Fluorine in PDB 3dyf: T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate

All present enzymatic activity of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate:
2.5.1.10;

The structure of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate, PDB code: 3dyf was solved by R.Cao, Y.Gao, H.Robinson, A.Goddard, E.Oldfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.48 / 2.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	133.939, 117.898, 63.274, 90.00, 111.27, 90.00
R / Rfree (%)	20.1 / 26.8

The structure of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Fluorine atom in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate (pdb code 3dyf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate, PDB code: 3dyf:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:F3001 b:43.9 occ:1.00 F A:NI93001 0.0 43.9 1.0 C7 A:NI93001 1.3 46.2 1.0 C3 A:NI93001 2.4 45.2 1.0 C4 A:NI93001 2.4 40.0 1.0 CD A:GLN172 3.0 25.1 1.0 NE2 A:GLN172 3.2 36.3 1.0 OE1 A:GLN172 3.2 29.8 1.0 N A:NI93001 3.6 46.3 1.0 CB A:TYR99 3.6 26.1 1.0 CG A:GLN172 3.6 25.2 1.0 C6 A:NI93001 3.6 44.8 1.0 CD1 A:TYR99 3.8 14.5 1.0 CG A:TYR99 3.9 11.9 1.0 O A:TYR99 4.1 30.8 1.0 C5 A:NI93001 4.1 41.9 1.0 CG2 A:THR168 4.3 11.1 1.0 CB A:ASP103 4.4 33.1 1.0 C A:TYR99 4.5 30.1 1.0 CA A:TYR99 4.6 26.7 1.0 OH A:TYR216 4.6 14.4 1.0 CE1 A:TYR99 4.7 12.1 1.0 CG A:ASP103 4.7 38.1 1.0 OD1 A:ASP103 4.8 41.0 1.0 C2 A:NI93001 4.8 41.4 1.0 CD2 A:TYR99 4.8 11.1 1.0 O A:LYS212 4.9 42.3 1.0

Fluorine binding site 2 out of 2 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 and Isopentyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:F4001 b:52.5 occ:1.00 F B:NI94001 0.0 52.5 1.0 C7 B:NI94001 1.3 52.3 1.0 C3 B:NI94001 2.3 50.5 1.0 C4 B:NI94001 2.4 56.8 1.0 CD B:GLN172 3.0 32.1 1.0 NE2 B:GLN172 3.1 36.5 1.0 OE1 B:GLN172 3.1 42.2 1.0 CB B:TYR99 3.5 19.6 1.0 N B:NI94001 3.6 54.8 1.0 C6 B:NI94001 3.6 58.8 1.0 CD1 B:TYR99 3.8 17.3 1.0 CG B:GLN172 3.8 28.0 1.0 CG B:TYR99 3.8 12.7 1.0 C5 B:NI94001 4.1 58.6 1.0 O B:TYR99 4.1 23.7 1.0 O B:HOH5004 4.3 26.8 1.0 CG2 B:THR168 4.3 11.1 1.0 C B:TYR99 4.5 27.5 1.0 CA B:TYR99 4.5 25.1 1.0 CB B:ASP103 4.5 32.3 1.0 OD2 B:ASP103 4.7 27.5 1.0 CE1 B:TYR99 4.7 11.1 1.0 CD2 B:TYR99 4.7 15.4 1.0 O B:LYS212 4.8 43.5 1.0 C2 B:NI94001 4.8 49.7 1.0 OH B:TYR216 4.8 28.2 1.0 CG B:ASP103 4.9 32.3 1.0

Y.Zhang, R.Cao, F.Yin, M.P.Hudock, R.T.Guo, K.Krysiak, S.Mukherjee, Y.G.Gao, H.Robinson, Y.Song, J.H.No, K.Bergan, A.Leon, L.Cass, A.Goddard, T.K.Chang, F.Y.Lin, E.Van Beek, S.Papapoulos, A.H.Wang, T.Kubo, M.Ochi, D.Mukkamala, E.Oldfield. Lipophilic Bisphosphonates As Dual Farnesyl/Geranylgeranyl Diphosphate Synthase Inhibitors: An X-Ray and uc(Nmr) Investigation. J.Am.Chem.Soc. V. 131 5153 2009.
ISSN: ISSN 0002-7863
PubMed: 19309137
DOI: 10.1021/JA808285E