Zinc in PDB 7cjd: Crystal Structure of the Sars-Cov-2 Plpro C111S Mutant

The structure of Crystal Structure of the Sars-Cov-2 Plpro C111S Mutant, PDB code: 7cjd was solved by X.Gao, S.Cui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.90 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	169.018, 108.626, 100.265, 90.00, 118.87, 90.00
R / Rfree (%)	23.3 / 28.2

The binding sites of Zinc atom in the Crystal Structure of the Sars-Cov-2 Plpro C111S Mutant (pdb code 7cjd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Sars-Cov-2 Plpro C111S Mutant, PDB code: 7cjd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Sars-Cov-2 Plpro C111S Mutant


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 the Sars-Cov-2 Plpro C111S Mutant within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:60.0 occ:1.00 HB2 D:CYS192 1.7 57.5 1.0 HB3 D:CYS192 2.0 57.5 1.0 SG D:CYS226 2.1 68.8 1.0 CB D:CYS192 2.2 48.0 1.0 HG D:CYS226 2.3 82.6 1.0 HB3 D:CYS226 2.3 65.1 1.0 HG D:CYS224 2.4 77.6 1.0 SG D:CYS189 2.5 64.9 1.0 CB D:CYS226 2.7 54.2 1.0 SG D:CYS224 2.7 64.7 1.0 H D:CYS192 2.9 66.2 1.0 HG D:CYS189 2.9 77.9 1.0 HG D:CYS192 3.0 0.1 1.0 H D:CYS226 3.1 71.7 1.0 SG D:CYS192 3.2 99.3 1.0 HB2 D:CYS226 3.3 65.1 1.0 N D:CYS192 3.4 55.2 1.0 HB D:THR191 3.4 68.9 1.0 CA D:CYS192 3.4 59.1 1.0 HB3 D:CYS189 3.6 67.3 1.0 CB D:CYS189 3.6 56.1 1.0 HB3 D:CYS224 3.7 71.5 1.0 HB2 D:CYS189 3.7 67.3 1.0 N D:CYS226 3.7 59.7 1.0 CA D:CYS226 3.8 59.4 1.0 CB D:CYS224 3.9 59.6 1.0 HA D:CYS192 3.9 71.0 1.0 HG22 D:THR191 4.0 69.0 1.0 HB2 D:LYS228 4.2 80.0 1.0 HA D:CYS226 4.3 71.3 1.0 CB D:THR191 4.3 57.4 1.0 HB3 C:LYS43 4.3 55.7 1.0 HB2 D:CYS224 4.3 71.5 1.0 C D:THR191 4.5 62.1 1.0 H D:THR191 4.5 81.5 1.0 H D:LYS228 4.6 73.9 1.0 CG2 D:THR191 4.6 57.5 1.0 C D:CYS192 4.6 56.6 1.0 HB2 C:LYS43 4.7 55.7 1.0 H D:GLY193 4.8 71.6 1.0 H D:GLY227 4.9 77.5 1.0 CA D:THR191 4.9 56.6 1.0 C D:CYS226 4.9 54.1 1.0 HG23 D:THR225 4.9 66.6 1.0 CB C:LYS43 5.0 46.4 1.0 HG21 D:THR191 5.0 69.0 1.0 CA D:CYS189 5.0 50.6 1.0 N D:THR191 5.0 67.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Sars-Cov-2 Plpro C111S Mutant


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 the Sars-Cov-2 Plpro C111S Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:61.4 occ:1.00 HB2 A:CYS226 1.6 75.8 1.0 SG A:CYS189 1.9 82.7 1.0 HG A:CYS226 2.0 0.4 1.0 CB A:CYS226 2.2 63.2 1.0 SG A:CYS226 2.4 87.9 1.0 HG A:CYS224 2.6 69.3 1.0 SG A:CYS224 2.6 57.7 1.0 HB3 A:CYS192 2.7 68.2 1.0 HB3 A:CYS226 2.7 75.8 1.0 HB2 A:CYS189 3.0 83.5 1.0 CB A:CYS189 3.0 69.5 1.0 HB3 A:CYS189 3.3 83.5 1.0 H A:CYS226 3.4 76.5 1.0 OG1 A:THR191 3.5 73.9 1.0 CA A:CYS226 3.5 69.0 1.0 HG1 A:THR191 3.5 88.7 1.0 HB3 A:CYS224 3.6 69.0 1.0 CB A:CYS192 3.6 56.8 1.0 HB2 A:CYS192 3.7 68.2 1.0 H A:CYS192 3.7 75.9 1.0 HA A:CYS226 3.7 82.8 1.0 CB A:CYS224 3.8 57.5 1.0 N A:CYS226 3.9 63.7 1.0 HG23 A:THR191 4.0 77.4 1.0 H A:THR191 4.0 83.2 1.0 HB2 A:CYS224 4.2 69.0 1.0 HB2 A:LYS228 4.2 78.5 1.0 N A:CYS192 4.2 63.2 1.0 CA A:CYS189 4.4 65.3 1.0 HE2 A:LYS228 4.5 90.7 1.0 H A:LYS228 4.5 67.0 1.0 HB3 B:LYS43 4.6 71.5 1.0 SG A:CYS192 4.6 0.6 1.0 CB A:THR191 4.6 72.1 1.0 CA A:CYS192 4.6 67.4 1.0 CG2 A:THR191 4.7 64.5 1.0 C A:CYS226 4.7 63.2 1.0 N A:THR191 4.8 69.3 1.0 C A:CYS189 4.8 67.4 1.0 H A:GLY227 4.8 78.6 1.0 HG21 A:THR191 4.9 77.4 1.0 HA A:CYS189 4.9 78.4 1.0 HB2 B:LYS43 5.0 71.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Sars-Cov-2 Plpro C111S Mutant


