Chlorine in PDB 8okk: Crystal Structure of F2F-2020184-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.

All present enzymatic activity of Crystal Structure of F2F-2020184-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.:
3.4.22.69;

The structure of Crystal Structure of F2F-2020184-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2., PDB code: 8okk was solved by E.Costanzi, N.Demitri, P.Storici, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.92 / 1.63
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.001, 99.431, 104.033, 90, 90, 90
R / Rfree (%)	15.2 / 17.8

The structure of Crystal Structure of F2F-2020184-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

The binding sites of Chlorine atom in the Crystal Structure of F2F-2020184-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. (pdb code 8okk). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of F2F-2020184-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2., PDB code: 8okk:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of F2F-2020184-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.


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 F2F-2020184-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl412 b:28.7 occ:1.00 H A:ALA285 2.3 25.0 1.0 H B:ALA285 2.3 23.0 1.0 O B:HOH509 2.8 41.7 1.0 O A:HOH605 3.0 38.0 1.0 N A:ALA285 3.1 20.9 1.0 N B:ALA285 3.1 19.2 1.0 HA B:SER284 3.2 21.4 1.0 H A:LEU286 3.2 21.4 1.0 HA A:SER284 3.2 24.3 1.0 H B:LEU286 3.3 22.3 1.0 OG A:SER284 3.3 31.0 1.0 HG A:LEU286 3.3 33.9 1.0 HG B:LEU286 3.4 38.1 1.0 OG B:SER284 3.4 28.4 1.0 HB3 A:ALA285 3.4 26.6 1.0 HB3 B:ALA285 3.4 25.5 1.0 HD12 A:LEU286 3.5 31.0 1.0 N A:LEU286 3.7 17.9 1.0 HD12 B:LEU286 3.7 33.9 1.0 HG A:SER284 3.8 37.2 1.0 HB2 A:LEU286 3.8 24.6 1.0 N B:LEU286 3.9 18.6 1.0 CA B:SER284 3.9 17.8 1.0 HG B:SER284 3.9 34.0 1.0 CA A:SER284 3.9 20.2 1.0 CA A:ALA285 3.9 18.2 1.0 HB2 B:LEU286 4.0 26.7 1.0 C A:SER284 4.0 19.9 1.0 C B:SER284 4.0 17.5 1.0 CA B:ALA285 4.0 17.3 1.0 CG A:LEU286 4.0 28.3 1.0 C A:ALA285 4.1 18.8 1.0 CB A:ALA285 4.1 22.1 1.0 CG B:LEU286 4.1 31.8 1.0 CB B:SER284 4.1 19.3 1.0 CB B:ALA285 4.1 21.3 1.0 CB A:SER284 4.2 22.4 1.0 CD1 A:LEU286 4.2 25.9 1.0 C B:ALA285 4.3 20.4 1.0 CB A:LEU286 4.3 20.5 1.0 CD1 B:LEU286 4.3 28.3 1.0 HB2 B:SER284 4.4 23.1 1.0 CB B:LEU286 4.4 22.3 1.0 HB2 A:ALA285 4.5 26.6 1.0 HB2 B:ALA285 4.5 25.5 1.0 HB2 A:SER284 4.5 26.9 1.0 HD11 A:LEU286 4.6 31.0 1.0 CA A:LEU286 4.6 18.7 1.0 HD11 B:LEU286 4.6 33.9 1.0 OE2 B:GLU288 4.7 26.5 0.4 CA B:LEU286 4.8 18.9 1.0 HA A:ALA285 4.8 21.8 1.0 HB1 A:ALA285 4.8 26.6 1.0 HA B:ALA285 4.9 20.8 1.0 HB1 B:ALA285 4.9 25.5 1.0 OE2 A:GLU288 4.9 24.4 0.4 HB3 A:SER284 5.0 26.9 1.0 O B:GLY283 5.0 25.1 1.0 HD13 A:LEU286 5.0 31.0 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of F2F-2020184-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.


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 F2F-2020184-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl411 b:15.0 occ:1.00 H B:THR224 2.5 22.7 1.0 HA B:PHE223 3.0 21.9 1.0 HD1 B:PHE223 3.0 23.9 1.0 N B:THR224 3.3 18.9 1.0 HG22 B:THR224 3.5 27.5 1.0 HB3 B:PHE223 3.6 23.4 1.0 O B:THR224 3.7 24.8 1.0 CA B:PHE223 3.7 18.2 1.0 HG23 B:THR224 3.8 27.5 1.0 CD1 B:PHE223 3.9 20.0 1.0 C B:PHE223 4.1 18.0 1.0 CB B:PHE223 4.1 19.5 1.0 CG2 B:THR224 4.1 23.0 1.0 CA B:THR224 4.3 20.2 1.0 C B:THR224 4.4 22.3 1.0 CG B:PHE223 4.5 18.9 1.0 O B:HOH688 4.7 40.0 1.0 O B:ARG222 4.7 18.3 1.0 CB B:THR224 4.7 22.3 1.0 HG21 B:THR224 4.9 27.5 1.0 CE1 B:PHE223 4.9 20.5 1.0 HE1 B:PHE223 4.9 24.5 1.0 HB B:THR224 4.9 26.7 1.0 N B:PHE223 5.0 17.5 1.0 HB2 B:PHE223 5.0 23.4 1.0

I.Stefanelli, A.Corona, C.Cerchia, E.Cassese, S.Improta, E.Costanzi, S.Pelliccia, S.Morasso, F.Esposito, A.Paulis, S.Scognamiglio, F.S.Di Leva, P.Storici, M.Brindisi, E.Tramontano, R.Cannalire, V.Summa. Broad-Spectrum Coronavirus 3C-Like Protease Peptidomimetic Inhibitors Effectively Block Sars-Cov-2 Replication in Cells: Design, Synthesis, Biological Evaluation, and X-Ray Structure Determination. Eur.J.Med.Chem. V. 253 15311 2023.
ISSN: ISSN 0223-5234
PubMed: 37043904
DOI: 10.1016/J.EJMECH.2023.115311