Zinc in PDB 7cmd: Crystal Structure of the Sars-Cov-2 Plpro with GRL0617

The structure of Crystal Structure of the Sars-Cov-2 Plpro with GRL0617, PDB code: 7cmd 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)	94.51 / 2.59
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.467, 123.510, 146.814, 90.00, 90.06, 90.00
R / Rfree (%)	24.4 / 29.8

The binding sites of Zinc atom in the Crystal Structure of the Sars-Cov-2 Plpro with GRL0617 (pdb code 7cmd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of the Sars-Cov-2 Plpro with GRL0617, PDB code: 7cmd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Crystal Structure of the Sars-Cov-2 Plpro with GRL0617


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 with GRL0617 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:0.4 occ:1.00 SG A:CYS189 2.6 72.6 1.0 SG A:CYS192 2.6 88.4 1.0 HB2 A:CYS192 2.8 0.5 1.0 HB2 A:CYS189 3.1 0.4 1.0 HG1 A:THR191 3.1 0.1 1.0 HB3 A:CYS189 3.2 0.4 1.0 CB A:CYS189 3.2 84.5 1.0 CB A:CYS192 3.2 97.0 1.0 OG1 A:THR191 3.5 0.9 1.0 H A:CYS192 3.5 0.6 1.0 HB3 A:CYS192 3.9 0.5 1.0 N A:CYS192 4.0 92.1 1.0 CA A:CYS192 4.3 92.8 1.0 H A:THR191 4.5 0.6 1.0 HA A:CYS192 4.7 0.4 1.0 CA A:CYS189 4.7 90.5 1.0 CB A:THR191 4.9 99.1 1.0 HA A:CYS189 5.0 0.6 1.0 C A:THR191 5.0 90.3 1.0

Zinc binding site 2 out of 9 in the Crystal Structure of the Sars-Cov-2 Plpro with GRL0617


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 with GRL0617 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:0.7 occ:1.00 C A:VAL220 3.4 58.7 1.0 O A:VAL220 3.6 47.9 1.0 HA A:THR231 4.3 79.3 1.0 H A:LYS232 4.7 73.7 1.0 CA A:VAL220 4.8 59.6 1.0 HB A:VAL220 4.8 77.5 1.0 HG23 A:VAL220 4.9 81.2 1.0

Zinc binding site 3 out of 9 in the Crystal Structure of the Sars-Cov-2 Plpro with GRL0617


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 with GRL0617 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:90.6 occ:0.00 OG1 B:THR191 2.0 92.2 1.0 SG B:CYS192 2.5 92.6 1.0 SG B:CYS189 2.7 80.5 1.0 H B:CYS192 3.0 0.3 1.0 HB2 B:CYS192 3.0 0.7 1.0 HB3 B:CYS189 3.3 0.6 1.0 CB B:CYS192 3.3 0.7 1.0 CB B:THR191 3.4 94.2 1.0 CB B:CYS189 3.5 99.6 1.0 N B:CYS192 3.5 0.9 1.0 HB2 B:CYS189 3.6 0.6 1.0 HB B:THR191 3.6 0.1 1.0 CA B:CYS192 4.1 0.1 1.0 HG21 B:THR191 4.1 0.5 1.0 HB3 B:CYS192 4.1 0.7 1.0 CG2 B:THR191 4.2 87.9 1.0 C B:THR191 4.3 0.6 1.0 H B:THR191 4.3 0.7 1.0 CA B:THR191 4.4 98.9 1.0 HG23 B:THR191 4.4 0.5 1.0 HA B:CYS192 4.7 0.4 1.0 O B:HOH608 4.7 53.2 1.0 N B:THR191 4.8 97.2 1.0 CA B:CYS189 5.0 0.1 1.0

Zinc binding site 4 out of 9 in the Crystal Structure of the Sars-Cov-2 Plpro with GRL0617


