Fluorine in PDB 7sea: Crystal Structure of Human Fibrillarin in Complex with Compound 2 From Cocktail Soak

The structure of Crystal Structure of Human Fibrillarin in Complex with Compound 2 From Cocktail Soak, PDB code: 7sea was solved by Y.Shi, I.M.El-Deeb, V.Masic, L.Hartley-Tassell, A.Maggioni, M.Vonitzstein, T.Ve, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.27 / 1.91
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	69.131, 138.651, 66.426, 90, 90, 90
R / Rfree (%)	19.6 / 22.9

The binding sites of Fluorine atom in the Crystal Structure of Human Fibrillarin in Complex with Compound 2 From Cocktail Soak (pdb code 7sea). 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 Human Fibrillarin in Complex with Compound 2 From Cocktail Soak, PDB code: 7sea:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Human Fibrillarin in Complex with Compound 2 From Cocktail Soak


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 Human Fibrillarin in Complex with Compound 2 From Cocktail Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:F407 b:46.5 occ:1.00 F A:8XF407 0.0 46.5 1.0 C A:8XF407 1.3 51.2 1.0 F2 A:8XF407 2.1 53.0 1.0 F1 A:8XF407 2.1 56.5 1.0 C1 A:8XF407 2.4 49.2 1.0 N2 A:8XF407 2.7 41.8 1.0 OD1 A:ASP216 2.7 30.2 1.0 HG3 A:ARG218 2.8 42.9 1.0 H A:ALA217 2.9 25.5 1.0 H A:ARG218 3.1 31.4 1.0 HB3 A:ALA217 3.1 29.9 1.0 HD13 A:ILE245 3.2 38.6 1.0 N A:ALA217 3.4 21.2 1.0 C2 A:8XF407 3.6 47.0 1.0 N A:ARG218 3.7 26.1 1.0 HH11 A:ARG218 3.7 56.0 1.0 HA A:ASP216 3.8 31.6 1.0 CG A:ASP216 3.8 30.6 1.0 CG A:ARG218 3.8 35.8 1.0 NH1 A:ARG218 3.9 46.7 1.0 CB A:ALA217 3.9 24.9 1.0 H A:8XF407 4.0 56.4 1.0 CA A:ALA217 4.0 24.1 1.0 C4 A:8XF407 4.0 37.7 1.0 HG21 A:ILE245 4.1 33.5 1.0 HH12 A:ARG218 4.1 56.0 1.0 C A:ASP216 4.1 22.4 1.0 CD1 A:ILE245 4.2 32.2 1.0 C A:ALA217 4.2 25.9 1.0 HG2 A:ARG218 4.3 42.9 1.0 HG3 A:GLN239 4.3 51.4 1.0 HB2 A:ARG218 4.3 43.4 1.0 HB2 A:ALA217 4.3 29.9 1.0 CA A:ASP216 4.3 26.3 1.0 HD11 A:ILE245 4.4 38.6 1.0 CZ A:ARG218 4.4 45.3 1.0 HD2 A:ARG218 4.4 50.8 1.0 CB A:ARG218 4.4 36.1 1.0 OD2 A:ASP216 4.5 34.7 1.0 CD A:ARG218 4.6 42.3 1.0 HD12 A:ILE245 4.6 38.6 1.0 CA A:ARG218 4.6 30.4 1.0 H3 A:8XF407 4.7 45.2 1.0 HB1 A:ALA217 4.7 29.9 1.0 HG11 A:VAL237 4.7 34.0 1.0 CB A:ASP216 4.7 29.9 1.0 NE A:ARG218 4.7 46.1 1.0 C3 A:8XF407 4.7 43.2 1.0 HB3 A:PHE192 4.7 52.8 1.0 HB A:VAL237 4.8 48.0 1.0 HA A:ARG218 4.8 36.5 1.0 N1 A:8XF407 4.9 30.6 1.0 HG12 A:ILE245 4.9 35.3 1.0 HA A:ALA217 4.9 28.9 1.0 CG2 A:ILE245 5.0 27.9 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Human Fibrillarin in Complex with Compound 2 From Cocktail Soak


