Fluorine in PDB 7se8: Crystal Structure of Human Fibrillarin in Complex with Fragment 1 From Cocktail Soak

The structure of Crystal Structure of Human Fibrillarin in Complex with Fragment 1 From Cocktail Soak, PDB code: 7se8 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)	48.40 / 1.75
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	68.038, 68.874, 138.653, 90, 90, 90
R / Rfree (%)	18.8 / 21.4

The binding sites of Fluorine atom in the Crystal Structure of Human Fibrillarin in Complex with Fragment 1 From Cocktail Soak (pdb code 7se8). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Human Fibrillarin in Complex with Fragment 1 From Cocktail Soak, PDB code: 7se8:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of Human Fibrillarin in Complex with Fragment 1 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 Fragment 1 From Cocktail Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:38.0 occ:1.00 F1 A:8W1401 0.0 38.0 1.0 C9 A:8W1401 1.4 48.7 1.0 F2 A:8W1401 2.2 50.9 1.0 F3 A:8W1401 2.3 45.2 1.0 C5 A:8W1401 2.4 34.8 1.0 HG22 A:ILE245 2.8 27.9 1.0 HB3 A:LEU166 2.8 23.1 1.0 HD13 A:LEU166 2.9 24.0 1.0 HB3 A:ALA217 3.0 22.4 1.0 C6 A:8W1401 3.0 47.2 1.0 H6 A:8W1401 3.1 56.6 1.0 HB1 A:ALA217 3.2 22.4 1.0 HG21 A:ILE245 3.4 27.9 1.0 CG2 A:ILE245 3.5 23.2 1.0 CB A:ALA217 3.5 18.7 1.0 CB A:LEU166 3.6 19.2 1.0 C4 A:8W1401 3.6 45.0 1.0 HB2 A:LEU166 3.6 23.1 1.0 CD1 A:LEU166 3.6 20.0 1.0 HD12 A:LEU166 3.7 24.0 1.0 HB2 A:ALA217 3.8 22.4 1.0 HB A:ILE245 3.8 27.6 1.0 H5 A:8W1401 3.8 54.0 1.0 HG22 A:VAL246 3.8 22.6 1.0 HG23 A:VAL246 4.0 22.6 1.0 HD22 A:LEU166 4.1 18.4 1.0 CG A:LEU166 4.1 15.6 1.0 CB A:ILE245 4.2 23.0 1.0 H A:FMT402 4.2 55.4 1.0 HG23 A:ILE245 4.2 27.9 1.0 C7 A:8W1401 4.3 47.0 1.0 CG2 A:VAL246 4.4 18.8 1.0 HB1 A:ALA235 4.4 21.2 1.0 HD11 A:LEU166 4.4 24.0 1.0 HA A:VAL246 4.5 15.3 1.0 N1 A:8W1401 4.5 57.2 1.0 HG2 A:GLN242 4.6 42.3 1.0 CD2 A:LEU166 4.7 15.4 1.0 HB3 A:GLN242 4.7 41.5 1.0 N A:VAL246 4.7 16.4 1.0 H A:VAL246 4.7 19.7 1.0 CA A:LEU166 4.8 15.5 1.0 CA A:ALA217 4.9 17.0 1.0 C A:LEU166 4.9 17.1 1.0 HG13 A:ILE245 4.9 38.1 1.0 C A:ILE245 4.9 19.1 1.0 HA A:LEU166 