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

The structure of Crystal Structure of Human Fibrillarin in Complex with Compound 2 From Single Soak, PDB code: 7seb 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)	48.03 / 1.81
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	69.21, 138.905, 66.483, 90, 90, 90
R / Rfree (%)	19.4 / 23.3

The binding sites of Fluorine atom in the Crystal Structure of Human Fibrillarin in Complex with Compound 2 From Single Soak (pdb code 7seb). 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 Single Soak, PDB code: 7seb:
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 Single 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 Single Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:53.2 occ:1.00 F A:8XF401 0.0 53.2 1.0 C A:8XF401 1.3 56.6 1.0 F2 A:8XF401 2.1 55.4 1.0 F1 A:8XF401 2.1 59.3 1.0 C1 A:8XF401 2.4 50.9 1.0 OD1 A:ASP216 2.4 38.2 1.0 N2 A:8XF401 2.8 42.3 1.0 HG3 A:ARG218 2.8 51.5 1.0 H A:ALA217 3.2 32.4 1.0 HH11 A:ARG218 3.2 66.9 1.0 H A:ARG218 3.3 33.6 1.0 CG A:ASP216 3.3 42.0 1.0 NH1 A:ARG218 3.3 55.8 1.0 HH12 A:ARG218 3.4 66.9 1.0 C2 A:8XF401 3.5 47.6 1.0 HA A:ASP216 3.5 38.3 1.0 N A:ALA217 3.7 27.0 1.0 HD13 A:ILE245 3.8 46.7 1.0 CG A:ARG218 3.8 42.9 1.0 HD2 A:PHE192 3.8 73.1 1.0 H A:8XF401 3.8 57.1 1.0 HE2 A:PHE192 3.8 77.5 1.0 HB3 A:ALA217 3.9 35.5 1.0 CD2 A:PHE192 3.9 61.0 1.0 OD2 A:ASP216 3.9 44.6 1.0 CE2 A:PHE192 3.9 64.6 1.0 CZ A:ARG218 3.9 56.1 1.0 N A:ARG218 4.0 28.0 1.0 C4 A:8XF401 4.0 32.6 1.0 CA A:ASP216 4.2 31.9 1.0 HG2 A:ARG218 4.2 51.5 1.0 C A:ASP216 4.2 27.9 1.0 CB A:ASP216 4.3 41.4 1.0 HB2 A:ARG218 4.3 48.2 1.0 NE A:ARG218 4.4 52.4 1.0 HG3 A:GLN239 4.5 60.7 1.0 CA A:ALA217 4.5 28.1 1.0 CD A:ARG218 4.5 51.2 1.0 HD2 A:ARG218 4.5 61.5 1.0 CG A:PHE192 4.5 51.8 1.0 CB A:ARG218 4.6 40.2 1.0 NH2 A:ARG218 4.6 62.3 1.0 CZ A:PHE192 4.6 61.7 1.0 HB3 A:PHE192 4.6 53.9 1.0 CB A:ALA217 4.6 29.6 1.0 HH22 A:ARG218 4.6 74.8 1.0 C3 A:8XF401 4.6 47.4 1.0 CD1 A:ILE245 4.7 38.9 1.0 C A:ALA217 4.7 31.9 1.0 H3 A:8XF401 4.7 39.1 1.0 HB2 A:ASP216 4.7 49.7 1.0 HG21 A:ILE245 4.8 39.4 1.0 N1 A:8XF401 4.8 32.5 1.0 HD11 A:ILE245 4.8 46.7 1.0 HB2 A:ALA217 4.9 35.5 1.0 CA A:ARG218 4.9 30.8 1.0 HZ A:PHE192 5.0 74.0 1.0 HE A:ARG218 5.0 62.8 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Human Fibrillarin in Complex with Compound 2 From Single 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 Single Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:59.3 occ:1.00 F1 A:8XF401 0.0 59.3 1.0 C A:8XF401 1.3 56.6 1.0 F A:8XF401 2.1 53.2 1.0 F2 A:8XF401 2.2 55.4 1.0 C1 A:8XF401 2.4 50.9 1.0 H A:8XF401 2.4 57.1 1.0 HG3 A:GLN239 2.6 60.7 1.0 C2 A:8XF401 2.8 47.6 1.0 CG A:GLN239 3.3 50.6 1.0 CD A:GLN239 3.5 54.7 1.0 N2 A:8XF401 3.6 42.3 1.0 HB A:VAL237 3.6 56.4 1.0 HH12 A:ARG218 3.6 66.9 1.0 HG2 A:GLN239 3.6 60.7 1.0 HD13 A:ILE245 