Chlorine in PDB 8uvm: Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Covalent Inhibitor JUN11313

Enzymatic activity of Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Covalent Inhibitor JUN11313

All present enzymatic activity of Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Covalent Inhibitor JUN11313:
3.4.19.12;

Protein crystallography data

The structure of Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Covalent Inhibitor JUN11313, PDB code: 8uvm was solved by A.Ansari, B.Tan, A.Chopra, 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) 41.90 / 2.85
Space group P 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 190.997, 190.997, 112.926, 90, 90, 120
R / Rfree (%) 17.8 / 20.4

Other elements in 8uvm:

The structure of Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Covalent Inhibitor JUN11313 also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Covalent Inhibitor JUN11313 (pdb code 8uvm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Covalent Inhibitor JUN11313, PDB code: 8uvm:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 8uvm

Go back to Chlorine Binding Sites List in 8uvm
Chlorine binding site 1 out of 5 in the Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Covalent Inhibitor JUN11313


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Covalent Inhibitor JUN11313 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:61.3
occ:1.00
 N A:PHE127 3.3 46.1 1.0
CB A:PHE127 3.9 48.3 1.0
CD A:LYS126 3.9 70.5 1.0
CD2 A:PHE127 3.9 45.2 1.0
CA A:GLN133 3.9 35.3 1.0
CG A:GLN133 3.9 40.8 1.0
CA A:LYS126 4.1 57.9 1.0
CA A:PHE127 4.1 47.8 1.0
C A:LYS126 4.1 50.6 1.0
CB A:GLN133 4.2 38.5 1.0
O A:PHE127 4.3 46.9 1.0
NZ A:LYS126 4.3 74.5 1.0
CG A:PHE127 4.4 50.5 1.0
CE A:LYS126 4.4 75.5 1.0
O A:LEU125 4.4 62.2 1.0
CD2 A:TYR136 4.6 59.0 1.0
C A:PHE127 4.6 43.7 1.0
O A:GLN133 4.7 46.4 1.0
N A:GLN133 4.8 40.9 1.0
C A:GLN133 4.9 41.0 1.0
CB A:LYS126 4.9 50.6 1.0
CG A:LYS126 4.9 60.3 1.0
CD A:GLN133 4.9 41.9 1.0
CB A:TYR136 4.9 35.2 1.0
O A:LEU132 5.0 43.8 1.0
CE2 A:PHE127 5.0 53.4 1.0

Chlorine binding site 2 out of 5 in 8uvm

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Chlorine binding site 2 out of 5 in the Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Covalent Inhibitor JUN11313


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Covalent Inhibitor JUN11313 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl403

b:59.3
occ:1.00
 N B:PHE127 3.1 43.8 1.0
CG B:GLN133 3.8 44.3 1.0
CB B:PHE127 3.8 44.2 1.0
CD2 B:PHE127 3.9 50.4 1.0
CA B:GLN133 3.9 51.3 1.0
CA B:LYS126 3.9 48.2 1.0
CA B:PHE127 4.0 48.6 1.0
C B:LYS126 4.0 46.9 1.0
CD B:LYS126 4.0 76.0 1.0
CB B:GLN133 4.1 37.6 1.0
O B:PHE127 4.2 53.2 1.0
CG B:PHE127 4.3 42.6 1.0
O B:LEU125 4.4 68.6 1.0
C B:PHE127 4.6 50.6 1.0
CD2 B:TYR136 4.6 74.7 1.0
N B:GLN133 4.7 48.2 1.0
CD B:GLN133 4.8 55.4 1.0
O B:GLN133 4.8 66.1 1.0
O B:LEU132 4.8 49.2 1.0
CB B:LYS126 4.8 50.2 1.0
CG B:LYS126 4.9 68.0 1.0
NZ B:LYS126 4.9 71.6 1.0
C B:GLN133 4.9 60.2 1.0
CE B:LYS126 4.9 68.2 1.0
N B:LYS126 4.9 56.9 1.0
CE2 B:PHE127 4.9 58.7 1.0