5.0 18.6 1.0 HD21 A:ASN249 5.0 19.5 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of Human Fibrillarin in Complex with Fragment 1 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 Fragment 1 From Cocktail Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:50.9 occ:1.00 F2 A:8W1401 0.0 50.9 1.0 C9 A:8W1401 1.4 48.7 1.0 F1 A:8W1401 2.2 38.0 1.0 F3 A:8W1401 2.2 45.2 1.0 C5 A:8W1401 2.3 34.8 1.0 H5 A:8W1401 2.7 54.0 1.0 C4 A:8W1401 2.9 45.0 1.0 HB3 A:GLN242 2.9 41.5 1.0 HG23 A:VAL246 3.2 22.6 1.0 HG22 A:VAL237 3.3 35.4 1.0 HG22 A:VAL246 3.4 22.6 1.0 HB1 A:ALA235 3.5 21.2 1.0 HG2 A:GLN242 3.6 42.3 1.0 C6 A:8W1401 3.7 47.2 1.0 CG2 A:VAL246 3.7 18.8 1.0 CB A:GLN242 3.8 34.6 1.0 O A:ASP236 3.8 41.4 1.0 HA A:VAL237 3.9 50.5 1.0 HB A:ILE245 3.9 27.6 1.0 HG21 A:VAL246 4.0 22.6 1.0 O A:GLN242 4.0 18.0 1.0 CG A:GLN242 4.1 35.2 1.0 H6 A:8W1401 4.1 56.6 1.0 OE1 A:GLN242 4.1 33.0 1.0 CG2 A:VAL237 4.1 29.5 1.0 HG22 A:ILE245 4.1 27.9 1.0 HB3 A:LEU166 4.1 23.1 1.0 HG23 A:VAL237 4.2 35.4 1.0 N1 A:8W1401 4.2 57.2 1.0 HB2 A:LEU166 4.3 23.1 1.0 CD A:GLN242 4.3 40.2 1.0 HA A:GLN242 4.4 33.0 1.0 HB2 A:GLN242 4.4 41.5 1.0 CB A:ALA235 4.4 17.6 1.0 HD13 A:LEU166 4.4 24.0 1.0 CA A:GLN242 4.5 27.5 1.0 C A:ASP236 4.5 46.0 1.0 H A:VAL246 4.6 19.7 1.0 C A:GLN242 4.6 27.2 1.0 HD12 A:LEU166 4.6 24.0 1.0 HG21 A:ILE245 4.6 27.9 1.0 HG21 A:VAL237 4.7 35.4 1.0 CB A:LEU166 4.7 19.2 1.0 CG2 A:ILE245 4.7 23.2 1.0 HB2 A:ALA235 4.7 21.2 1.0 C7 A:8W1401 4.7 47.0 1.0 CA A:VAL237 4.7 42.1 1.0 CB A:ILE245 4.7 23.0 1.0 H A:ASP236 4.8 24.5 1.0 HB3 A:ALA235 4.8 21.2 1.0 N A:VAL246 4.9 16.4 1.0 CD1 A:LEU166 5.0 20.0 1.0 N A:VAL237 5.0 32.5 1.0 HG3 A:GLN242 5.0 42.3 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of Human Fibrillarin in Complex with Fragment 1 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 Fragment 1 From Cocktail Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:45.2 occ:1.00 F3 A:8W1401 0.0 45.2 1.0 C9 A:8W1401 1.4 48.7 1.0 F2 A:8W1401 2.2 50.9 1.0 F1 A:8W1401 2.3 38.0 1.0 C5 A:8W1401 2.4 34.8 1.0 HG2 A:GLN242 2.4 42.3 1.0 HG21 A:ILE245 3.0 27.9 1.0 HB A:ILE245 3.0 27.6 1.0 H6 A:8W1401 