Zinc in PDB 8uob: Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12682

Enzymatic activity of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12682

All present enzymatic activity of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12682:
3.4.19.12;

Protein crystallography data

The structure of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12682, PDB code: 8uob was solved by A.Ansari, B.Tan, F.X.Ruiz, J.Wang, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.74 / 2.52
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 115.825, 115.825, 219.317, 90, 90, 90
R / Rfree (%) 20.6 / 24.5

Other elements in 8uob:

The structure of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12682 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12682 (pdb code 8uob). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12682, PDB code: 8uob:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8uob

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Zinc binding site 1 out of 6 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12682


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12682 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:103.2
occ:1.00
 SG A:CYS192 2.3 84.2 1.0
SG A:CYS226 2.4 119.1 1.0
SG A:CYS189 2.5 96.3 1.0
SG A:CYS224 2.6 95.9 1.0
CB A:CYS192 3.1 99.5 1.0
CB A:CYS226 3.1 126.4 1.0
CB A:CYS224 3.3 105.5 1.0
CB A:CYS189 3.3 96.1 1.0
N A:CYS192 3.7 103.5 1.0
N A:CYS226 3.8 121.0 1.0
CA A:CYS192 4.0 98.6 1.0
CA A:CYS226 4.1 121.7 1.0
O A:HOH518 4.2 88.1 1.0
N A:THR225 4.6 126.5 1.0
CA A:CYS224 4.7 112.4 1.0
CB A:THR191 4.7 96.8 1.0
C A:THR191 4.8 103.7 1.0
OG1 A:THR225 4.8 125.7 1.0
CA A:CYS189 4.8 103.0 1.0
C A:CYS224 4.8 121.9 1.0
C A:CYS226 4.9 126.7 1.0
C A:THR225 5.0 119.6 1.0

Zinc binding site 2 out of 6 in 8uob

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Zinc binding site 2 out of 6 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12682


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12682 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:56.9
occ:1.00
 ND1 A:HIS73 2.0 45.3 1.0
CL A:CL409 2.3 57.1 1.0
CL A:CL408 2.3 64.2 1.0
CG A:HIS73 2.9 51.9 1.0
CE1 A:HIS73 3.0 53.5 1.0
CB A:HIS73 3.2 50.1 1.0
CD2 A:HIS73 4.1 50.6 1.0
NE2 A:HIS73 4.1 54.3 1.0
CB A:ASN128 4.1 55.5 1.0
CA A:HIS73 4.6 53.7 1.0
CG A:PRO129 4.7 52.3 1.0
O A:HIS73 4.8 61.7 1.0
CD A:PRO129 4.8 56.0 1.0
ND2 A:ASN128 4.8 64.4 1.0
N A:PRO129 4.9 54.2 1.0
CG A:ASN128 5.0 62.7 1.0

Zinc binding site 3 out of 6 in 8uob

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Zinc binding site 3 out of 6 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12682


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12682 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:72.1
occ:1.00
 ZN A:ZN406 1.7 157.0 1.0
OD2 A:ASP108 2.0 77.8 1.0
ND1 A:HIS89 2.5 66.5 1.0
O A:HOH670 2.9 69.6 1.0
CG A:ASP108 3.1 64.7 1.0
CG A:HIS89 3.3 69.7 1.0
CE1 A:HIS89 3.4 71.1 1.0
CB A:HIS89 3.5 57.0 1.0
OD1 A:ASP108 3.6 76.9 1.0
CG1 A:VAL159 4.1 66.7 1.0
NE1 A:TRP93 4.2 62.8 1.0
O A:HOH663 4.2 89.5 1.0
CA A:HIS89 4.3 60.6 1.0
CB A:ASP108 4.3 46.4 1.0
CD2 A:HIS89 4.4 76.6 1.0
NE2 A:HIS89 4.5 69.3 1.0
O A:HOH505 4.6 87.9 1.0
O A:HOH693 4.7 76.9 1.0
C A:HIS89 5.0 60.1 1.0
O A:HIS89 5.0 57.7 1.0

Zinc binding site 4 out of 6 in 8uob

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Zinc binding site 4 out of 6 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12682


