Zinc in PDB 8uuw: Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12145

Enzymatic activity of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12145

All present enzymatic activity of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12145:
3.4.19.12;

Protein crystallography data

The structure of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12145, PDB code: 8uuw was solved by A.Ansari, B.Tan, F.X.Ruiz, E.Arnold, J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.83 / 3.20
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 115.028, 115.028, 218.357, 90, 90, 90
R / Rfree (%) 26.9 / 30.6

Other elements in 8uuw:

The structure of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12145 also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12145 (pdb code 8uuw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12145, PDB code: 8uuw:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 8uuw

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Zinc binding site 1 out of 5 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12145


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 JUN12145 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:136.6
occ:1.00
 SG A:CYS226 2.3 110.8 1.0
CB A:CYS226 2.3 144.1 1.0
O A:HOH567 3.2 64.0 1.0
N A:CYS226 3.3 140.9 1.0
CA A:CYS226 3.4 146.2 1.0
C A:THR225 4.5 144.8 1.0
C A:CYS226 4.6 151.9 1.0
N A:GLY227 4.8 141.4 1.0
N A:THR225 4.9 134.4 1.0

Zinc binding site 2 out of 5 in 8uuw

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Zinc binding site 2 out of 5 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12145


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 JUN12145 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:59.3
occ:1.00
 CL A:CL411 2.2 84.1 1.0
ND1 A:HIS73 2.3 56.4 1.0
CL A:CL410 2.6 49.6 1.0
CG A:HIS73 3.1 58.2 1.0
CB A:HIS73 3.2 53.4 1.0
CE1 A:HIS73 3.4 76.4 1.0
CB A:ASN128 4.2 47.5 1.0
CD2 A:HIS73 4.3 70.3 1.0
NE2 A:HIS73 4.4 81.9 1.0
CA A:HIS73 4.5 60.9 1.0
O A:HIS73 4.6 64.4 1.0
CG A:PRO129 4.7 57.2 1.0
CD A:PRO129 4.9 62.7 1.0
ND2 A:ASN128 4.9 55.0 1.0

Zinc binding site 3 out of 5 in 8uuw

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Zinc binding site 3 out of 5 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12145


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 JUN12145 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:128.9
occ:1.00
 O A:HOH549 2.3 94.2 1.0
ND1 A:HIS255 2.3 93.8 1.0
O A:HOH533 2.5 90.6 1.0
O A:HOH587 2.5 101.2 1.0
O A:HOH583 2.7 84.7 1.0
O A:HOH523 2.9 77.1 1.0
CG A:HIS255 3.2 89.3 1.0
CB A:HIS255 3.3 76.8 1.0
CE1 A:HIS255 3.4 88.6 1.0
CD2 A:HIS255 4.4 92.0 1.0
NE2 A:HIS255 4.4 89.9 1.0
O A:HOH510 4.5 75.4 1.0
CA A:HIS255 4.7 63.8 1.0
O A:HOH502 4.9 67.9 1.0
O A:HIS255 5.0 93.7 1.0
O A:GLU280 5.0 98.1 1.0

Zinc binding site 4 out of 5 in 8uuw

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Zinc binding site 4 out of 5 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12145


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 JUN12145 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:91.7
occ:1.00
 O A:HOH553 2.0 57.9 1.0
OD2 A:ASP108 2.1 49.6 1.0
ND1 A:HIS89 2.3 65.0 1.0
O A:HOH515 2.7 76.2 1.0
CG A:HIS89 3.1 69.2 1.0
CB A:HIS89 3.2 72.5 1.0
CG A:ASP108 3.3 57.4 1.0
CE1 A:HIS89 3.4 76.5 1.0
O A:HOH573 3.6 51.8 1.0
O A:HOH527 3.6 63.6 1.0
OD1 A:ASP108 3.9 65.4 1.0
CA A:HIS89 3.9 70.4 1.0
NE1 A:TRP93 4.1 59.4 1.0
CG1 A:VAL159 4.3 38.9 1.0
CD2 A:HIS89 4.3 69.6 1.0
CB A:ASP108 4.4 56.0 1.0
NE2 A:HIS89 4.4 64.8 1.0
O A:HIS89 4.4 72.5 1.0
C A:HIS89 4.6 71.7 1.0
O A:HOH504 4.6 55.4 1.0
CD1 A:TRP93 4.9 55.4 1.0
CD A:LYS92 4.9 84.8 1.0
CE2 A:TRP93 5.0 54.9 1.0

Zinc binding site 5 out of 5 in 8uuw

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Zinc binding site 5 out of 5 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12145


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 JUN12145 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn408

b:88.3
occ:1.00
 O A:HOH555 2.3 87.2 1.0
SG A:CYS111 2.3 66.4 1.0
O A:HOH543 2.3 133.9 1.0
CD2 A:HIS272 2.7 88.8 1.0
NE1 A:TRP106 2.7 80.0 1.0
CB A:CYS111 2.9 73.0 1.0
NE2 A:HIS272 3.3 90.2 1.0
CE2 A:TRP106 3.4 91.5 1.0
CG A:HIS272 3.5 82.5 1.0
CZ2 A:TRP106 3.6 103.9 1.0
CD1 A:TRP106 3.9 108.7 1.0
O A:HOH576 4.0 72.9 1.0
CA A:HIS272 4.0 76.6 1.0
CB A:HIS272 4.1 78.7 1.0
N A:CYS111 4.1 59.6 1.0
CA A:CYS111 4.1 49.7 1.0
CE1 A:HIS272 4.2 90.9 1.0
ND1 A:HIS272 4.3 82.0 1.0
CA A:ASN109 4.4 70.1 1.0
N A:TYR273 4.5 73.6 1.0
O A:GLY271 4.6 72.9 1.0
C A:ASN109 4.7 66.9 1.0
CD2 A:TRP106 4.7 98.5 1.0
C A:HIS272 4.8 74.9 1.0
CH2 A:TRP106 4.9 103.1 1.0
CG A:TRP106 4.9 110.3 1.0
CB A:ASN109 5.0 76.4 1.0
N A:HIS272 5.0 77.4 1.0
OD1 A:ASN109 5.0 68.0 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 12:31:42 2024

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