Chlorine in PDB 8cyz: Crystal Structure of Sars-Cov-2 Mpro with Compound C4

Enzymatic activity of Crystal Structure of Sars-Cov-2 Mpro with Compound C4

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Mpro with Compound C4:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Mpro with Compound C4, PDB code: 8cyz was solved by L.J.Worrall, J.Lee, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.75 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.43, 102.62, 102.22, 90, 100.19, 90
R / Rfree (%) 24.5 / 27.8

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Sars-Cov-2 Mpro with Compound C4 (pdb code 8cyz). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Sars-Cov-2 Mpro with Compound C4, PDB code: 8cyz:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 8cyz

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Chlorine binding site 1 out of 4 in the Crystal Structure of Sars-Cov-2 Mpro with Compound C4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Sars-Cov-2 Mpro with Compound C4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:36.4
occ:1.00
 CL01 A:P6I401 0.0 36.4 1.0
C18 A:P6I401 1.8 31.6 1.0
C09 A:P6I401 2.8 29.4 1.0
C12 A:P6I401 2.8 28.9 1.0
CE A:MET165 3.3 35.1 1.0
CB A:ASP187 3.4 23.4 1.0
CA A:ASP187 3.5 24.0 1.0
O A:HIS164 3.7 22.2 1.0
CB A:MET165 3.7 28.4 1.0
CD2 A:HIS41 3.7 28.9 1.0
CB A:HIS164 3.8 20.9 1.0
C19 A:P6I401 4.0 29.1 1.0
C A:HIS164 4.0 21.7 1.0
CZ A:PHE181 4.2 25.2 1.0
NE2 A:HIS41 4.2 30.4 1.0
C A:ASP187 4.3 24.1 1.0
S01 A:P6I401 4.3 34.3 1.0
O A:VAL186 4.5 21.5 1.0
CA A:HIS164 4.5 20.0 1.0
CE A:MET49 4.5 45.3 1.0
N A:ASP187 4.5 23.8 1.0
CG A:HIS164 4.6 21.2 1.0
N A:MET165 4.6 23.3 1.0
CA A:MET165 4.6 26.7 1.0
CD2 A:HIS164 4.6 19.8 1.0
O A:HOH620 4.6 18.1 1.0
SD A:MET165 4.7 39.6 1.0
CG A:HIS41 4.7 27.6 1.0
CG A:MET165 4.7 32.9 1.0
N A:ARG188 4.8 24.4 1.0
C A:VAL186 4.9 23.5 1.0
O A:ASP187 4.9 25.8 1.0
CG A:ASP187 4.9 25.1 1.0
CE1 A:PHE181 4.9 23.4 1.0

Chlorine binding site 2 out of 4 in 8cyz

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Chlorine binding site 2 out of 4 in the Crystal Structure of Sars-Cov-2 Mpro with Compound C4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Sars-Cov-2 Mpro with Compound C4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:41.1
occ:1.00
 CL01 B:P6I401 0.0 41.1 1.0
C18 B:P6I401 1.9 33.4 1.0
C12 B:P6I401 2.8 33.9 1.0
C09 B:P6I401 2.8 34.3 1.0
CB B:ASP187 3.3 26.6 1.0
CA B:ASP187 3.3 26.1 1.0
CE B:MET165 3.7 40.8 1.0
CD2 B:HIS41 3.7 23.3 1.0
CB B:HIS164 3.7 19.9 1.0
O B:HIS164 3.8 19.7 1.0
CB B:MET165 3.9 27.8 1.0
C19 B:P6I401 4.1 34.8 1.0
CZ B:PHE181 4.1 26.5 1.0
C B:HIS164 4.1 20.2 1.0
C B:ASP187 4.2 24.1 1.0
NE2 B:HIS41 4.3 26.6 1.0
S01 B:P6I401 4.3 38.7 1.0
CG B:MET165 4.4 35.2 1.0
CE B:MET49 4.4 43.3 1.0
N B:ASP187 4.4 25.1 1.0
ND1 B:HIS164 4.5 20.9 1.0
O B:VAL186 4.5 25.8 1.0
O B:HOH596 4.5 15.6 1.0
CA B:HIS164 4.5 20.0 1.0
CG B:HIS164 4.6 20.6 1.0
CA B:MET165 4.6 26.5 1.0
N B:MET165 4.7 22.3 1.0
CG B:HIS41 4.7 23.6 1.0
N B:ARG188 4.7 25.4 1.0
CG B:ASP187 4.8 30.4 1.0
O B:ASP187 4.8 26.1 1.0
C B:VAL186 4.8 24.7 1.0
CE1 B:PHE181 4.8 25.4 1.0
SD B:MET165 4.8 45.9 1.0
CE2 B:PHE181 5.0 27.1 1.0