3.7 46.7 1.0 NE2 A:GLN239 3.7 59.4 1.0 HE21 A:GLN239 3.7 71.3 1.0 NH1 A:ARG218 3.7 55.8 1.0 HH22 A:ARG218 3.8 74.8 1.0 CZ A:ARG218 3.9 56.1 1.0 NH2 A:ARG218 3.9 62.3 1.0 HE2 A:PHE192 3.9 77.5 1.0 CE2 A:PHE192 4.0 64.6 1.0 OE1 A:GLN239 4.0 52.1 1.0 HG3 A:ARG218 4.0 51.5 1.0 CZ A:PHE192 4.1 61.7 1.0 HZ A:PHE192 4.1 74.0 1.0 HH11 A:ARG218 4.1 66.9 1.0 C3 A:8XF401 4.1 47.4 1.0 HE22 A:GLN239 4.1 71.3 1.0 CD1 A:ILE245 4.3 38.9 1.0 HH21 A:ARG218 4.3 74.8 1.0 HD12 A:ILE245 4.3 46.7 1.0 HD11 A:ILE245 4.4 46.7 1.0 HG11 A:VAL237 4.5 36.9 1.0 CB A:VAL237 4.5 47.0 1.0 OD1 A:ASP216 4.5 38.2 1.0 CD2 A:PHE192 4.6 61.0 1.0 C4 A:8XF401 4.6 32.6 1.0 NE A:ARG218 4.6 52.4 1.0 CB A:GLN239 4.6 44.6 1.0 HG21 A:VAL237 4.7 51.0 1.0 HG12 A:VAL237 4.7 36.9 1.0 HB2 A:GLN239 4.7 53.5 1.0 CE1 A:PHE192 4.7 55.8 1.0 HB3 A:ALA217 4.7 35.5 1.0 HB3 A:GLN239 4.8 53.5 1.0 O A:HOH501 4.8 44.6 1.0 H A:ALA217 4.8 32.4 1.0 CG1 A:VAL237 4.8 30.8 1.0 O A:VAL237 4.8 49.5 1.0 HD2 A:PHE192 4.9 73.1 1.0 CG A:ARG218 4.9 42.9 1.0 N1 A:8XF401 4.9 32.5 1.0 H1 A:8XF401 4.9 58.8 1.0 HE A:ARG218 5.0 62.8 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Human Fibrillarin in Complex with Compound 2 From Single 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 Single Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:55.4 occ:1.00 F2 A:8XF401 0.0 55.4 1.0 C A:8XF401 1.3 56.6 1.0 F A:8XF401 2.1 53.2 1.0 F1 A:8XF401 2.2 59.3 1.0 C1 A:8XF401 2.3 50.9 1.0 HD13 A:ILE245 2.4 46.7 1.0 HB3 A:ALA217 2.7 35.5 1.0 N2 A:8XF401 2.9 42.3 1.0 HG21 A:ILE245 3.0 39.4 1.0 HG11 A:VAL237 3.2 36.9 1.0 HG3 A:ARG218 3.3 51.5 1.0 CD1 A:ILE245 3.3 38.9 1.0 HD12 A:ILE245 3.4 46.7 1.0 C2 A:8XF401 3.4 47.6 1.0 H A:ALA217 3.5 32.4 1.0 HB A:VAL237 3.6 56.4 1.0 H A:8XF401 3.6 57.1 1.0 HG3 A:GLN239 3.6 60.7 1.0 CB A:ALA217 3.7 29.6 1.0 H A:ARG218 3.7 33.6 1.0 HD11 A:ILE245 3.8 46.7 1.0 HG21 A:VAL237 3.9 51.0 1.0 CG1 A:VAL237 4.0 30.8 1.0 CG2 A:ILE245 4.0 32.9 1.0 OD1 A:ASP216 4.0 38.2 1.0 HG2 A:ARG218 4.0 51.5 1.0 CG A:ARG218 4.0 42.9 1.0 N A:ALA217 4.0 27.0 1.0 N A:ARG218 4.1 28.0 1.0 HG12 A:VAL237 4.1 36.9 1.0 HB2 A:ALA217 4.1 35.5 1.0 CB A:VAL237 4.2 47.0 1.0 C4 A:8XF401 4.2 32.6 1.0 CA A:ALA217 4.2 28.1 1.0 HB1 A:ALA217 4.2 35.5 1.0 C A:ALA217 4.3 31.9 1.0 CG1 A:ILE245 4.3 34.0 1.0 HG12 A:ILE245 4.4 40.9 1.0 HG23 A:ILE245 4.4 39.4 1.0 HG22 A:ILE245 4.4 39.4 1.0 CG A:GLN239 4.5 50.6 1.0 C3 A:8XF401 4.5 47.4 1.0 CG2 A:VAL237 4.6 42.5 1.0 NH1 A:ARG218 4.6 55.8 1.0 CZ A:ARG218 4.6 56.1 1.0 HH11 A:ARG218 4.7 66.9 1.0 CB A:ILE245 4.7 28.2 1.0 HG2 A:GLN239 4.8 60.7 1.0 NE A:ARG218 4.8 52.4 1.0 HG13 A:VAL237 4.8 36.9 1.0 HB A:ILE245 4.8 33.9 1.0 HH12 A:ARG218 4.8 66.9 1.0 N1 A:8XF401 4.9 32.5 1.0 HA A:ASP216 4.9 38.3 1.0 H3 A:8XF401 4.9 39.1 1.0 HA A:ARG218 4.9 36.9 1.0 CA A:ARG218 5.0 30.8 1.0 CB A:ARG218 5.0 40.2 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