Zinc in PDB 8uuh: Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12199

Enzymatic activity of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12199

All present enzymatic activity of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12199:
3.4.19.12;

Protein crystallography data

The structure of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12199, PDB code: 8uuh 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) 37.67 / 2.80
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 114.713, 114.713, 218.719, 90, 90, 90
R / Rfree (%) 22.7 / 26.2

Other elements in 8uuh:

The structure of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12199 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12199 (pdb code 8uuh). 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 JUN12199, PDB code: 8uuh:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 8uuh

Go back to Zinc Binding Sites List in 8uuh
Zinc binding site 1 out of 5 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12199


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 JUN12199 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:123.6
occ:1.00
 SG A:CYS226 2.3 114.1 1.0
SG A:CYS192 2.3 88.1 1.0
SG A:CYS224 2.3 103.6 1.0
SG A:CYS189 2.3 118.0 1.0
CB A:CYS192 3.3 97.5 1.0
CB A:CYS226 3.3 113.0 1.0
CB A:CYS224 3.4 108.9 1.0
CB A:CYS189 3.6 106.0 1.0
N A:CYS192 3.8 99.2 1.0
N A:CYS226 4.0 111.0 1.0
CA A:CYS192 4.2 98.6 1.0
CA A:CYS226 4.2 116.5 1.0
O A:HOH559 4.3 69.7 1.0
CB A:THR191 4.5 100.5 1.0
N A:GLY227 4.6 116.0 1.0
O A:GLY227 4.7 97.0 1.0
CA A:CYS224 4.8 107.4 1.0
C A:CYS226 4.8 113.2 1.0
N A:THR225 4.9 119.1 1.0
C A:THR191 4.9 103.0 1.0
C A:CYS224 5.0 114.1 1.0
CA A:CYS189 5.0 93.9 1.0

Zinc binding site 2 out of 5 in 8uuh

Go back to Zinc Binding Sites List in 8uuh
Zinc binding site 2 out of 5 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12199


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 JUN12199 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:47.0
occ:1.00
 CL A:CL411 2.2 55.3 1.0
ND1 A:HIS73 2.3 38.0 1.0
CL A:CL412 2.3 59.6 1.0
CG A:HIS73 3.0 45.3 1.0
CB A:HIS73 3.1 40.3 1.0
CE1 A:HIS73 3.4 54.3 1.0
CD2 A:HIS73 4.3 47.0 1.0
CB A:ASN128 4.3 42.2 1.0
NE2 A:HIS73 4.4 48.2 1.0
CA A:HIS73 4.5 45.9 1.0
O A:HIS73 4.6 53.6 1.0
CG A:PRO129 4.6 44.8 1.0
CD A:PRO129 4.7 48.3 1.0
N A:PRO129 4.9 49.1 1.0

Zinc binding site 3 out of 5 in 8uuh

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Zinc binding site 3 out of 5 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12199


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 JUN12199 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:75.3
occ:1.00
 OD2 A:ASP108 2.2 51.5 1.0
ZN A:ZN407 2.3 131.6 1.0
ND1 A:HIS89 2.3 60.0 1.0
CG A:ASP108 3.2 54.6 1.0
CE1 A:HIS89 3.2 72.9 1.0
CG A:HIS89 3.3 57.4 1.0
CB A:HIS89 3.6 63.9 1.0
OD1 A:ASP108 3.7 72.7 1.0
CG1 A:VAL159 4.3 41.8 1.0
CA A:HIS89 4.3 52.6 1.0
NE2 A:HIS89 4.4 61.2 1.0
CD2 A:HIS89 4.4 59.7 1.0
CB A:ASP108 4.4 45.9 1.0
NE1 A:TRP93 4.5 45.3 1.0

Zinc binding site 4 out of 5 in 8uuh

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Zinc binding site 4 out of 5 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12199


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 JUN12199 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:131.6
occ:1.00
 ZN A:ZN406 2.3 75.3 1.0
ND1 A:HIS89 3.1 60.0 1.0
CG A:HIS89 3.8 57.4 1.0
CA A:HIS89 3.9 52.6 1.0
CB A:HIS89 4.0 63.9 1.0
CE1 A:HIS89 4.0 72.9 1.0
CD A:LYS92 4.0 80.3 1.0
NZ A:LYS92 4.1 86.6 1.0
OD2 A:ASP108 4.2 51.5 1.0
O A:HIS89 4.4 55.5 1.0
CG A:LYS92 4.5 63.4 1.0
O A:ASN88 4.5 53.1 1.0
CB A:LYS92 4.5 48.0 1.0
C A:HIS89 4.6 55.0 1.0
CE A:LYS92 4.7 91.9 1.0
N A:HIS89 4.9 57.9 1.0
CD2 A:HIS89 4.9 59.7 1.0
NE2 A:HIS89 5.0 61.2 1.0

Zinc binding site 5 out of 5 in 8uuh

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Zinc binding site 5 out of 5 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12199


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 JUN12199 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn408

b:73.5
occ:1.00
 O A:HOH503 2.2 87.4 1.0
SG A:CYS111 2.3 57.0 1.0
ND1 A:HIS272 2.3 101.7 1.0
O A:HOH531 2.4 53.2 1.0
CB A:CYS111 2.9 52.1 1.0
CE1 A:HIS272 3.0 80.0 1.0
NE1 A:TRP106 3.0 84.4 1.0
CG A:HIS272 3.5 80.9 1.0
CZ2 A:TRP106 3.5 128.1 1.0
CE2 A:TRP106 3.6 115.5 1.0
CA A:HIS272 3.9 60.7 1.0
O A:GLY271 4.0 67.5 1.0
CB A:HIS272 4.0 55.5 1.0
CA A:CYS111 4.2 47.8 1.0
NE2 A:HIS272 4.2 67.6 1.0
CD1 A:TRP106 4.2 112.8 1.0
N A:CYS111 4.3 43.3 1.0
OD1 A:ASN109 4.4 62.9 1.0
CD2 A:HIS272 4.4 60.8 1.0
N A:TYR273 4.5 58.8 1.0
CA A:ASN109 4.6 67.3 1.0
C A:GLY271 4.8 71.5 1.0
CH2 A:TRP106 4.8 128.8 1.0
C A:HIS272 4.8 59.9 1.0
N A:HIS272 4.8 56.9 1.0
CD2 A:TRP106 4.9 114.9 1.0
C A:ASN109 4.9 62.2 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 12:30:22 2024

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