Fluorine in PDB 8gfu: Room Temperature X-Ray Structure of Truncated Sars-Cov-2 Main Protease C145A Mutant, Residues 1-304, in Complex with Nirmatrelvir (Nmv)

The structure of Room Temperature X-Ray Structure of Truncated Sars-Cov-2 Main Protease C145A Mutant, Residues 1-304, in Complex with Nirmatrelvir (Nmv), PDB code: 8gfu was solved by A.Kovalevsky, L.Coates, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.25 / 1.80
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	52.223, 81.711, 91.702, 90, 95.39, 90
R / Rfree (%)	16.6 / 19.3

The binding sites of Fluorine atom in the Room Temperature X-Ray Structure of Truncated Sars-Cov-2 Main Protease C145A Mutant, Residues 1-304, in Complex with Nirmatrelvir (Nmv) (pdb code 8gfu). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Room Temperature X-Ray Structure of Truncated Sars-Cov-2 Main Protease C145A Mutant, Residues 1-304, in Complex with Nirmatrelvir (Nmv), PDB code: 8gfu:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Room Temperature X-Ray Structure of Truncated Sars-Cov-2 Main Protease C145A Mutant, Residues 1-304, in Complex with Nirmatrelvir (Nmv)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Room Temperature X-Ray Structure of Truncated Sars-Cov-2 Main Protease C145A Mutant, Residues 1-304, in Complex with Nirmatrelvir (Nmv) within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:49.0 occ:1.00 F33 A:ZGW401 0.0 49.0 1.0 C32 A:ZGW401 1.3 48.7 1.0 F34 A:ZGW401 2.2 52.9 1.0 F35 A:ZGW401 2.2 49.1 1.0 C21 A:ZGW401 2.4 44.2 1.0 N20 A:ZGW401 2.9 36.5 1.0 O A:GLU166 3.2 28.0 1.0 O22 A:ZGW401 3.3 47.1 1.0 O A:HOH539 3.3 51.5 1.0 CD A:PRO168 3.5 40.8 1.0 CA A:LEU167 3.7 31.6 1.0 CG A:PRO168 3.9 45.0 1.0 N A:PRO168 3.9 39.6 1.0 O A:THR190 4.0 55.0 1.0 C A:LEU167 4.1 34.7 1.0 CD2 A:LEU167 4.1 36.6 1.0 C A:GLU166 4.2 29.9 1.0 C15 A:ZGW401 4.3 34.0 1.0 N A:LEU167 4.4 29.0 1.0 O A:GLN192 4.6 45.3 1.0 CB A:LEU167 4.6 28.1 1.0 C19 A:ZGW401 4.7 37.8 1.0 CA A:PRO168 4.9 40.2 1.0 N A:GLN192 4.9 50.6 1.0 C16 A:ZGW401 5.0 40.0 1.0 O A:LEU167 5.0 34.7 1.0 CB A:PRO168 5.0 41.2 1.0 CG A:LEU167 5.0 33.6 1.0

Fluorine binding site 2 out of 3 in the Room Temperature X-Ray Structure of Truncated Sars-Cov-2 Main Protease C145A Mutant, Residues 1-304, in Complex with Nirmatrelvir (Nmv)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Room Temperature X-Ray Structure of Truncated Sars-Cov-2 Main Protease C145A Mutant, Residues 1-304, in Complex with Nirmatrelvir (Nmv) within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:52.9 occ:1.00 F34 A:ZGW401 0.0 52.9 1.0 C32 A:ZGW401 1.3 48.7 1.0 F33 A:ZGW401 2.2 49.0 1.0 F35 A:ZGW401 2.2 49.1 1.0 C21 A:ZGW401 2.4 44.2 1.0 N20 A:ZGW401 2.8 36.5 1.0 O A:GLU166 2.9 28.0 1.0 CD2 A:LEU167 3.3 36.6 1.0 O22 A:ZGW401 3.3 47.1 1.0 C A:GLU166 3.6 29.9 1.0 CE A:MET165 3.7 34.5 1.0 CG A:MET165 3.7 25.2 1.0 CA A:LEU167 3.8 31.6 1.0 SD A:MET165 4.0 34.3 1.0 N A:LEU167 4.0 29.0 1.0 CB A:MET165 4.1 25.6 1.0 C15 A:ZGW401 4.1 34.0 1.0 CG A:LEU167 4.3 33.6 1.0 NE2 A:GLN192 4.3 33.2 1.0 C14 A:ZGW401 4.5 37.0 1.0 N A:GLU166 4.5 21.0 1.0 CB A:LEU167 4.6 28.1 1.0 O23 A:ZGW401 4.6 33.7 1.0 CA A:GLU166 4.7 22.1 1.0 CD A:GLN192 4.8 33.4 1.0 O A:HOH539 4.9 51.5 1.0 C A:LEU167 4.9 34.7 1.0 O A:THR190 4.9 55.0 1.0 CD A:PRO168 5.0 40.8 1.0 C A:MET165 5.0 22.9 1.0

Fluorine binding site 3 out of 3 in the Room Temperature X-Ray Structure of Truncated Sars-Cov-2 Main Protease C145A Mutant, Residues 1-304, in Complex with Nirmatrelvir (Nmv)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Room Temperature X-Ray Structure of Truncated Sars-Cov-2 Main Protease C145A Mutant, Residues 1-304, in Complex with Nirmatrelvir (Nmv) within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:49.1 occ:1.00 F35 A:ZGW401 0.0 49.1 1.0 C32 A:ZGW401 1.4 48.7 1.0 F34 A:ZGW401 2.2 52.9 1.0 F33 A:ZGW401 2.2 49.0 1.0 C21 A:ZGW401 2.4 44.2 1.0 O22 A:ZGW401 2.7 47.1 1.0 O A:THR190 2.7 55.0 1.0 NE2 A:GLN192 3.3 33.2 1.0 N20 A:ZGW401 3.6 36.5 1.0 CG A:GLN192 3.6 40.2 1.0 CD A:GLN192 3.8 33.4 1.0 C A:THR190 3.9 48.4 1.0 O A:ARG188 4.0 33.8 1.0 N A:THR190 4.1 47.5 1.0 N A:GLN192 4.2 50.6 1.0 CB A:GLN192 4.2 38.6 1.0 CD2 A:LEU167 4.4 36.6 1.0 CE A:MET165 4.6 34.5 1.0 CA A:THR190 4.6 51.5 1.0 O A:GLU166 4.7 28.0 1.0 CA A:GLN189 4.7 47.0 1.0 CA A:GLN192 4.8 41.4 1.0 C A:GLN189 4.8 53.1 1.0 C15 A:ZGW401 4.8 34.0 1.0 OE1 A:GLN192 4.9 30.2 1.0 O A:GLN192 4.9 45.3 1.0 N A:ALA191 4.9 51.7 1.0

A.Kovalevsky, A.Aniana, L.Coates, P.V.Bonnesen, N.T.Nashed, J.M.Louis. Contribution of the Catalytic Dyad of Sars-Cov-2 Main Protease to Binding Covalent and Noncovalent Inhibitors. J.Biol.Chem. V. 299 04886 2023.
ISSN: ESSN 1083-351X
PubMed: 37271339
DOI: 10.1016/J.JBC.2023.104886