Fluorine in PDB 9f2h: Crystal Structure of Sars-Cov-2 N-Protein C-Terminal Domain in Complex with Riluzole

The structure of Crystal Structure of Sars-Cov-2 N-Protein C-Terminal Domain in Complex with Riluzole, PDB code: 9f2h was solved by M.A.Marquez-Monino, B.Gonzalez, J.M.Perez-Canadillas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.56 / 1.30
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	93.056, 43.383, 109.326, 90, 91.44, 90
R / Rfree (%)	16.8 / 18.9

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 N-Protein C-Terminal Domain in Complex with Riluzole (pdb code 9f2h). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Sars-Cov-2 N-Protein C-Terminal Domain in Complex with Riluzole, PDB code: 9f2h:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Sars-Cov-2 N-Protein C-Terminal Domain in Complex with Riluzole


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 N-Protein C-Terminal Domain in Complex with Riluzole within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:31.1 occ:0.80 F1 A:657401 0.0 31.1 0.8 C7 A:657401 1.3 30.0 0.8 F2 A:657401 2.1 26.8 0.8 F3 A:657401 2.1 31.3 0.8 O1 A:657401 2.2 29.1 0.8 CD2 A:TRP330 3.3 16.0 1.0 CE3 A:TRP330 3.4 16.3 1.0 CB B:ALA336 3.4 14.5 1.0 C6 A:657401 3.5 26.8 0.8 CG A:TRP330 3.5 15.5 1.0 CG2 A:THR282 3.6 23.7 1.0 CB A:TRP330 3.8 15.4 1.0 CE2 A:TRP330 3.9 16.8 1.0 CZ3 A:TRP330 4.1 17.0 1.0 C5 A:657401 4.1 26.1 0.8 CD1 A:TRP330 4.1 15.8 1.0 NE1 A:TRP330 4.4 16.5 1.0 C1 A:657401 4.5 27.3 0.8 CZ2 A:TRP330 4.5 17.9 1.0 CH2 A:TRP330 4.6 18.1 1.0 CA B:ALA336 4.9 14.0 1.0 CG2 A:THR325 4.9 21.2 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Sars-Cov-2 N-Protein C-Terminal Domain in Complex with Riluzole


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 N-Protein C-Terminal Domain in Complex with Riluzole within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:26.8 occ:0.80 F2 A:657401 0.0 26.8 0.8 C7 A:657401 1.3 30.0 0.8 F1 A:657401 2.1 31.1 0.8 F3 A:657401 2.1 31.3 0.8 O1 A:657401 2.2 29.1 0.8 C6 A:657401 2.7 26.8 0.8 C5 A:657401 2.8 26.1 0.8 CG2 A:THR332 3.2 14.3 1.0 CB B:ALA336 3.3 14.5 1.0 CB A:TRP330 3.4 15.4 1.0 C1 A:657401 3.7 27.3 0.8 CG A:TRP330 3.9 15.5 1.0 C4 A:657401 4.0 25.2 0.8 CB A:GLU323 4.3 19.7 1.0 CD2 A:TRP330 4.4 16.0 1.0 CG A:GLU323 4.4 21.5 1.0 CE3 A:TRP330 4.6 16.3 1.0 CB A:THR332 4.6 13.0 1.0 C2 A:657401 4.6 26.0 0.8 CA B:ALA336 4.7 14.0 1.0 CD1 A:TRP330 4.7 15.8 1.0 CA A:TRP330 4.7 14.7 1.0 C3 A:657401 4.8 24.9 0.8 O A:TRP330 4.8 14.9 1.0 C A:TRP330 4.9 14.1 1.0 CG2 A:THR325 5.0 21.2 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Sars-Cov-2 N-Protein C-Terminal Domain in Complex with Riluzole


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 N-Protein C-Terminal Domain in Complex with Riluzole within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:31.3 occ:0.80 F3 A:657401 0.0 31.3 0.8 C7 A:657401 1.3 30.0 0.8 F2 A:657401 2.1 26.8 0.8 F1 A:657401 2.1 31.1 0.8 O1 A:657401 2.2 29.1 0.8 C6 A:657401 2.9 26.8 0.8 CG2 A:THR325 3.0 21.2 1.0 C1 A:657401 3.3 27.3 0.8 CG A:TRP330 3.4 15.5 1.0 CD1 A:TRP330 3.6 15.8 1.0 CB A:TRP330 3.6 15.4 1.0 C5 A:657401 3.9 26.1 0.8 CD2 A:TRP330 4.0 16.0 1.0 CB A:GLU323 4.0 19.7 1.0 NE1 A:TRP330 4.2 16.5 1.0 CB A:THR325 4.2 20.5 1.0 CE2 A:TRP330 4.4 16.8 1.0 OG1 A:THR325 4.4 21.5 1.0 O C:HOH639 4.5 35.4 1.0 C2 A:657401 4.5 26.0 0.8 O A:GLU323 4.7 18.0 1.0 CE3 A:TRP330 4.7 16.3 1.0 CG A:GLU323 4.8 21.5 1.0 C4 A:657401 5.0 25.2 0.8 CB B:ALA336 5.0 14.5 1.0 CA A:TRP330 5.0 14.7 1.0

M.A.Marquez-Monino, C.M.Santiveri, P.De Leon, S.Camero, R.Campos-Olivas, M.A.Jimenez, M.Saiz, B.Gonzalez, J.M.Perez-Canadillas. The Als Drug Riluzole Binds to the C-Terminal Domain of Sars-Cov-2 Nucleocapsid Protein and Has Antiviral Activity. Structure 2024.
ISSN: ISSN 0969-2126
DOI: 10.1016/J.STR.2024.10.025