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 Human Fibrillarin in Complex with Compound 2 From Cocktail Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:F407 b:56.5 occ:1.00 F1 A:8XF407 0.0 56.5 1.0 C A:8XF407 1.3 51.2 1.0 F A:8XF407 2.1 46.5 1.0 F2 A:8XF407 2.1 53.0 1.0 C1 A:8XF407 2.4 49.2 1.0 N2 A:8XF407 3.1 41.8 1.0 CE2 A:PHE192 3.1 59.1 1.0 CD2 A:PHE192 3.2 51.6 1.0 C2 A:8XF407 3.2 47.0 1.0 HH12 A:ARG218 3.2 56.0 1.0 OD1 A:ASP216 3.3 30.2 1.0 H A:8XF407 3.3 56.4 1.0 HH11 A:ARG218 3.3 56.0 1.0 HE2 A:PHE192 3.4 70.9 1.0 HD2 A:PHE192 3.4 61.9 1.0 NH1 A:ARG218 3.4 46.7 1.0 CZ A:PHE192 3.5 55.6 1.0 CG A:PHE192 3.6 48.0 1.0 CG A:ASP216 3.8 30.6 1.0 HA A:ASP216 3.8 31.6 1.0 CE1 A:PHE192 3.9 51.0 1.0 CD1 A:PHE192 3.9 51.5 1.0 HZ A:PHE192 4.0 66.8 1.0 HB3 A:PHE192 4.0 52.8 1.0 H A:ALA217 4.1 25.5 1.0 OD2 A:ASP216 4.1 34.7 1.0 C4 A:8XF407 4.2 37.7 1.0 HG3 A:ARG218 4.2 42.9 1.0 C3 A:8XF407 4.3 43.2 1.0 CB A:PHE192 4.4 44.0 1.0 CZ A:ARG218 4.4 45.3 1.0 HE1 A:PHE192 4.5 61.3 1.0 HD1 A:PHE192 4.5 61.8 1.0 HG3 A:GLN239 4.5 51.4 1.0 O A:HOH507 4.6 44.7 1.0 CA A:ASP216 4.6 26.3 1.0 H A:ARG218 4.6 31.4 1.0 CB A:ASP216 4.7 29.9 1.0 HB2 A:PHE192 4.7 52.8 1.0 N A:ALA217 4.7 21.2 1.0 N1 A:8XF407 4.7 30.6 1.0 HB2 A:ASP216 4.8 35.9 1.0 HD2 A:ARG218 4.8 50.8 1.0 HH22 A:ARG218 4.9 58.0 1.0 HD13 A:ILE245 4.9 38.6 1.0 H3 A:8XF407 4.9 45.2 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Human Fibrillarin in Complex with Compound 2 From Cocktail Soak


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 Human Fibrillarin in Complex with Compound 2 From Cocktail Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:F407 b:53.0 occ:1.00 F2 A:8XF407 0.0 53.0 1.0 C A:8XF407 1.3 51.2 1.0 F A:8XF407 2.1 46.5 1.0 F1 A:8XF407 2.1 56.5 1.0 C1 A:8XF407 2.4 49.2 1.0 HG3 A:GLN239 2.5 51.4 1.0 H A:8XF407 2.6 56.4 1.0 C2 A:8XF407 2.8 47.0 1.0 CG A:GLN239 3.3 42.8 1.0 HH12 A:ARG218 3.4 56.0 1.0 N2 A:8XF407 3.5 41.8 1.0 HD13 A:ILE245 3.5 38.6 1.0 HG2 A:GLN239 3.6 51.4 1.0 NH1 A:ARG218 3.6 46.7 1.0 CD A:GLN239 3.6 47.6 1.0 HB A:VAL237 3.7 48.0 1.0 HH11 A:ARG218 3.8 56.0 1.0 HE21 A:GLN239 3.9 66.4 1.0 NE2 A:GLN239 3.9 55.3 1.0 CZ A:ARG218 4.0 45.3 1.0 HG3 A:ARG218 4.0 42.9 1.0 HH22 A:ARG218 4.0 58.0 1.0 OE1 A:GLN239 4.1 39.6 1.0 NH2 A:ARG218 4.1 48.3 1.0 HD11 A:ILE245 4.2 38.6 1.0 CD1 A:ILE245 4.2 32.2 1.0 C3 A:8XF407 4.2 43.2 1.0 HD12 A:ILE245 4.3 38.6 1.0 HE22 A:GLN239 4.4 66.4 1.0 OD1 A:ASP216 4.5 30.2 1.0 CB A:GLN239 4.5 42.7 1.0 CB A:VAL237 4.6 40.0 1.0 HB2 A:GLN239 4.6 51.2 1.0 C4 A:8XF407 4.6 37.7 1.0 HB3 A:ALA217 4.6 29.9 1.0 HG11 A:VAL237 4.6 34.0 1.0 CZ A:PHE192 4.7 55.6 1.0 HB3 A:GLN239 4.7 51.2 1.0 HH21 A:ARG218 4.7 58.0 1.0 NE A:ARG218 4.7 46.1 1.0 H A:ALA217 4.8 25.5 1.0 CE2 A:PHE192 4.8 59.1 1.0 HZ A:PHE192 4.8 66.8 1.0 HG21 A:VAL237 4.8 43.9 1.0 CE1 A:PHE192 4.8 51.0 1.0 HG12 A:VAL237 4.9 34.0 1.0 O A:VAL237 4.9 39.2 1.0 CG A:ARG218 4.9 35.8 1.0 HG21 A:ILE245 4.9 33.5 1.0 CG1 A:VAL237 4.9 28.4 1.0 N1 A:8XF407 4.9 30.6 1.0

Y.Shi, I.M.El-Deeb, V.Masic, L.Hartley-Tassell, A.Maggioni, M.V.Itzstein, T.Ve. Discovery of Cofactor Competitive Inhibitors Against the Human Methyltransferase Fibrillarin. Pharmaceuticals V. 15 2021.
ISSN: ESSN 1424-8247
PubMed: 35056083
DOI: 10.3390/PH15010026