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12682 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:65.1
occ:1.00
 O A:HOH634 2.2 75.5 1.0
O A:HOH504 2.3 75.6 1.0
SG A:CYS111 2.5 63.5 1.0
ND1 A:HIS272 2.8 82.2 1.0
CB A:CYS111 3.0 53.3 1.0
NE1 A:TRP106 3.0 93.0 1.0
CE1 A:HIS272 3.4 70.2 1.0
CE2 A:TRP106 3.7 114.0 1.0
CZ2 A:TRP106 3.7 120.9 1.0
O A:GLY271 3.9 65.3 1.0
CG A:HIS272 4.0 79.4 1.0
N A:CYS111 4.0 62.1 1.0
O A:HOH667 4.0 88.5 1.0
CA A:CYS111 4.1 51.4 1.0
CA A:HIS272 4.2 60.2 1.0
CD1 A:TRP106 4.2 130.6 1.0
CA A:ASN109 4.4 63.5 1.0
CB A:HIS272 4.5 61.5 1.0
C A:ASN109 4.5 64.6 1.0
OD1 A:ASN109 4.6 70.4 1.0
O A:HOH635 4.6 68.7 1.0
NE2 A:HIS272 4.6 62.7 1.0
N A:TYR273 4.7 64.4 1.0
O A:ASN109 4.8 64.5 1.0
C A:GLY271 4.8 59.1 1.0
CD2 A:HIS272 4.9 58.6 1.0
O A:HOH506 4.9 62.4 1.0
CB A:ASN109 4.9 68.3 1.0
N A:ASN110 5.0 58.0 1.0

Zinc binding site 5 out of 6 in 8uob

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Zinc binding site 5 out of 6 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12682


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12682 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:157.0
occ:1.00
 ZN A:ZN404 1.7 72.1 1.0
O A:HOH670 2.1 69.6 1.0
ND1 A:HIS89 2.5 66.5 1.0
O A:HOH505 3.1 87.9 1.0
CG A:HIS89 3.4 69.7 1.0
CE1 A:HIS89 3.4 71.1 1.0
OD2 A:ASP108 3.6 77.8 1.0
CB A:HIS89 3.6 57.0 1.0
CA A:HIS89 3.7 60.6 1.0
CD A:LYS92 4.3 91.4 1.0
O A:HIS89 4.5 57.7 1.0
O A:HOH663 4.5 89.5 1.0
NE2 A:HIS89 4.6 69.3 1.0
CD2 A:HIS89 4.6 76.6 1.0
O A:HOH693 4.6 76.9 1.0
C A:HIS89 4.6 60.1 1.0
CG A:ASP108 4.7 64.7 1.0
N A:HIS89 4.8 54.5 1.0
NZ A:LYS92 4.8 102.2 1.0
NE1 A:TRP93 4.8 62.8 1.0
O A:ASN88 4.9 52.6 1.0

Zinc binding site 6 out of 6 in 8uob

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Zinc binding site 6 out of 6 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12682


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12682 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:218.1
occ:1.00
 NE2 A:HIS17 2.3 83.4 1.0
OE2 A:GLU67 2.7 85.9 1.0
CE1 A:HIS17 2.9 90.4 1.0
CD2 A:HIS17 3.1 94.9 1.0
CD A:GLU67 3.7 76.1 1.0
ND1 A:HIS17 3.8 95.0 1.0
CG A:HIS17 3.9 93.4 1.0
CB A:ASN15 3.9 82.2 1.0
OE1 A:GLU67 4.0 71.0 1.0
O A:HOH569 4.2 81.8 1.0
CG2 A:THR63 4.4 60.0 1.0
CG A:ASN15 4.5 86.2 1.0
ND2 A:ASN15 4.7 80.7 1.0
O A:HOH690 4.8 86.0 1.0
CA A:ASN15 4.9 78.4 1.0
C A:ASN15 5.0 83.7 1.0

Reference:

B.Tan, X.Zhang, A.Ansari, P.Jadhav, H.Tan, K.Li, A.Chopra, A.Ford, X.Chi, F.X.Ruiz, E.Arnold, X.Deng, J.Wang. Design of A Sars-Cov-2 Papain-Like Protease Inhibitor with Antiviral Efficacy in A Mouse Model Science V. 383 1434 2024.
ISSN: ESSN 1095-9203
DOI: 10.1126/SCIENCE.ADM9724
Page generated: Thu Oct 31 12:24:37 2024

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