Fluorine in PDB 8dz1: Crystal Structure of Sars-Cov-2 Main Protease Mutant M49I in Complex with Ensitrelvir

The structure of Crystal Structure of Sars-Cov-2 Main Protease Mutant M49I in Complex with Ensitrelvir, PDB code: 8dz1 was solved by G.D.Noske, G.Oliva, A.S.Godoy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.52 / 2.08
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.59, 99.066, 103.352, 90, 90, 90
R / Rfree (%)	21.8 / 25.6

The structure of Crystal Structure of Sars-Cov-2 Main Protease Mutant M49I in Complex with Ensitrelvir also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease Mutant M49I in Complex with Ensitrelvir (pdb code 8dz1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Sars-Cov-2 Main Protease Mutant M49I in Complex with Ensitrelvir, PDB code: 8dz1:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease Mutant M49I in Complex with Ensitrelvir


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 Sars-Cov-2 Main Protease Mutant M49I in Complex with Ensitrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:99.1 occ:1.00 F28 A:7YY403 0.0 99.1 1.0 C27 A:7YY403 1.4 75.2 1.0 NE2 A:GLN189 2.0 85.8 1.0 C26 A:7YY403 2.4 64.9 1.0 C29 A:7YY403 2.4 62.9 1.0 C25 A:7YY403 2.8 75.0 1.0 CD A:GLN189 3.2 92.2 1.0 C34 A:7YY403 3.6 58.2 1.0 C30 A:7YY403 3.6 48.6 1.0 OE1 A:GLN189 3.9 93.6 1.0 C32 A:7YY403 4.1 64.3 1.0 N24 A:7YY403 4.2 70.8 1.0 CB A:GLN189 4.2 56.8 1.0 CG A:GLN189 4.2 59.4 1.0 CA A:GLN189 4.6 48.6 1.0 O36 A:7YY403 4.6 57.4 1.0 CG2 A:ILE49 4.6 55.4 1.0 F31 A:7YY403 4.8 48.5 1.0 C35 A:7YY403 4.9 64.5 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease Mutant M49I in Complex with Ensitrelvir


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 Sars-Cov-2 Main Protease Mutant M49I in Complex with Ensitrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:48.5 occ:1.00 F31 A:7YY403 0.0 48.5 1.0 C30 A:7YY403 1.4 48.6 1.0 C32 A:7YY403 2.4 64.3 1.0 C29 A:7YY403 2.4 62.9 1.0 F33 A:7YY403 2.7 68.2 1.0 C A:ASP187 3.1 33.7 1.0 CA A:ASP187 3.2 24.2 1.0 N A:ARG188 3.3 36.4 1.0 O A:ASP187 3.5 29.8 1.0 CB A:ASP187 3.5 28.5 1.0 C27 A:7YY403 3.6 75.2 1.0 C34 A:7YY403 3.6 58.2 1.0 CA A:ARG188 4.0 38.2 1.0 SD A:MET165 4.0 40.7 1.0 C26 A:7YY403 4.1 64.9 1.0 C A:ARG188 4.2 40.0 1.0 O A:ARG188 4.3 38.7 1.0 CE A:MET165 4.3 47.8 1.0 CB A:HIS41 4.4 32.4 1.0 CG A:HIS41 4.6 34.2 1.0 N A:ASP187 4.6 31.0 1.0 O A:VAL186 4.6 32.3 1.0 ND1 A:HIS41 4.7 41.9 1.0 OH A:TYR54 4.7 35.1 1.0 CB A:MET165 4.7 33.9 1.0 F28 A:7YY403 4.8 99.1 1.0 N A:GLN189 4.8 41.4 1.0 O A:HOH533 4.9 37.0 1.0 CG A:MET165 4.9 35.8 1.0 CG A:ASP187 4.9 30.6 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease Mutant M49I in Complex with Ensitrelvir


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 Sars-Cov-2 Main Protease Mutant M49I in Complex with Ensitrelvir within 5.0Å range: probe atom residue distance (Å) B Occ A:F403 b:68.2 occ:1.00 F33 A:7YY403 0.0 68.2 1.0 C32 A:7YY403 1.4 64.3 1.0 C30 A:7YY403 2.4 48.6 1.0 ND1 A:HIS41 2.4 41.9 1.0 C34 A:7YY403 2.4 58.2 1.0 CE1 A:HIS41 2.7 43.8 1.0 F31 A:7YY403 2.7 48.5 1.0 CG A:HIS41 2.9 34.2 1.0 NE2 A:HIS41 3.2 48.0 1.0 O A:HIS164 3.2 35.3 1.0 CD2 A:HIS41 3.3 45.1 1.0 CB A:HIS41 3.6 32.4 1.0 C29 A:7YY403 3.6 62.9 1.0 C26 A:7YY403 3.6 64.9 1.0 C A:HIS164 3.9 31.3 1.0 O A:HOH533 4.1 37.0 1.0 C27 A:7YY403 4.1 75.2 1.0 CB A:HIS164 4.4 28.7 1.0 CB A:MET165 4.5 33.9 1.0 CA A:HIS164 4.5 25.2 1.0 CB A:ASP187 4.6 28.5 1.0 N A:MET165 4.7 27.2 1.0 CA A:MET165 4.8 29.5 1.0 ND1 A:HIS164 4.8 25.6 1.0 C25 A:7YY403 4.9 75.0 1.0 CG A:MET165 5.0 35.8 1.0 SG A:CYS145 5.0 46.1 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease Mutant M49I in Complex with Ensitrelvir


