Fluorine in PDB 6fe3: Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1439

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1439, PDB code: 6fe3 was solved by A.K.Singh, D.G.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.41 / 1.62
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.530, 114.820, 68.310, 90.00, 108.25, 90.00
R / Rfree (%)	16.5 / 19

The structure of Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1439 also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Zinc	(Zn)	2 atoms

The binding sites of Fluorine atom in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1439 (pdb code 6fe3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1439, PDB code: 6fe3:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1439


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 T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1439 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1003 b:39.4 occ:1.00 F1 A:D681003 0.0 39.4 1.0 C16 A:D681003 1.4 37.4 1.0 O3 A:D681003 2.2 33.2 1.0 F2 A:D681003 2.2 30.8 1.0 C15 A:D681003 2.7 34.8 1.0 O A:HOH1148 2.9 49.1 1.0 O A:HOH1140 2.9 35.4 1.0 C14 A:D681003 3.0 36.9 1.0 CB A:ASN825 3.3 21.1 1.0 CG1 A:VAL826 3.5 21.7 1.0 OE1 A:GLN874 3.8 27.2 1.0 C17 A:D681003 3.9 36.2 1.0 OD1 A:ASN825 3.9 25.1 1.0 O A:HOH1269 3.9 27.5 1.0 CE2 A:PHE877 3.9 29.1 1.0 N A:VAL826 4.0 21.0 1.0 CD2 A:PHE877 4.1 24.1 1.0 CG A:ASN825 4.1 22.2 1.0 C13 A:D681003 4.2 34.2 1.0 O4 A:D681003 4.3 39.1 1.0 CA A:ASN825 4.3 21.2 1.0 C A:ASN825 4.4 21.4 1.0 NE2 A:GLN874 4.6 27.0 1.0 CD A:GLN874 4.6 26.1 1.0 CB A:VAL826 4.6 21.7 1.0 N A:ASN825 4.7 19.5 1.0 CA A:VAL826 4.7 22.2 1.0 CZ A:PHE877 4.7 29.6 1.0 C19 A:D681003 4.9 34.9 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1439


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 T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1439 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1003 b:30.8 occ:1.00 F2 A:D681003 0.0 30.8 1.0 C16 A:D681003 1.4 37.4 1.0 F1 A:D681003 2.2 39.4 1.0 O3 A:D681003 2.2 33.2 1.0 O A:HOH1148 2.8 49.1 1.0 C15 A:D681003 2.9 34.8 1.0 C14 A:D681003 3.0 36.9 1.0 OD1 A:ASN825 3.1 25.1 1.0 N A:ALA837 3.4 23.6 1.0 CB A:ASN825 3.5 21.1 1.0 CA A:ALA837 3.5 26.9 1.0 C A:TRP836 3.7 23.9 1.0 CG A:ASN825 3.7 22.2 1.0 CB A:TRP836 3.8 23.0 1.0 O A:TRP836 3.9 24.0 1.0 CB A:ALA837 4.0 26.1 1.0 CG1 A:VAL840 4.2 32.6 1.0 C17 A:D681003 4.2 36.2 1.0 OE1 A:GLN874 4.2 27.2 1.0 C13 A:D681003 4.3 34.2 1.0 CA A:TRP836 4.4 25.5 1.0 O A:SER833 4.4 23.4 1.0 NE2 A:GLN874 4.6 27.0 1.0 O A:HOH1269 4.7 27.5 1.0 O4 A:D681003 4.7 39.1 1.0 CD A:GLN874 4.8 26.1 1.0 CB A:VAL840 4.8 29.5 1.0 CE1 A:TYR668 4.8 27.5 1.0 C A:ALA837 4.8 27.0 1.0 O A:HOH1140 4.9 35.4 1.0 CA A:ASN825 4.9 21.2 1.0 CG A:TRP836 5.0 21.0 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1439


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 T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1439 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1003 b:47.5 occ:1.00 F3 A:D681003 0.0 47.5 1.0 C18 A:D681003 1.3 50.7 1.0 F4 A:D681003 2.1 54.8 1.0 O4 A:D681003 2.2 39.1 1.0 C17 A:D681003 2.8 36.2 1.0 C19 A:D681003 2.9 34.9 1.0 SD A:MET861 3.4 84.7 1.0 CE2 A:PHE844 3.6 31.3 1.0 C15 A:D681003 4.1 34.8 1.0 O A:HOH1216 4.1 48.5 1.0 CE A:MET861 4.2 68.1 1.0 C12 A:D681003 4.2 29.8 1.0 CD2 A:PHE844 4.4 31.4 1.0 CZ A:PHE844 4.4 30.9 1.0 CG A:MET861 4.5 68.7 1.0 O3 A:D681003 4.5 33.2 1.0 N4 A:D681003 4.5 32.9 1.0 CD1 A:PHE877 4.6 28.9 1.0 O6 A:D681003 4.7 53.9 1.0 O A:HOH1263 4.7 37.0 1.0 CG1 A:VAL840 4.7 32.6 1.0 NE2 A:GLN874 4.9 27.0 1.0 CG A:PHE877 4.9 27.3 1.0 CB A:PHE877 4.9 24.4 1.0 C11 A:D681003 4.9 31.6 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1439


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 T. Brucei Pde-B1 Catalytic Domain with Inhibitor Npd-1439 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1003 b:54.8 occ:1.00 F4 A:D681003 0.0 54.8 1.0 C18 A:D681003 1.3 50.7 1.0 F3 A:D681003 2.1 47.5 1.0 O4 A:D681003 2.2 39.1 1.0 O A:HOH1216 2.8 48.5 1.0 O A:GLY873 3.4 26.8 1.0 CB A:PHE877 3.4 24.4 1.0 C17 A:D681003 3.5 36.2 1.0 O A:HOH1263 3.5 37.0 1.0 NE2 A:GLN874 3.6 27.0 1.0 C A:GLY873 3.9 27.1 1.0 CG A:PHE877 4.0 27.3 1.0 O6 A:D681003 4.1 53.9 1.0 C19 A:D681003 4.1 34.9 1.0 SD A:MET861 4.2 84.7 1.0 CD1 A:PHE877 4.2 28.9 1.0 O3 A:D681003 4.4 33.2 1.0 C15 A:D681003 4.5 34.8 1.0 CA A:GLY873 4.5 28.4 1.0 CA A:PHE877 4.6 23.3 1.0 N A:GLN874 4.6 23.1 1.0 N A:PHE877 4.7 23.8 1.0 CD A:GLN874 4.8 26.1 1.0 CD2 A:PHE877 4.9 24.1 1.0 CA A:GLN874 4.9 24.8 1.0

I.G.Salado, C.Moreno, G.Sakaine, A.K.Singh, A.R.Blaazer, M.Siderius, A.Matheeussen, S.Gul, L.Maes, R.Leurs, D.G.Brown, K.Augustyns. TBRPDEB1 Structure with Inhibitor Npd-1439 To Be Published.