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 with GRL0617 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:0.2 occ:1.00 H B:ARG166 2.3 44.7 1.0 OD1 B:ASP164 2.6 60.8 1.0 OD2 B:ASP302 2.9 64.3 1.0 HB2 B:ARG166 2.9 83.3 1.0 H01A B:TTT502 3.0 57.8 1.0 OH B:TYR273 3.0 40.8 1.0 N B:ARG166 3.2 37.2 1.0 HB3 B:ARG166 3.3 83.3 1.0 O B:HOH604 3.3 32.0 1.0 HB B:VAL165 3.3 44.7 1.0 CB B:ARG166 3.4 69.4 1.0 HE1 B:TYR273 3.5 37.0 1.0 HG23 B:THR301 3.5 55.8 1.0 HH B:TYR273 3.5 49.0 1.0 H B:VAL165 3.6 52.7 1.0 OD1 B:ASP302 3.6 64.4 1.0 CG B:ASP302 3.6 58.0 1.0 CG B:ASP164 3.7 52.0 1.0 H01B B:TTT502 3.7 57.8 1.0 HG21 B:THR301 3.7 55.8 1.0 C01 B:TTT502 3.7 48.1 1.0 OG1 B:THR301 3.8 48.2 1.0 CA B:ARG166 3.9 50.0 1.0 CZ B:TYR273 4.0 31.2 1.0 N B:VAL165 4.0 43.9 1.0 CG2 B:THR301 4.0 46.4 1.0 CE1 B:TYR273 4.0 30.8 1.0 OD2 B:ASP164 4.1 56.5 1.0 HN2 B:TTT502 4.1 51.4 1.0 CB B:VAL165 4.1 37.2 1.0 C B:VAL165 4.2 29.7 1.0 H01 B:TTT502 4.2 57.8 1.0 CA B:VAL165 4.3 37.3 1.0 HG B:SER262 4.3 46.5 1.0 HA B:ARG166 4.4 60.0 1.0 HG1 B:THR301 4.4 57.9 1.0 HG12 B:VAL165 4.5 46.0 1.0 HE B:ARG166 4.5 0.3 1.0 CB B:THR301 4.6 47.9 1.0 HA B:ASP164 4.6 52.4 1.0 HD3 B:ARG166 4.7 0.3 1.0 C B:ASP164 4.7 45.6 1.0 N2 B:TTT502 4.8 42.8 1.0 H B:GLU167 4.8 61.4 1.0 CG B:ARG166 4.8 80.6 1.0 H4 B:TTT502 4.8 39.3 1.0 CG1 B:VAL165 4.9 38.3 1.0 HG22 B:THR301 4.9 55.8 1.0 CB B:ASP164 4.9 50.0 1.0 C6 B:TTT502 4.9 39.6 1.0 O B:THR301 5.0 12.3 1.0 CA B:ASP164 5.0 43.6 1.0

Zinc binding site 5 out of 9 in the Crystal Structure of the Sars-Cov-2 Plpro with GRL0617


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Sars-Cov-2 Plpro with GRL0617 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn504 b:0.0 occ:1.00 HG2 B:PRO59 2.9 65.7 1.0 HB1 B:ALA68 3.2 43.6 1.0 HA B:THR75 3.2 79.8 1.0 HD23 B:LEU80 3.6 54.2 0.4 O B:THR74 3.6 51.6 1.0 O B:ASP76 3.7 49.0 1.0 HG23 B:THR74 3.7 64.8 1.0 CG B:PRO59 3.8 54.7 1.0 HB3 B:ALA68 3.8 43.6 1.0 HG3 B:PRO59 3.8 65.7 1.0 CB B:ALA68 3.9 36.3 1.0 CA B:THR75 4.0 66.5 1.0 C B:THR75 4.1 58.5 1.0 HB3 B:PHE79 4.1 49.8 1.0 C B:THR74 4.4 55.4 1.0 HA B:PRO77 4.4 68.1 1.0 C B:ASP76 4.4 54.5 1.0 N B:ASP76 4.4 54.9 1.0 HD12 B:LEU80 4.5 52.0 0.6 CD2 B:LEU80 4.5 45.2 0.4 HB2 B:ALA68 4.5 43.6 1.0 HD3 B:PRO59 4.5 65.3 1.0 CD B:PRO59 4.5 54.4 1.0 HG B:LEU80 4.5 53.4 0.6 O B:THR75 4.5 58.3 1.0 HD2 B:PRO59 4.6 65.3 1.0 H B:ASP76 4.6 65.9 1.0 HD21 B:LEU80 4.6 54.2 0.4 N B:THR75 4.6 63.5 1.0 CG2 B:THR74 4.6 53.9 1.0 H B:LEU80 4.8 52.9 0.4 H B:LEU80 4.8 52.9 0.6 O B:ALA68 4.8 51.8 1.0 C B:ALA68 4.8 49.0 1.0 HG22 B:THR74 4.8 64.8 1.0 HG22 B:THR75 4.9 89.1 1.0 HD2 B:TYR72 4.9 44.2 1.0 CB B:PRO59 4.9 54.7 1.0 HD22 B:LEU80 4.9 54.2 0.4 HB2 B:PRO59 5.0 65.6 1.0

Zinc binding site 6 out of 9 in the Crystal Structure of the Sars-Cov-2 Plpro with GRL0617


