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Fluorine in PDB 2opm: Human Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph- 461

Enzymatic activity of Human Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph- 461

All present enzymatic activity of Human Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph- 461:
2.5.1.10;

Protein crystallography data

The structure of Human Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph- 461, PDB code: 2opm was solved by R.Cao, Y.G.Gao, H.Robinson, A.Goddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.40
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 111.783, 111.783, 66.525, 90.00, 90.00, 90.00
R / Rfree (%) 23.4 / 26.9

Other elements in 2opm:

The structure of Human Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph- 461 also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph- 461 (pdb code 2opm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Human Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph- 461, PDB code: 2opm:

Fluorine binding site 1 out of 1 in 2opm

Go back to Fluorine Binding Sites List in 2opm
Fluorine binding site 1 out of 1 in the Human Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph- 461


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph- 461 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:63.2
occ:1.00
 F A:NI9901 0.0 63.2 1.0
C7 A:NI9901 1.3 68.1 1.0
C4 A:NI9901 2.3 65.0 1.0
C3 A:NI9901 2.4 72.3 1.0
CG A:GLN185 3.6 61.1 1.0
N A:NI9901 3.6 73.7 1.0
C6 A:NI9901 3.6 65.4 1.0
OD1 A:ASP117 3.7 59.5 1.0
NE2 A:GLN185 4.0 82.9 1.0
C5 A:NI9901 4.1 69.2 1.0
CG2 A:THR181 4.2 32.9 1.0
O A:HOH3072 4.2 53.4 1.0
CB A:PHE113 4.3 35.5 1.0
O A:PHE113 4.3 46.2 1.0
CD A:GLN185 4.3 72.5 1.0
CB A:ASP117 4.4 43.9 1.0
CG A:ASP117 4.4 54.1 1.0
O A:HOH3123 4.4 64.7 1.0
CG A:PHE113 4.6 42.5 1.0
O A:LYS214 4.7 23.3 1.0
CD2 A:PHE113 4.7 49.7 1.0
O4 A:NI9901 4.8 65.6 1.0
CB A:GLN185 4.9 47.5 1.0
C2 A:NI9901 4.9 73.5 1.0
C A:PHE113 4.9 35.3 1.0
CA A:PHE113 5.0 26.8 1.0

Reference:

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
Page generated: Mon Jul 14 13:53:34 2025

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