Fluorine in PDB 8wts: Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor

All present enzymatic activity of Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor:
3.4.22.69;

The structure of Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor, PDB code: 8wts was solved by J.Peng, D.Sun, X.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.31 / 1.56
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	98.46, 80.98, 51.34, 90, 115.69, 90
R / Rfree (%)	17.9 / 20.7

The structure of Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Fluorine atom in the Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor (pdb code 8wts). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor, PDB code: 8wts:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:29.6 occ:1.00 F17 A:XDQ401 0.0 29.6 1.0 C15 A:XDQ401 1.4 28.0 1.0 C14 A:XDQ401 2.3 25.8 1.0 O16 A:XDQ401 2.6 26.9 1.0 SG A:CYS145 2.7 24.9 1.0 CB A:CYS145 3.0 20.5 1.0 N A:CYS145 3.2 18.0 1.0 CA A:GLY143 3.2 20.4 1.0 N A:GLY143 3.2 19.5 1.0 O A:HOH713 3.3 43.9 1.0 C A:GLY143 3.4 21.7 1.0 N A:SER144 3.6 19.0 1.0 N5 A:XDQ401 3.6 22.1 1.0 CA A:CYS145 3.7 19.3 1.0 O A:GLY143 4.1 20.3 1.0 C13 A:XDQ401 4.2 21.1 1.0 C A:SER144 4.3 18.2 1.0 CB A:LEU27 4.4 23.8 1.0 C A:ASN142 4.5 21.5 1.0 CE1 A:HIS41 4.5 23.1 1.0 CA A:SER144 4.5 19.4 1.0 C20 A:XDQ401 4.6 26.1 1.0 OD1 A:ASN142 4.6 31.4 0.5 C A:CYS145 4.7 18.2 1.0 O A:CYS145 4.7 19.2 1.0 C4 A:XDQ401 4.8 23.9 1.0 C8 A:XDQ401 4.9 20.1 1.0 C19 A:XDQ401 4.9 18.5 1.0 OG A:SER144 5.0 19.5 1.0

Fluorine binding site 2 out of 3 in the Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:40.5 occ:1.00 F26 A:XDQ401 0.0 40.5 1.0 C25 A:XDQ401 1.4 36.5 1.0 O24 A:XDQ401 2.3 27.5 1.0 CL2 A:XDQ401 2.4 44.4 1.0 F27 A:XDQ401 2.4 27.2 1.0 C22 A:XDQ401 3.1 24.6 1.0 C23 A:XDQ401 3.1 21.5 1.0 O A:ASP187 3.2 23.9 1.0 C A:ASP187 3.3 23.5 1.0 CB A:HIS41 3.4 21.1 1.0 CG A:HIS41 3.6 21.8 1.0 N A:ARG188 3.7 23.7 1.0 CE A:MET165 3.7 30.1 0.5 CA A:ASP187 3.7 19.5 1.0 CD2 A:HIS41 3.7 22.9 1.0 CB A:ASP187 3.9 20.3 1.0 OH A:TYR54 3.9 27.4 1.0 CA A:ARG188 4.0 28.2 1.0 C19 A:XDQ401 4.4 18.5 1.0 C21 A:XDQ401 4.4 26.1 1.0 ND1 A:HIS41 4.4 23.9 1.0 NE2 A:HIS41 4.6 24.8 1.0 C A:ARG188 4.6 30.7 1.0 CA A:HIS41 4.9 20.4 1.0 CE1 A:HIS41 5.0 23.1 1.0 O A:ARG188 5.0 28.6 1.0 C31 A:XDQ401 5.0 36.3 1.0 CG A:ASP187 5.0 18.6 1.0

Fluorine binding site 3 out of 3 in the Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:27.2 occ:1.00 F27 A:XDQ401 0.0 27.2 1.0 C25 A:XDQ401 1.5 36.5 1.0 O24 A:XDQ401 2.4 27.5 1.0 F26 A:XDQ401 2.4 40.5 1.0 CL2 A:XDQ401 2.6 44.4 1.0 OH A:TYR54 3.5 27.4 1.0 SG A:CYS44 3.6 32.7 0.5 O A:ASP187 3.7 23.9 1.0 C22 A:XDQ401 3.7 24.6 1.0 CG A:MET49 3.7 74.5 1.0 CB A:HIS41 3.9 21.1 1.0 SG A:CYS44 3.9 40.0 0.5 CB A:CYS44 3.9 33.5 0.5 CA A:ARG188 4.0 28.2 1.0 CB A:CYS44 4.0 37.4 0.5 C A:ASP187 4.3 23.5 1.0 O A:MET49 4.3 41.6 1.0 CA A:MET49 4.4 65.6 1.0 N A:ARG188 4.5 23.7 1.0 C23 A:XDQ401 4.5 21.5 1.0 CB A:MET49 4.6 71.0 1.0 C21 A:XDQ401 4.6 26.1 1.0 CG A:HIS41 4.7 21.8 1.0 CZ A:TYR54 4.8 24.5 1.0 C A:ARG188 4.8 30.7 1.0 SD A:MET49 4.8 78.5 1.0 CB A:ARG188 4.8 36.7 1.0 CA A:HIS41 4.9 20.4 1.0 N A:GLN189 4.9 28.5 1.0 C A:MET49 4.9 54.6 1.0 CG A:PRO52 5.0 43.5 1.0

J.Peng, D.Sun, X.Ding. Sars-Cov-2 3CLPRO Bound to Covalent Inhibitor To Be Published.