Chlorine binding site 3 out of 5 in 8uvm

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Chlorine binding site 3 out of 5 in the Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Covalent Inhibitor JUN11313


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Covalent Inhibitor JUN11313 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl403

b:79.2
occ:1.00
 CD2 C:PHE127 3.3 54.7 1.0
N C:PHE127 3.4 64.6 1.0
CD2 C:TYR136 3.6 67.8 1.0
CA C:LYS126 3.8 63.4 1.0
C C:LYS126 4.1 73.4 1.0
O C:LEU125 4.1 69.9 1.0
CG C:PHE127 4.1 59.8 1.0
CA C:GLN133 4.1 46.4 1.0
CB C:PHE127 4.1 57.9 1.0
CE2 C:PHE127 4.1 55.7 1.0
CG C:GLN133 4.2 52.9 1.0
CA C:PHE127 4.3 53.6 1.0
CB C:LYS126 4.4 60.3 1.0
CE2 C:TYR136 4.4 77.3 1.0
CB C:TYR136 4.5 62.5 1.0
CB C:GLN133 4.5 40.5 1.0
CG C:TYR136 4.5 65.7 1.0
O C:LEU132 4.7 53.2 1.0
O C:GLN133 4.8 65.0 1.0
N C:LYS126 4.8 67.5 1.0
N C:GLN133 4.8 50.5 1.0
C C:LEU125 4.9 73.0 1.0
O C:PHE127 4.9 61.9 1.0
C C:GLN133 5.0 60.0 1.0

Chlorine binding site 4 out of 5 in 8uvm

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Chlorine binding site 4 out of 5 in the Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Covalent Inhibitor JUN11313


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Covalent Inhibitor JUN11313 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl403

b:90.5
occ:1.00
 N D:SER294 3.1 85.5 1.0
CB D:SER294 3.6 84.7 1.0
OG D:SER294 3.6 88.8 1.0
CA D:SER293 3.9 77.2 1.0
CA D:SER294 3.9 85.9 1.0
C D:SER293 4.0 77.2 1.0
CB D:SER293 4.3 74.7 1.0
N D:GLU295 4.7 74.9 1.0
C D:SER294 4.8 76.3 1.0

Chlorine binding site 5 out of 5 in 8uvm

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Chlorine binding site 5 out of 5 in the Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Covalent Inhibitor JUN11313


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Sars-Cov-2 Papain-Like Protease (Plpro) Complex with Covalent Inhibitor JUN11313 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl404

b:54.5
occ:1.00
 N D:PHE127 3.1 46.6 1.0
CG D:LYS126 3.7 52.9 1.0
CA D:LYS126 3.7 40.6 1.0
CD2 D:TYR136 3.8 49.4 1.0
C D:LYS126 3.9 49.3 1.0
CG D:GLN133 4.0 38.8 1.0
CA D:GLN133 4.0 34.0 1.0
CB D:PHE127 4.0 46.7 1.0
CA D:PHE127 4.1 51.4 1.0
CD2 D:PHE127 4.1 40.9 1.0
CB D:GLN133 4.2 31.6 1.0
CB D:LYS126 4.3 38.6 1.0
O D:PHE127 4.3 48.8 1.0
CG D:PHE127 4.5 52.4 1.0
CE2 D:TYR136 4.5 39.7 1.0
O D:GLN133 4.6 40.0 1.0
O D:LEU125 4.6 42.9 1.0
CB D:TYR136 4.7 38.3 1.0
C D:PHE127 4.7 51.4 1.0
CG D:TYR136 4.7 47.3 1.0
C D:GLN133 4.8 35.0 1.0
N D:LYS126 4.9 45.9 1.0
CD D:LYS126 4.9 60.5 1.0
O D:LEU132 4.9 50.6 1.0
CD D:GLN133 4.9 32.7 1.0
CE D:LYS126 5.0 68.0 1.0
N D:GLN133 5.0 45.8 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: Tue Jul 30 13:26:34 2024

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