Chlorine binding site 3 out of 4 in 8cyz

Go back to Chlorine Binding Sites List in 8cyz
Chlorine binding site 3 out of 4 in the Crystal Structure of Sars-Cov-2 Mpro with Compound C4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Sars-Cov-2 Mpro with Compound C4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl401

b:33.2
occ:1.00
 CL01 C:P6I401 0.0 33.2 1.0
C18 C:P6I401 1.8 32.5 1.0
C09 C:P6I401 2.8 32.1 1.0
C12 C:P6I401 2.8 33.1 1.0
CB C:ASP187 3.3 22.9 1.0
CA C:ASP187 3.3 22.9 1.0
CE C:MET165 3.6 32.7 1.0
CD2 C:HIS41 3.7 28.8 1.0
O C:HIS164 3.8 19.9 1.0
CB C:MET165 3.8 24.4 1.0
CB C:HIS164 3.8 18.8 1.0
C19 C:P6I401 4.0 31.4 1.0
C C:HIS164 4.1 20.4 1.0
CZ C:PHE181 4.1 14.9 1.0
C C:ASP187 4.2 25.4 1.0
NE2 C:HIS41 4.3 29.4 1.0
S01 C:P6I401 4.3 31.9 1.0
O C:VAL186 4.4 19.8 1.0
N C:ASP187 4.4 21.0 1.0
CE C:MET49 4.4 35.0 1.0
CA C:HIS164 4.5 19.6 1.0
CG C:HIS164 4.6 18.8 1.0
CD2 C:HIS164 4.6 19.2 1.0
O C:HOH588 4.6 19.6 1.0
CA C:MET165 4.6 22.3 1.0
N C:MET165 4.6 19.6 1.0
C C:VAL186 4.8 20.4 1.0
N C:ARG188 4.8 29.6 1.0
CG C:HIS41 4.8 29.2 1.0
SD C:MET165 4.8 34.6 1.0
CG C:ASP187 4.8 24.0 1.0
CG C:MET165 4.8 30.9 1.0
O C:ASP187 4.8 24.7 1.0
CE1 C:PHE181 4.9 15.3 1.0

Chlorine binding site 4 out of 4 in 8cyz

Go back to Chlorine Binding Sites List in 8cyz
Chlorine binding site 4 out of 4 in the Crystal Structure of Sars-Cov-2 Mpro with Compound C4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Sars-Cov-2 Mpro with Compound C4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:32.7
occ:1.00
 CL01 D:P6I401 0.0 32.7 1.0
C18 D:P6I401 1.8 32.6 1.0
C12 D:P6I401 2.8 34.7 1.0
C09 D:P6I401 2.8 32.0 1.0
CB D:ASP187 3.3 27.4 1.0
CA D:ASP187 3.3 27.4 1.0
CB D:MET165 3.7 31.4 1.0
CB D:HIS164 3.8 23.5 1.0
CD2 D:HIS41 3.8 31.6 1.0
O D:HIS164 3.8 24.5 1.0
C19 D:P6I401 4.0 34.0 1.0
CZ D:PHE181 4.1 17.5 1.0
C D:HIS164 4.2 24.5 1.0
C D:ASP187 4.2 28.0 1.0
S01 D:P6I401 4.2 37.3 1.0
O D:VAL186 4.3 22.9 1.0
N D:ASP187 4.4 26.9 1.0
NE2 D:HIS41 4.4 30.1 1.0
CE D:MET49 4.4 34.9 1.0
O D:HOH570 4.5 18.3 1.0
CA D:HIS164 4.6 22.8 1.0
CG D:HIS164 4.6 21.8 1.0
CD2 D:HIS164 4.6 20.8 1.0
CE D:MET165 4.6 41.5 1.0
CA D:MET165 4.6 28.4 1.0
N D:MET165 4.7 25.3 1.0
C D:VAL186 4.7 25.1 1.0
SD D:MET165 4.7 42.5 1.0
CG D:MET165 4.7 37.1 1.0
N D:ARG188 4.8 31.2 1.0
O D:ASP187 4.8 29.1 1.0
CG D:ASP187 4.8 27.5 1.0
CG D:HIS41 4.9 31.3 1.0
CE1 D:PHE181 4.9 18.0 1.0
CE2 D:PHE181 5.0 16.9 1.0

Reference:

J.Perez-Vargas, L.J.Worrall, A.D.Olmstead, A.T.Ton, J.Lee, I.Villanueva, C.A.H.Thompson, S.Dudek, S.Ennis, J.R.Smith, T.Shapira, J.De Guzman, S.Gang, F.Ban, M.Vuckovic, M.Bielecki, S.Kovacic, C.Kenward, C.Y.Hong, D.G.Gordon, P.N.Levett, M.Krajden, R.Leduc, P.L.Boudreault, M.Niikura, M.Paetzel, R.N.Young, A.Cherkasov, N.C.J.Strynadka, F.Jean. A Novel Class of Broad-Spectrum Active-Site-Directed 3C-Like Protease Inhibitors with Nanomolar Antiviral Activity Against Highly Immune-Evasive Sars-Cov-2 Omicron Subvariants. Emerg Microbes Infect V. 12 46594 2023.
ISSN: ESSN 2222-1751
PubMed: 37555275
DOI: 10.1080/22221751.2023.2246594
Page generated: Tue Jul 30 08:19:06 2024

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