3.1 56.6 1.0 C6 A:8W1401 3.2 47.2 1.0 HG22 A:ILE245 3.3 27.9 1.0 CG A:GLN242 3.3 35.2 1.0 HB3 A:GLN242 3.3 41.5 1.0 CG2 A:ILE245 3.4 23.2 1.0 C4 A:8W1401 3.4 45.0 1.0 HG13 A:ILE245 3.5 38.1 1.0 H A:FMT402 3.5 55.4 1.0 CB A:ILE245 3.6 23.0 1.0 O2 A:FMT402 3.7 55.0 1.0 HA A:GLN242 3.7 33.0 1.0 CB A:GLN242 3.7 34.6 1.0 HB3 A:ALA217 3.8 22.4 1.0 CD A:GLN242 3.8 40.2 1.0 H5 A:8W1401 3.8 54.0 1.0 C A:FMT402 3.9 46.2 1.0 CG1 A:ILE245 3.9 31.8 1.0 HG3 A:GLN242 4.0 42.3 1.0 HG12 A:ILE245 4.1 38.1 1.0 OE1 A:GLN242 4.2 33.0 1.0 CA A:GLN242 4.2 27.5 1.0 HG23 A:ILE245 4.4 27.9 1.0 NE2 A:GLN242 4.4 34.4 1.0 HO2 A:FMT402 4.4 66.0 1.0 HE21 A:GLN242 4.4 41.2 1.0 O A:GLN242 4.4 18.0 1.0 C7 A:8W1401 4.4 47.0 1.0 N1 A:8W1401 4.5 57.2 1.0 HG23 A:VAL246 4.5 22.6 1.0 HB1 A:ALA217 4.5 22.4 1.0 CB A:ALA217 4.6 18.7 1.0 HB2 A:GLN242 4.6 41.5 1.0 C A:GLN242 4.8 27.2 1.0 HG2 A:ARG218 4.9 49.5 1.0 HG22 A:VAL237 4.9 35.4 1.0 HB3 A:LEU166 4.9 23.1 1.0 H A:VAL246 4.9 19.7 1.0 HE22 A:GLN242 4.9 41.2 1.0 HD13 A:LEU166 5.0 24.0 1.0 CA A:ILE245 5.0 17.8 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of Human Fibrillarin in Complex with Fragment 1 From Cocktail Soak


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human Fibrillarin in Complex with Fragment 1 From Cocktail Soak within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:26.8 occ:1.00 F1 B:8W1401 0.0 26.8 1.0 C9 B:8W1401 1.4 40.9 1.0 F2 B:8W1401 2.2 37.7 1.0 F3 B:8W1401 2.3 36.2 1.0 C5 B:8W1401 2.4 26.4 1.0 HB3 B:LEU166 2.5 20.2 1.0 HD13 B:LEU166 2.7 25.5 1.0 HG22 B:ILE245 2.9 28.0 1.0 HB3 B:ALA217 3.0 21.3 1.0 C6 B:8W1401 3.1 30.4 1.0 H6 B:8W1401 3.1 36.5 1.0 HB1 B:ALA217 3.1 21.3 1.0 CB B:LEU166 3.3 16.8 1.0 HB2 B:LEU166 3.3 20.2 1.0 CB B:ALA217 3.4 17.8 1.0 CD1 B:LEU166 3.4 21.3 1.0 HD12 B:LEU166 3.5 25.5 1.0 HB2 B:ALA217 3.5 21.3 1.0 HG21 B:ILE245 3.6 28.0 1.0 C4 B:8W1401 3.6 34.5 1.0 CG2 B:ILE245 3.7 23.3 1.0 HG22 B:VAL246 3.7 21.8 1.0 HD22 B:LEU166 3.8 19.5 1.0 H5 B:8W1401 3.8 41.4 1.0 HG23 B:VAL246 3.8 21.8 1.0 CG B:LEU166 3.9 17.9 1.0 HB B:ILE245 4.0 24.5 1.0 CG2 B:VAL246 4.2 18.1 1.0 HD11 B:LEU166 4.2 25.5 1.0 HA B:VAL246 4.3 17.7 1.0 C7 