Bromine in PDB 8okm: Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.

All present enzymatic activity of Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.:
3.4.22.69;

The structure of Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2., PDB code: 8okm 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)	41.33 / 1.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.025, 100.036, 104.065, 90, 90, 90
R / Rfree (%)	16.3 / 18.7

The structure of Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Sodium	(Na)	1 atom

The binding sites of Bromine atom in the Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. (pdb code 8okm). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2., PDB code: 8okm:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. within 5.0Å range: probe atom residue distance (Å) B Occ A:Br406 b:31.1 occ:0.49 CL A:CL403 0.0 31.2 0.5 H B:ALA285 2.5 31.6 1.0 H A:ALA285 2.6 29.4 1.0 O B:HOH668 3.2 46.2 1.0 H A:LEU286 3.2 29.5 1.0 H B:LEU286 3.2 28.6 1.0 N B:ALA285 3.3 26.3 1.0 HA B:SER284 3.3 28.0 1.0 N A:ALA285 3.3 24.5 1.0 OG B:SER284 3.4 36.2 1.0 HG B:LEU286 3.4 37.6 1.0 OG A:SER284 3.4 38.9 1.0 HA A:SER284 3.4 30.9 1.0 HB3 A:ALA285 3.4 32.0 1.0 HG A:LEU286 3.5 37.1 1.0 HB3 B:ALA285 3.5 32.0 1.0 HD12 A:LEU286 3.7 36.1 1.0 HD12 B:LEU286 3.7 41.8 1.0 HG A:SER284 3.8 46.7 1.0 HB2 A:LEU286 3.8 31.3 1.0 N A:LEU286 3.8 24.6 1.0 HG B:SER284 3.8 43.4 1.0 N B:LEU286 3.9 23.8 1.0 HB2 B:LEU286 3.9 29.5 1.0 CA B:SER284 4.0 23.4 1.0 CA A:SER284 4.1 25.7 1.0 CA A:ALA285 4.1 24.5 1.0 CG B:LEU286 4.1 31.3 1.0 CA B:ALA285 4.1 23.9 1.0 C B:SER284 4.1 23.4 1.0 CB A:ALA285 4.2 26.6 1.0 CG A:LEU286 4.2 30.9 1.0 C A:SER284 4.2 26.9 1.0 CB B:SER284 4.2 23.4 1.0 CB B:ALA285 4.2 26.6 1.0 C A:ALA285 4.2 24.2 1.0 CB A:SER284 4.3 28.4 1.0 CD1 B:LEU286 4.3 34.9 1.0 CB A:LEU286 4.4 26.1 1.0 CD1 A:LEU286 4.4 30.1 1.0 C B:ALA285 4.4 27.4 1.0 CB B:LEU286 4.4 24.6 1.0 HB2 B:SER284 4.5 28.1 1.0 HB2 A:SER284 4.5 34.1 1.0 HB2 B:ALA285 4.6 32.0 1.0 HD11 B:LEU286 4.6 41.8 1.0 HB2 A:ALA285 4.6 32.0 1.0 CA A:LEU286 4.7 21.7 1.0 CA B:LEU286 4.8 24.0 1.0 HD11 A:LEU286 4.8 36.1 1.0 O A:HOH669 4.8 48.9 1.0 HB1 A:ALA285 4.9 32.0 1.0

Bromine binding site 2 out of 2 in the Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of F2F-2020197-00X Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2. within 5.0Å range: probe atom residue distance (Å) B Occ A:Br407 b:24.3 occ:0.47 CL A:CL404 0.0 24.0 0.5 H A:GLN107 2.5 23.3 1.0 HE21 A:GLN110 2.5 24.3 1.0 HA A:ILE106 3.1 22.0 1.0 HB2 A:GLN110 3.2 20.9 1.0 O A:HOH731 3.2 39.6 1.0 N A:GLN107 3.3 19.4 1.0 HB A:ILE106 3.3 20.7 1.0 NE2 A:GLN110 3.3 20.3 1.0 HB2 A:GLN107 3.4 29.8 1.0 HG2 A:GLN110 3.4 21.2 1.0 HG2 A:GLN107 3.5 35.0 1.0 HG22 A:ILE106 3.6 25.2 1.0 CA A:ILE106 3.8 18.3 1.0 HE22 A:GLN110 3.9 24.3 1.0 CB A:GLN110 3.9 17.5 1.0 CB A:ILE106 3.9 17.3 1.0 CG A:GLN110 3.9 17.6 1.0 CB A:GLN107 4.0 24.8 1.0 C A:ILE106 4.0 22.7 1.0 CG A:GLN107 4.1 29.2 1.0 CD A:GLN110 4.1 20.1 1.0 HB3 A:GLN110 4.2 20.9 1.0 CA A:GLN107 4.2 22.4 1.0 CG2 A:ILE106 4.2 20.9 1.0 O A:HOH519 4.4 36.2 1.0 HG3 A:GLN107 4.4 35.0 1.0 O A:GLN107 4.6 20.1 1.0 HG21 A:ILE106 4.6 25.2 1.0 HG3 A:GLN110 4.8 21.2 1.0 C A:GLN107 4.9 20.5 1.0 HB3 A:GLN107 4.9 29.8 1.0 O A:HOH718 4.9 37.1 1.0 O A:ARG105 4.9 24.2 1.0 O A:HOH567 5.0 41.2 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