Fluorine in PDB 7lzv: Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 19B

All present enzymatic activity of Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 19B:
3.4.22.69;

The structure of Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 19B, PDB code: 7lzv was solved by S.Lovell, M.M.Kashipathy, K.P.Battaile, S.D.Chamandi, A.D.Rathnayake, Y.Kim, K.D.Perera, A.R.M.Jesri, H.N.Nguyen, M.A.Baird, M.J.Miller, W.C.Groutas, K.O.Chang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.04 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.466, 98.588, 59.114, 90, 108.31, 90
R / Rfree (%)	18.5 / 21.2

The binding sites of Fluorine atom in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 19B (pdb code 7lzv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 19B, PDB code: 7lzv:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 19B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 19B within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:37.0 occ:0.50 F28 A:YLM401 0.0 37.0 0.5 C27 A:YLM401 1.3 29.5 0.5 C29 A:YLM401 2.3 22.0 0.5 C26 A:YLM401 2.4 30.7 0.5 CB A:ALA191 3.5 36.2 1.0 C30 A:YLM401 3.6 27.1 0.5 C25 A:YLM401 3.6 28.0 0.5 N A:ALA191 3.7 30.7 1.0 O A:HOH578 3.8 33.2 1.0 CA A:ALA191 3.9 32.8 1.0 C24 A:YLM401 4.2 27.4 0.5 C A:THR190 4.4 29.3 1.0 CA A:THR190 4.9 34.3 1.0

Fluorine binding site 2 out of 4 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 19B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 19B within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:31.1 occ:0.50 F28 A:YLS402 0.0 31.1 0.5 C27 A:YLS402 1.3 29.8 0.5 C29 A:YLS402 2.3 34.0 0.5 C26 A:YLS402 2.4 25.9 0.5 O A:HOH651 3.2 41.8 1.0 C30 A:YLS402 3.6 28.7 0.5 C25 A:YLS402 3.6 27.3 0.5 ND2 A:ASN142 3.9 28.7 1.0 O A:HOH579 4.1 34.0 1.0 C24 A:YLS402 4.2 22.2 0.5 C16 A:YLM401 4.2 25.0 0.5 C16 A:YLS402 4.3 24.9 0.5 CG A:ASN142 4.6 39.6 1.0 OD1 A:ASN142 4.8 41.8 1.0 O A:HOH571 4.8 34.6 1.0

Fluorine binding site 3 out of 4 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 19B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 19B within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:50.6 occ:0.50 F28 B:YLM401 0.0 50.6 0.5 F28 B:YLS402 0.1 50.6 0.5 C27 B:YLS402 1.3 44.1 0.5 C27 B:YLM401 1.3 44.1 0.5 C26 B:YLS402 2.3 42.1 0.5 C29 B:YLS402 2.4 45.4 0.5 C29 B:YLM401 2.4 45.4 0.5 C26 B:YLM401 2.4 42.1 0.5 C25 B:YLS402 3.6 39.8 0.5 C30 B:YLS402 3.6 40.7 0.5 C30 B:YLM401 3.6 40.7 0.5 C25 B:YLM401 3.6 39.8 0.5 C16 B:YLM401 4.0 36.0 0.5 OD1 B:ASN142 4.1 44.7 1.0 C16 B:YLS402 4.1 36.0 0.5 C24 B:YLS402 4.1 39.0 0.5 C24 B:YLM401 4.2 39.0 0.5 ND2 B:ASN142 4.5 49.0 1.0 CG B:ASN142 4.6 41.9 1.0 C17 B:YLS402 4.9 31.3 0.5 C17 B:YLM401 4.9 31.3 0.5

Fluorine binding site 4 out of 4 in the Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 19B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 19B within 5.0Å range: probe atom residue distance (Å) B Occ B:F402 b:50.6 occ:0.50 F28 B:YLS402 0.0 50.6 0.5 F28 B:YLM401 0.1 50.6 0.5 C27 B:YLS402 1.3 44.1 0.5 C27 B:YLM401 1.4 44.1 0.5 C29 B:YLS402 2.4 45.4 0.5 C29 B:YLM401 2.4 45.4 0.5 C26 B:YLS402 2.4 42.1 0.5 C26 B:YLM401 2.4 42.1 0.5 C30 B:YLS402 3.6 40.7 0.5 C25 B:YLS402 3.6 39.8 0.5 C30 B:YLM401 3.6 40.7 0.5 C25 B:YLM401 3.7 39.8 0.5 C16 B:YLM401 4.0 36.0 0.5 OD1 B:ASN142 4.1 44.7 1.0 C16 B:YLS402 4.1 36.0 0.5 C24 B:YLS402 4.2 39.0 0.5 C24 B:YLM401 4.2 39.0 0.5 ND2 B:ASN142 4.5 49.0 1.0 CG B:ASN142 4.7 41.9 1.0 C17 B:YLS402 4.9 31.3 0.5 C17 B:YLM401 4.9 31.3 0.5

S.D.Chamandi, A.D.Rathnayake, J.Zhang, Y.Kim, K.D.Perera, A.R.M.Jesri, H.N.Nguyen, M.A.Baird, S.Makin, D.K.Meyerholz, M.M.Kashipathy, K.P.Battaile, S.Lovell, S.Perlman, K.O.Chang, W.C.Groutas. Structure of Sars-Cov-2 3CL Protease in Complex with Inhibitor 19B To Be Published.