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 Sars-Cov-2 Main Protease Mutant M49I in Complex with Ensitrelvir within 5.0Å range: probe atom residue distance (Å) B Occ B:F402 b:93.7 occ:1.00 F28 B:7YY402 0.0 93.7 1.0 C27 B:7YY402 1.4 86.8 1.0 C29 B:7YY402 2.4 77.4 1.0 C26 B:7YY402 2.4 82.3 1.0 C25 B:7YY402 2.8 87.8 1.0 O36 B:7YY402 3.5 67.8 1.0 C30 B:7YY402 3.6 74.0 1.0 C34 B:7YY402 3.6 79.9 1.0 N24 B:7YY402 4.0 87.1 1.0 C32 B:7YY402 4.1 78.3 1.0 C35 B:7YY402 4.2 76.7 1.0 OE1 B:GLN189 4.6 109.8 1.0 F31 B:7YY402 4.8 68.2 1.0 CG B:GLN189 5.0 101.7 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease Mutant M49I in Complex with Ensitrelvir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Sars-Cov-2 Main Protease Mutant M49I in Complex with Ensitrelvir within 5.0Å range: probe atom residue distance (Å) B Occ B:F402 b:68.2 occ:1.00 F31 B:7YY402 0.0 68.2 1.0 C30 B:7YY402 1.4 74.0 1.0 C32 B:7YY402 2.4 78.3 1.0 C29 B:7YY402 2.4 77.4 1.0 F33 B:7YY402 2.7 84.2 1.0 C B:ASP187 3.1 61.0 1.0 N B:ARG188 3.2 64.9 1.0 CA B:ASP187 3.2 52.1 1.0 SD B:MET165 3.5 54.6 1.0 C27 B:7YY402 3.6 86.8 1.0 C34 B:7YY402 3.6 79.9 1.0 O B:ASP187 3.7 63.3 1.0 CB B:ASP187 3.8 51.4 1.0 O B:ARG188 3.9 64.2 1.0 CA B:ARG188 4.0 67.1 1.0 C B:ARG188 4.0 71.2 1.0 C26 B:7YY402 4.1 82.3 1.0 O B:VAL186 4.3 50.9 1.0 CB B:MET165 4.4 43.1 1.0 N B:ASP187 4.5 49.8 1.0 CD1 B:ILE49 4.5 83.4 1.0 CG B:MET165 4.6 41.8 1.0 ND1 B:HIS41 4.7 58.5 1.0 CG1 B:ILE49 4.7 80.5 1.0 F28 B:7YY402 4.8 93.7 1.0 N B:GLN189 4.8 80.4 1.0 C B:VAL186 4.9 49.3 1.0 CE B:MET165 5.0 42.9 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease Mutant M49I in Complex with Ensitrelvir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Sars-Cov-2 Main Protease Mutant M49I in Complex with Ensitrelvir within 5.0Å range: probe atom residue distance (Å) B Occ B:F402 b:84.2 occ:1.00 F33 B:7YY402 0.0 84.2 1.0 C32 B:7YY402 1.4 78.3 1.0 ND1 B:HIS41 2.1 58.5 1.0 C30 B:7YY402 2.3 74.0 1.0 C34 B:7YY402 2.4 79.9 1.0 F31 B:7YY402 2.7 68.2 1.0 CG B:HIS41 2.7 65.2 1.0 CE1 B:HIS41 2.9 54.5 1.0 CB B:HIS41 3.1 52.8 1.0 CD2 B:HIS41 3.6 63.2 1.0 C29 B:7YY402 3.6 77.4 1.0 C26 B:7YY402 3.6 82.3 1.0 NE2 B:HIS41 3.7 69.7 1.0 O B:HIS164 3.8 42.3 1.0 CD1 B:ILE49 4.0 83.4 1.0 C27 B:7YY402 4.1 86.8 1.0 CB B:ASP187 4.5 51.4 1.0 CA B:HIS41 4.7 50.1 1.0 C B:HIS164 4.7 37.0 1.0 CA B:ASP187 4.9 52.1 1.0 CB B:MET165 4.9 43.1 1.0 CG1 B:ILE49 4.9 80.5 1.0 C25 B:7YY402 4.9 87.8 1.0 C B:ASP187 4.9 61.0 1.0 O B:ASP187 5.0 63.3 1.0

G.D.Noske, G.Oliva, A.S.Godoy. Crystal Structure of Sars-Cov-2 Main Protease Mutant M49I in Complex with Ensitrelvir To Be Published.