B:8W1401 4.4 34.7 1.0 CD2 B:LEU166 4.4 16.2 1.0 HG23 B:ILE245 4.4 28.0 1.0 CB B:ILE245 4.4 20.4 1.0 HB1 B:ALA235 4.4 16.9 1.0 CA B:LEU166 4.5 16.1 1.0 N1 B:8W1401 4.6 34.4 1.0 HB3 B:GLN242 4.6 30.4 1.0 H B:FMT402 4.6 51.5 1.0 N B:VAL246 4.6 15.1 1.0 HG2 B:GLN242 4.7 34.8 1.0 H B:VAL246 4.7 18.1 1.0 C B:LEU166 4.7 15.2 1.0 HA B:LEU166 4.7 19.2 1.0 HG B:LEU166 4.8 21.5 1.0 HD22 B:ASN249 4.8 20.4 1.0 HB2 B:ALA235 4.8 16.9 1.0 CA B:ALA217 4.8 17.6 1.0 C B:ILE245 4.9 19.0 1.0 HD21 B:LEU166 4.9 19.5 1.0 HG21 B:VAL246 4.9 21.8 1.0 HD21 B:ASN249 4.9 20.4 1.0 CA B:VAL246 4.9 14.8 1.0 O B:GLN242 5.0 18.2 1.0 ND2 B:ASN249 5.0 17.0 1.0 O B:LEU166 5.0 16.4 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of Human Fibrillarin in Complex with Fragment 1 From Cocktail Soak


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Human Fibrillarin in Complex with Fragment 1 From Cocktail Soak within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:37.7 occ:1.00 F2 B:8W1401 0.0 37.7 1.0 C9 B:8W1401 1.4 40.9 1.0 F1 B:8W1401 2.2 26.8 1.0 F3 B:8W1401 2.3 36.2 1.0 C5 B:8W1401 2.3 26.4 1.0 H5 B:8W1401 2.6 41.4 1.0 HB3 B:GLN242 2.7 30.4 1.0 C4 B:8W1401 2.8 34.5 1.0 HG23 B:VAL246 2.8 21.8 1.0 HG22 B:VAL246 3.1 21.8 1.0 HG22 B:VAL237 3.3 31.9 1.0 CG2 B:VAL246 3.4 18.1 1.0 HB1 B:ALA235 3.4 16.9 1.0 CB B:GLN242 3.6 25.3 1.0 HG21 B:VAL246 3.6 21.8 1.0 HG2 B:GLN242 3.7 34.8 1.0 C6 B:8W1401 3.7 30.4 1.0 O B:GLN242 3.8 18.2 1.0 HG23 B:VAL237 3.9 31.9 1.0 HB3 B:LEU166 4.0 20.2 1.0 CG B:GLN242 4.0 29.0 1.0 HB2 B:LEU166 4.0 20.2 1.0 HB B:ILE245 4.0 24.5 1.0 CG2 B:VAL237 4.0 26.6 1.0 HA B:VAL237 4.0 25.4 1.0 H6 B:8W1401 4.1 36.5 1.0 HG22 B:ILE245 4.1 28.0 1.0 CD B:GLN242 4.2 21.1 1.0 OE1 B:GLN242 4.2 26.3 1.0 N1 B:8W1401 4.2 34.4 1.0 HA B:GLN242 4.2 35.4 1.0 HD13 B:LEU166 4.3 25.5 1.0 HB2 B:GLN242 4.3 30.4 1.0 HD12 B:LEU166 4.3 25.5 1.0 O B:ASP236 4.3 24.9 1.0 CB B:ALA235 4.3 14.1 1.0 H B:VAL246 4.3 18.1 1.0 CA B:GLN242 4.3 29.5 1.0 C B:GLN242 4.3 20.5 1.0 HB2 B:ALA235 4.4 16.9 1.0 CB B:LEU166 4.5 16.8 1.0 HG21 B:VAL237 4.6 31.9 1.0 C7 B:8W1401 4.7 34.7 1.0 N B:VAL246 4.7 15.1 1.0 CD1 B:LEU166 4.7 21.3 1.0 CB