Bromine in PDB 7grf: Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-2

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-2:
3.4.22.69;

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-2, PDB code: 7grf was solved by C.-Y.Huang, A.Metz, M.Sharpe, A.Sweeney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.68 / 1.84
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.71, 99.47, 103.64, 90, 90, 90
R / Rfree (%)	19.7 / 23.9

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-2 also contains other interesting chemical elements:

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

The binding sites of Bromine atom in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-2 (pdb code 7grf). 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 Sars-Cov-2 Main Protease in Complex with Cpd-2, PDB code: 7grf:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-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 Sars-Cov-2 Main Protease in Complex with Cpd-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br501 b:73.4 occ:0.70 BR07 A:XWZ501 0.0 73.4 0.7 C06 A:XWZ501 1.9 29.1 0.7 C05 A:XWZ501 2.9 23.4 0.7 C08 A:XWZ501 2.9 32.7 0.7 O B:HOH560 3.2 33.4 1.0 OE1 A:GLU166 3.5 26.3 1.0 N B:SER1 3.7 24.0 1.0 OD1 A:ASN142 3.8 39.0 1.0 O A:PHE140 3.9 23.6 1.0 CD A:GLU166 3.9 28.1 1.0 O A:HOH608 4.0 27.4 1.0 OE2 A:GLU166 4.0 34.7 1.0 N04 A:XWZ501 4.1 17.4 0.7 N A:ASN142 4.2 26.1 1.0 C02 A:XWZ501 4.2 30.4 0.7 C A:LEU141 4.3 22.3 1.0 CA A:LEU141 4.4 21.9 1.0 CG A:ASN142 4.4 45.1 1.0 CB A:GLU166 4.6 24.8 1.0 OG B:SER1 4.6 40.2 1.0 C03 A:XWZ501 4.6 26.8 0.7 C A:PHE140 4.7 25.2 1.0 ND2 A:ASN142 4.8 56.5 1.0 CG A:GLU166 4.8 27.0 1.0 CA A:ASN142 4.9 28.4 1.0 O A:LEU141 4.9 23.7 1.0 CA B:SER1 5.0 29.6 1.0

Bromine binding site 2 out of 2 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with Cpd-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 Sars-Cov-2 Main Protease in Complex with Cpd-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br401 b:84.4 occ:0.61 BR07 B:XWZ401 0.0 84.4 0.6 C06 B:XWZ401 1.9 40.7 0.6 C05 B:XWZ401 2.9 28.2 0.6 C08 B:XWZ401 2.9 41.5 0.6 OE1 B:GLU166 3.5 31.5 1.0 OD1 B:ASN142 3.6 53.0 1.0 N A:SER1 3.7 25.9 1.0 O A:HOH719 3.7 43.5 1.0 O B:PHE140 3.8 34.4 1.0 CD B:GLU166 3.9 34.7 1.0 CA B:LEU141 4.0 34.1 1.0 OE2 B:GLU166 4.0 34.7 1.0 C B:LEU141 4.0 37.3 1.0 N B:ASN142 4.0 37.9 1.0 N04 B:XWZ401 4.1 23.6 0.6 C02 B:XWZ401 4.2 31.9 0.6 C B:PHE140 4.5 34.3 1.0 O B:LEU141 4.6 33.6 1.0 CG B:ASN142 4.6 52.0 1.0 N B:LEU141 4.6 32.0 1.0 C03 B:XWZ401 4.6 29.7 0.6 CB B:GLU166 4.6 26.3 1.0 CA B:ASN142 4.8 30.7 1.0 CG B:GLU166 4.9 24.2 1.0

C.Y.Huang, A.Metz, R.Lange, N.Artico, C.Potot, J.Hazemann, M.Muller, M.Dos Santos, A.Chambovey, D.Ritz, D.Eris, S.Meyer, G.Bourquin, M.Sharpe, A.Mac Sweeney. Fragment-Based Screening Targeting An Open Form of the Sars-Cov-2 Main Protease Binding Pocket. Acta Crystallogr D Struct V. 80 123 2024BIOL.
ISSN: ISSN 2059-7983
PubMed: 38289714
DOI: 10.1107/S2059798324000329