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Sars-Cov-2 Plpro with GRL0617 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn505 b:0.1 occ:1.00 O B:GLU307 3.0 40.5 1.0 HB2 B:ASN308 3.4 40.8 1.0 HA B:PRO240 3.5 45.4 1.0 OE1 B:GLU124 3.9 76.0 1.0 HB3 B:PRO240 4.0 51.2 1.0 C B:GLU307 4.2 35.8 1.0 HD2 D:HIS272 4.2 46.0 1.0 HA B:ASN308 4.2 37.6 1.0 CA B:PRO240 4.2 37.8 1.0 H B:GLU307 4.2 50.8 1.0 O B:PRO240 4.3 43.8 1.0 CB B:ASN308 4.3 34.0 1.0 CD2 D:HIS272 4.3 38.3 1.0 HB2 B:PRO240 4.3 51.2 1.0 HE2 D:HIS272 4.4 44.1 1.0 CB B:PRO240 4.4 42.7 1.0 NE2 D:HIS272 4.4 36.7 1.0 CA B:ASN308 4.6 31.3 1.0 C B:PRO240 4.7 40.8 1.0 N B:ASN308 4.8 32.3 1.0 HB3 B:ASN308 4.8 40.8 1.0 NE1 D:TRP106 4.8 54.0 1.0 HE1 D:TRP106 5.0 64.8 1.0 CG D:HIS272 5.0 38.9 1.0 OD1 B:ASN308 5.0 19.4 1.0 CD B:GLU124 5.0 70.7 1.0 CD1 D:TRP106 5.0 49.3 1.0 CE2 D:TRP106 5.0 50.3 1.0

Zinc binding site 7 out of 9 in the Crystal Structure of the Sars-Cov-2 Plpro with GRL0617


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Sars-Cov-2 Plpro with GRL0617 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn602 b:0.0 occ:1.00 HB C:THR191 1.7 0.9 1.0 CB C:THR191 2.6 94.9 1.0 SG C:CYS189 2.8 88.2 1.0 H C:CYS192 2.8 0.4 1.0 HG1 C:THR191 2.8 0.0 1.0 HB3 C:CYS189 2.9 0.3 1.0 HG21 C:THR191 3.0 0.9 1.0 OG1 C:THR191 3.1 88.3 1.0 CG2 C:THR191 3.2 93.2 1.0 CB C:CYS189 3.3 0.2 1.0 HG22 C:THR191 3.4 0.9 1.0 N C:CYS192 3.5 0.2 1.0 SG C:CYS192 3.5 0.2 1.0 HB2 C:CYS189 3.6 0.3 1.0 O C:HOH707 3.6 61.4 1.0 HB2 C:CYS192 3.6 0.9 1.0 H C:THR191 3.7 0.2 1.0 CA C:THR191 3.8 98.1 1.0 CB C:CYS192 4.0 0.1 1.0 C C:THR191 4.1 0.8 1.0 HG23 C:THR191 4.1 0.9 1.0 N C:THR191 4.2 87.6 1.0 CA C:CYS192 4.4 0.4 1.0 HA C:THR191 4.6 0.8 1.0 CA C:CYS189 4.7 0.1 1.0 HB3 C:CYS192 4.9 0.9 1.0 HA C:CYS192 5.0 0.9 1.0

Zinc binding site 8 out of 9 in the Crystal Structure of the Sars-Cov-2 Plpro with GRL0617


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Sars-Cov-2 Plpro with GRL0617 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn602 b:1.0 occ:1.00 SG D:CYS192 2.3 85.8 1.0 O D:HOH751 2.8 59.9 1.0 SG D:CYS189 2.8 73.1 1.0 H D:CYS192 3.0 0.4 1.0 OG1 D:THR191 3.0 0.9 1.0 HB2 D:CYS192 3.1 0.5 1.0 CB D:CYS192 3.3 87.9 1.0 N D:CYS192 3.7 91.1 1.0 HB2 D:CYS189 3.9 0.7 1.0 CB D:CYS189 3.9 88.9 1.0 HB3 D:CYS189 4.0 0.7 1.0 HB3 D:CYS192 4.1 0.5 1.0 CA D:CYS192 4.2 86.6 1.0 CB D:THR191 4.5 0.1 1.0 HA D:CYS192 4.7 0.0 1.0 H D:THR191 4.8 0.9 1.0 C D:THR191 4.8 89.4 1.0

Zinc binding site 9 out of 9 in the Crystal Structure of the Sars-Cov-2 Plpro with GRL0617


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the Sars-Cov-2 Plpro with GRL0617 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:0.1 occ:1.00 CD1 D:TYR268 3.9 51.6 1.0 CG D:TYR268 4.1 44.4 1.0 HB2 D:TYR268 4.1 35.2 1.0 HD1 D:TYR268 4.1 61.9 1.0 CE1 D:TYR268 4.2 55.9 1.0 H18 D:TTT601 4.2 39.5 1.0 CD2 D:TYR268 4.4 58.8 1.0 CZ D:TYR268 4.5 56.2 1.0 HE1 D:TYR268 4.5 67.2 1.0 CB D:TYR268 4.6 29.3 1.0 CE2 D:TYR268 4.6 63.3 1.0 C18 D:TTT601 4.6 32.9 1.0 HA2 B:GLY100 4.7 58.7 1.0 HB3 D:TYR268 4.8 35.2 1.0 HD2 D:TYR268 4.8 70.6 1.0 H22 D:TTT601 4.9 39.0 1.0 C22 D:TTT601 5.0 32.5 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