B:VAL246 4.7 15.0 1.0 CG2 B:ILE245 4.8 23.3 1.0 HB3 B:ALA235 4.8 16.9 1.0 HG21 B:ILE245 4.8 28.0 1.0 H B:ASP236 4.8 24.6 1.0 HA B:VAL246 4.8 17.7 1.0 CB B:ILE245 4.8 20.4 1.0 C B:ASP236 4.8 28.8 1.0 CA B:VAL237 4.8 21.2 1.0 NE2 B:GLN242 4.9 36.6 1.0 HD11 B:ILE245 4.9 38.9 1.0 HB3 B:ALA217 4.9 21.3 1.0 HG3 B:GLN242 4.9 34.8 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of Human Fibrillarin in Complex with Fragment 1 From Cocktail Soak


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Human Fibrillarin in Complex with Fragment 1 From Cocktail Soak within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:36.2 occ:1.00 F3 B:8W1401 0.0 36.2 1.0 C9 B:8W1401 1.4 40.9 1.0 F2 B:8W1401 2.3 37.7 1.0 F1 B:8W1401 2.3 26.8 1.0 C5 B:8W1401 2.3 26.4 1.0 HG2 B:GLN242 2.5 34.8 1.0 HB B:ILE245 2.9 24.5 1.0 HG21 B:ILE245 3.0 28.0 1.0 H6 B:8W1401 3.0 36.5 1.0 HD11 B:ILE245 3.1 38.9 1.0 HG22 B:ILE245 3.1 28.0 1.0 HB3 B:GLN242 3.1 30.4 1.0 C6 B:8W1401 3.1 30.4 1.0 CG B:GLN242 3.3 29.0 1.0 HD12 B:ILE245 3.4 38.9 1.0 CG2 B:ILE245 3.4 23.3 1.0 C4 B:8W1401 3.4 34.5 1.0 HB3 B:ALA217 3.4 21.3 1.0 HA B:GLN242 3.5 35.4 1.0 CB B:ILE245 3.6 20.4 1.0 CB B:GLN242 3.6 25.3 1.0 CD1 B:ILE245 3.6 32.4 1.0 H B:FMT402 3.7 51.5 1.0 CD B:GLN242 3.8 21.1 1.0 H5 B:8W1401 3.8 41.4 1.0 HE21 B:GLN242 3.9 43.9 1.0 CA B:GLN242 4.0 29.5 1.0 O2 B:FMT402 4.0 45.8 1.0 HG3 B:GLN242 4.0 34.8 1.0 NE2 B:GLN242 4.1 36.6 1.0 C B:FMT402 4.1 43.0 1.0 O B:GLN242 4.2 18.2 1.0 HG23 B:VAL246 4.2 21.8 1.0 CG1 B:ILE245 4.2 20.6 1.0 CB B:ALA217 4.3 17.8 1.0 HG23 B:ILE245 4.3 28.0 1.0 HB1 B:ALA217 4.4 21.3 1.0 C7 B:8W1401 4.4 34.7 1.0 OE1 B:GLN242 4.4 26.3 1.0 N1 B:8W1401 4.4 34.4 1.0 HD13 B:ILE245 4.5 38.9 1.0 HB2 B:GLN242 4.5 30.4 1.0 C B:GLN242 4.6 20.5 1.0 HB2 B:ALA217 4.6 21.3 1.0 HE22 B:GLN242 4.6 43.9 1.0 H B:VAL246 4.7 18.1 1.0 HB3 B:LEU166 4.7 20.2 1.0 HO2 B:FMT402 4.7 54.9 1.0 HD13 B:LEU166 4.8 25.5 1.0 HG22 B:VAL246 4.8 21.8 1.0 HG13 B:ILE245 4.8 24.8 1.0 HG12 B:ILE245 4.8 24.8 1.0 CA B:ILE245 4.9 16.9 1.0 N B:VAL246 4.9 15.1 1.0 CG2 B:VAL246 4.9 18.1 1.0 HG22 B:VAL237 5.0 31.9 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