Fluorine in PDB 8u40: Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor

All present enzymatic activity of Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor:
3.4.22.69;

The structure of Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor, PDB code: 8u40 was solved by P.Chen, E.Arutyunova, J.Lu, H.S.Young, M.J.Lemieux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.02 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.11, 54.093, 113.458, 90, 101.64, 90
R / Rfree (%)	22.6 / 27.4

The binding sites of Fluorine atom in the Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor (pdb code 8u40). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor, PDB code: 8u40:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:58.9 occ:1.00 F18 A:V8X401 0.0 58.9 1.0 C17 A:V8X401 1.4 56.4 1.0 C19 A:V8X401 2.4 52.8 1.0 C16 A:V8X401 2.4 53.0 1.0 H191 A:V8X401 2.6 63.5 1.0 H161 A:V8X401 2.6 63.6 1.0 N A:ALA191 3.6 69.3 1.0 C20 A:V8X401 3.6 53.3 1.0 C15 A:V8X401 3.7 52.6 1.0 CB A:ALA191 3.7 74.9 1.0 CA A:ALA191 3.9 68.2 1.0 C A:THR190 4.0 58.7 1.0 C22 A:V8X401 4.1 52.1 1.0 O A:THR190 4.5 53.5 1.0 CA A:THR190 4.6 58.3 1.0 F21 A:V8X401 4.8 54.5 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:54.5 occ:1.00 F21 A:V8X401 0.0 54.5 1.0 C20 A:V8X401 1.4 53.3 1.0 C22 A:V8X401 2.4 52.1 1.0 C19 A:V8X401 2.4 52.8 1.0 H191 A:V8X401 2.7 63.5 1.0 N23 A:V8X401 2.9 46.8 1.0 N A:PRO168 2.9 49.0 1.0 C A:LEU167 3.0 50.8 1.0 O A:GLU166 3.0 44.7 1.0 O A:LEU167 3.3 52.9 1.0 CD A:PRO168 3.4 51.5 1.0 CA A:LEU167 3.5 48.9 1.0 CA A:PRO168 3.5 50.0 1.0 C15 A:V8X401 3.7 52.6 1.0 C17 A:V8X401 3.7 56.4 1.0 CG A:PRO168 3.7 54.4 1.0 C A:GLU166 3.8 48.7 1.0 N A:LEU167 4.0 46.1 1.0 CB A:PRO168 4.2 51.8 1.0 C16 A:V8X401 4.2 53.0 1.0 C13 A:V8X401 4.2 49.1 1.0 C14 A:V8X401 4.6 49.8 1.0 F18 A:V8X401 4.8 58.9 1.0 C A:PRO168 4.8 53.3 1.0 CB A:LEU167 4.8 47.0 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:67.0 occ:1.00 F18 B:V8X401 0.0 67.0 1.0 C17 B:V8X401 1.4 64.0 1.0 C19 B:V8X401 2.4 62.6 1.0 C16 B:V8X401 2.4 62.4 1.0 H191 B:V8X401 2.6 75.2 1.0 H161 B:V8X401 2.6 75.0 1.0 N B:ALA191 3.6 79.7 1.0 CB B:ALA191 3.6 83.3 1.0 C20 B:V8X401 3.6 61.0 1.0 C15 B:V8X401 3.7 61.7 1.0 CA B:ALA191 3.8 78.2 1.0 C B:THR190 3.9 66.8 1.0 C22 B:V8X401 4.1 60.0 1.0 O B:THR190 4.3 61.5 1.0 CA B:THR190 4.6 64.9 1.0 F21 B:V8X401 4.8 58.3 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:58.3 occ:1.00 F21 B:V8X401 0.0 58.3 1.0 C20 B:V8X401 1.4 61.0 1.0 C19 B:V8X401 2.4 62.6 1.0 C22 B:V8X401 2.4 60.0 1.0 H191 B:V8X401 2.7 75.2 1.0 N B:PRO168 2.9 48.3 1.0 N23 B:V8X401 3.0 52.8 1.0 C B:LEU167 3.0 50.4 1.0 O B:GLU166 3.1 46.7 1.0 CD B:PRO168 3.4 56.2 1.0 O B:LEU167 3.4 51.1 1.0 CA B:PRO168 3.5 50.5 1.0 CA B:LEU167 3.5 50.6 1.0 C17 B:V8X401 3.7 64.0 1.0 C15 B:V8X401 3.7 61.7 1.0 C B:GLU166 3.9 49.8 1.0 N B:LEU167 4.0 48.8 1.0 CG B:PRO168 4.1 56.9 1.0 CB B:PRO168 4.2 50.1 1.0 C16 B:V8X401 4.2 62.4 1.0 C13 B:V8X401 4.3 55.6 1.0 C14 B:V8X401 4.7 56.5 1.0 C B:PRO168 4.8 51.8 1.0 F18 B:V8X401 4.8 67.0 1.0 CB B:LEU167 4.9 46.9 1.0

P.Chen, E.Arutyunova, J.Lu, H.S.Young, M.J.Lemieux. Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor To Be Published.