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Zinc Bound Sars-Cov-2 Main Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:41.2 occ:0.85 NE2 A:HIS41 2.1 35.5 1.0 O A:HOH688 2.1 53.0 1.0 O A:HOH704 2.2 37.5 1.0 SG A:CYS145 2.3 34.9 1.0 CD2 A:HIS41 3.0 33.2 1.0 CE1 A:HIS41 3.1 35.5 1.0 CB A:CYS145 3.1 27.8 1.0 O A:HOH602 3.6 76.4 1.0 O A:HOH531 3.6 49.8 1.0 O A:HIS164 4.2 29.6 1.0 CG A:HIS41 4.2 32.0 1.0 ND1 A:HIS41 4.2 34.4 1.0 CD2 A:LEU27 4.2 27.1 1.0 O A:HOH523 4.4 51.4 1.0 N A:GLY404 4.4 47.7 1.0 O A:HOH728 4.5 70.6 1.0 CA A:CYS145 4.6 25.5 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Zinc Bound Sars-Cov-2 Main Protease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Zinc Bound Sars-Cov-2 Main Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:35.1 occ:0.90 OD1 A:ASP155 1.9 42.6 1.0 OD2 A:ASP153 2.0 35.7 1.0 SG A:CYS156 2.3 36.4 1.0 CG A:ASP153 2.7 34.9 1.0 OD1 A:ASP153 2.7 33.8 1.0 CG A:ASP155 2.8 42.0 1.0 OD2 A:ASP155 3.1 43.0 1.0 N A:CYS156 3.5 35.1 1.0 CB A:CYS156 3.5 32.6 1.0 NZ A:LYS102 3.9 43.4 1.0 CA A:CYS156 4.0 33.0 1.0 CB A:ASP155 4.2 39.2 1.0 CB A:ASP153 4.2 35.2 1.0 O A:HOH557 4.2 32.7 1.0 C A:ASP155 4.3 37.3 1.0 N A:ASP155 4.3 39.2 1.0 CA A:ASP155 4.4 38.5 1.0 CE A:LYS102 4.5 42.9 1.0 O A:CYS156 4.5 30.2 1.0 C A:CYS156 4.6 31.2 1.0 CD A:LYS102 4.7 40.5 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Zinc Bound Sars-Cov-2 Main Protease


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Zinc Bound Sars-Cov-2 Main Protease within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:40.2 occ:0.80 NE2 B:HIS41 1.9 39.8 1.0 O B:HOH628 2.0 45.7 1.0 O B:HOH636 2.2 27.7 1.0 SG B:CYS145 2.4 40.3 1.0 CE1 B:HIS41 2.9 39.5 1.0 CD2 B:HIS41 3.0 38.6 1.0 CB B:CYS145 3.1 32.2 1.0 O B:HOH591 3.9 53.5 1.0 ND1 B:HIS41 4.0 39.1 1.0 CG B:HIS41 4.0 37.8 1.0 O B:HIS164 4.1 30.1 1.0 CD2 B:LEU27 4.2 35.5 1.0 CA B:CYS145 4.6 30.0 1.0 O B:GLY405 4.9 60.0 0.8

L.Panchariya, W.A.Khan, S.Kuila, K.S.Sonkar, S.Sahoo, A.Ghoshal, A.Kumar, D.P.Verma, A.Hasan, S.Das, J.K.Thakur, R.Halder, S.Sunil, A.Arockiasamy. ZINC2+ Ion Inhibits Sars-Cov-2 Main Protease and Viral Replication in Vitro Biorxiv 2021.
DOI: 10.1101/2021.06.15.448551