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 the Sars-Cov-2 Plpro C111S Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:94.9 occ:1.00 HB3 B:CYS226 2.1 0.2 1.0 SG B:CYS192 2.1 0.1 1.0 HG B:CYS226 2.2 0.2 1.0 HG B:CYS224 2.6 0.8 1.0 SG B:CYS189 2.6 0.3 1.0 SG B:CYS226 2.7 0.7 1.0 CB B:CYS226 2.8 91.9 1.0 SG B:CYS224 2.8 96.5 1.0 HB B:THR191 2.9 0.8 1.0 HB2 B:CYS192 3.1 0.5 1.0 H B:CYS226 3.1 0.9 1.0 CB B:CYS192 3.2 99.6 1.0 H B:CYS192 3.3 1.0 1.0 HB3 B:CYS224 3.3 0.3 1.0 HB2 B:CYS226 3.4 0.2 1.0 HB3 B:CYS189 3.4 0.6 1.0 CB B:CYS189 3.5 98.0 1.0 HB2 B:CYS189 3.6 0.6 1.0 N B:CYS192 3.7 0.8 1.0 CB B:CYS224 3.7 94.5 1.0 N B:CYS226 3.8 94.1 1.0 CB B:THR191 3.9 0.7 1.0 CA B:CYS226 3.9 90.4 1.0 HB3 B:CYS192 4.0 0.5 1.0 CA B:CYS192 4.0 0.3 1.0 HB2 B:CYS224 4.2 0.3 1.0 H B:THR191 4.3 0.9 1.0 HG22 B:THR191 4.4 0.6 1.0 HA B:CYS192 4.4 0.3 1.0 C B:THR191 4.5 98.0 1.0 HA B:CYS226 4.5 0.4 1.0 H B:LYS228 4.6 0.6 1.0 HB3 B:LYS228 4.6 0.7 1.0 H B:GLY227 4.6 0.4 1.0 CG2 B:THR191 4.6 0.3 1.0 CA B:THR191 4.6 0.8 1.0 HG1 B:THR191 4.6 0.8 1.0 HG21 B:THR191 4.6 0.6 1.0 OG1 B:THR191 4.6 0.8 1.0 N B:THR191 4.8 0.7 1.0 C B:CYS224 4.9 88.8 1.0 CA B:CYS224 4.9 90.1 1.0 H B:THR225 4.9 0.4 1.0 N B:THR225 4.9 95.3 1.0 CA B:CYS189 4.9 96.5 1.0 C B:CYS226 5.0 98.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Sars-Cov-2 Plpro C111S Mutant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Sars-Cov-2 Plpro C111S Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:0.6 occ:0.00 O C:LYS190 2.2 0.4 1.0 CG2 C:THR191 2.2 0.7 1.0 HB2 C:CYS226 2.6 0.7 1.0 SG C:CYS226 2.7 0.2 1.0 OG1 C:THR191 2.8 0.8 1.0 CB C:THR191 2.8 0.5 1.0 HA C:THR191 2.8 0.3 1.0 C C:LYS190 3.0 0.8 1.0 CE C:LYS190 3.1 0.8 1.0 CB C:CYS226 3.1 0.6 1.0 CA C:THR191 3.1 0.4 1.0 N C:THR191 3.3 0.6 1.0 HB3 C:CYS226 3.4 0.7 1.0 NZ C:LYS190 3.7 0.8 1.0 HB2 C:LYS228 4.0 0.8 1.0 H C:THR191 4.0 0.7 1.0 H C:CYS226 4.2 0.3 1.0 HA C:LYS190 4.2 0.6 1.0 HB3 C:LYS228 4.3 0.8 1.0 CA C:LYS190 4.3 0.4 1.0 CD C:LYS190 4.4 0.5 1.0 CA C:CYS226 4.5 0.3 1.0 H C:LYS228 4.6 0.2 1.0 C C:THR191 4.6 0.7 1.0 CB C:LYS228 4.6 0.5 1.0 N C:CYS226 4.7 0.1 1.0 CG C:LYS190 4.9 1.0 1.0

X.Gao, B.Qin, P.Chen, K.Zhu, P.Hou, J.A.Wojdyla, M.Wang, S.Cui. Crystal Structure of Sars-Cov-2 Papain-Like Protease. Acta Pharm Sin B 2020.
ISSN: ISSN 2211-3835
PubMed: 32895623
DOI: 10.1016/J.APSB.2020.08.014