Zinc in PDB 8uuu: Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12162

Enzymatic activity of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12162

All present enzymatic activity of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12162:
3.4.19.12;

Protein crystallography data

The structure of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12162, PDB code: 8uuu 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) 29.35 / 3.01
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 115.393, 115.393, 220.691, 90, 90, 90
R / Rfree (%) 20.6 / 24.4

Other elements in 8uuu:

The structure of Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12162 also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12162 (pdb code 8uuu). 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 JUN12162, PDB code: 8uuu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8uuu

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Zinc binding site 1 out of 6 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12162


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 JUN12162 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:196.8
occ:1.00
 SG A:CYS111 1.9 64.2 1.0
O A:HOH570 2.4 79.0 1.0
O A:HOH529 2.4 97.9 1.0
ND1 A:HIS272 2.8 101.2 1.0
CB A:CYS111 3.0 65.2 1.0
NE1 A:TRP106 3.0 93.3 1.0
CZ2 A:TRP106 3.3 121.1 1.0
CE2 A:TRP106 3.4 95.2 1.0
CE1 A:HIS272 3.5 98.7 1.0
CG A:HIS272 3.9 101.9 1.0
N A:CYS111 4.0 42.9 1.0
CA A:CYS111 4.1 38.6 1.0
CD1 A:TRP106 4.2 124.3 1.0
CA A:HIS272 4.2 60.9 1.0
CB A:HIS272 4.3 71.8 1.0
CA A:ASN109 4.3 65.0 1.0
O A:GLY271 4.5 73.2 1.0
CH2 A:TRP106 4.5 123.0 1.0
C A:ASN109 4.6 52.3 1.0
CD2 A:TRP106 4.7 103.0 1.0
NE2 A:HIS272 4.7 114.8 1.0
CB A:ASN109 4.8 52.8 1.0
N A:TYR273 4.8 57.8 1.0
N A:ASN110 5.0 43.5 1.0
CD2 A:HIS272 5.0 116.8 1.0
O A:ASN109 5.0 62.4 1.0
OD1 A:ASN109 5.0 80.0 1.0

Zinc binding site 2 out of 6 in 8uuu

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Zinc binding site 2 out of 6 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12162


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 JUN12162 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:48.7
occ:1.00
 CL A:CL411 2.2 47.0 1.0
CL A:CL410 2.3 47.2 1.0
ND1 A:HIS73 2.3 42.6 1.0
CG A:HIS73 3.0 44.1 1.0
CE1 A:HIS73 3.1 37.1 1.0
CB A:HIS73 3.3 46.7 1.0
CD2 A:HIS73 4.0 43.5 1.0
NE2 A:HIS73 4.0 37.2 1.0
CB A:ASN128 4.2 37.7 1.0
CA A:HIS73 4.7 41.1 1.0
CG A:PRO129 4.8 35.4 1.0
CD A:PRO129 4.8 36.6 1.0
O A:HIS73 4.9 47.7 1.0
N A:PRO129 5.0 40.6 1.0

Zinc binding site 3 out of 6 in 8uuu

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Zinc binding site 3 out of 6 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12162


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 JUN12162 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:124.6
occ:1.00
 SG A:CYS192 2.3 89.9 1.0
SG A:CYS224 2.3 88.6 1.0
O A:THR225 3.0 115.1 1.0
CB A:CYS192 3.1 95.0 1.0
SG A:CYS189 3.2 99.1 1.0
CB A:CYS224 3.4 110.1 1.0
CB A:CYS189 3.8 106.6 1.0
N A:CYS192 3.8 111.5 1.0
CA A:CYS192 4.1 104.2 1.0
C A:THR225 4.1 105.9 1.0
N A:THR225 4.2 124.0 1.0
O A:HOH510 4.2 76.0 1.0
OG1 A:THR225 4.3 121.7 1.0
C A:CYS224 4.3 121.9 1.0
CA A:CYS224 4.5 116.3 1.0
CB A:THR191 4.7 105.4 1.0
CA A:THR225 4.7 118.2 1.0
O A:CYS224 4.8 114.2 1.0
C A:THR191 4.9 108.6 1.0

Zinc binding site 4 out of 6 in 8uuu

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Zinc binding site 4 out of 6 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12162


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 JUN12162 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:64.6
occ:1.00
 OD2 A:ASP108 2.1 49.8 1.0
ZN A:ZN407 2.3 110.8 1.0
ND1 A:HIS89 2.3 56.5 1.0
CE1 A:HIS89 3.0 67.7 1.0
CG A:ASP108 3.2 58.3 1.0
CG A:HIS89 3.4 52.7 1.0
OD1 A:ASP108 3.9 70.7 1.0
CB A:HIS89 3.9 58.5 1.0
O A:HOH546 4.0 64.3 1.0
CG1 A:VAL159 4.1 54.6 1.0
NE2 A:HIS89 4.2 45.1 1.0
CB A:ASP108 4.3 27.0 1.0
CD2 A:HIS89 4.4 48.2 1.0
NE1 A:TRP93 4.5 56.7 1.0
CA A:HIS89 4.6 46.3 1.0
O A:HOH572 4.8 62.6 1.0

Zinc binding site 5 out of 6 in 8uuu

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Zinc binding site 5 out of 6 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12162


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 JUN12162 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:110.8
occ:1.00
 ZN A:ZN406 2.3 64.6 1.0
CD A:LYS92 3.0 90.3 1.0
ND1 A:HIS89 3.2 56.5 1.0
O A:HOH572 3.3 62.6 1.0
CG A:LYS92 3.6 78.0 1.0
OD2 A:ASP108 3.7 49.8 1.0
CE A:LYS92 3.9 78.4 1.0
NZ A:LYS92 4.0 80.6 1.0
O A:HOH546 4.1 64.3 1.0
CE1 A:HIS89 4.1 67.7 1.0
CG A:HIS89 4.1 52.7 1.0
CA A:HIS89 4.2 46.3 1.0
O A:HIS89 4.2 43.1 1.0
CB A:HIS89 4.2 58.5 1.0
NE1 A:TRP93 4.5 56.7 1.0
C A:HIS89 4.7 45.8 1.0
CG A:ASP108 4.8 58.3 1.0
CD1 A:TRP93 4.9 50.7 1.0

Zinc binding site 6 out of 6 in 8uuu

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Zinc binding site 6 out of 6 in the Sars-Cov-2 Papain-Like Protease (Plpro) with Inhibitor JUN12162


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 JUN12162 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn408

b:242.5
occ:1.00
 NE2 A:HIS17 2.3 75.7 1.0
OE2 A:GLU67 2.3 94.0 1.0
CD2 A:HIS17 3.1 89.8 1.0
CE1 A:HIS17 3.3 89.5 1.0
CD A:GLU67 3.4 66.4 1.0
OE1 A:GLU67 3.7 75.7 1.0
CB A:ASN15 3.9 63.2 1.0
O A:HOH521 4.0 52.7 1.0
CG A:HIS17 4.3 85.6 1.0
ND1 A:HIS17 4.4 84.3 1.0
CG A:ASN15 4.7 77.9 1.0
CG A:GLU67 4.7 57.3 1.0
OD1 A:ASN15 4.9 75.4 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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