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

Enzymatic activity of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461

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

Protein crystallography data

The structure of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461, PDB code: 3dyg 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) 29.22 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 135.565, 118.520, 63.186, 90.00, 112.36, 90.00
R / Rfree (%) 20.7 / 25

Other elements in 3dyg:

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

Magnesium (Mg) 6 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 (pdb code 3dyg). 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, PDB code: 3dyg:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 3dyg

Go back to Fluorine Binding Sites List in 3dyg
Fluorine binding site 1 out of 2 in the T. Brucei 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 T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F3001

b:25.5
occ:1.00
F A:NI93001 0.0 25.5 1.0
C7 A:NI93001 1.3 21.0 1.0
C3 A:NI93001 2.3 17.5 1.0
C4 A:NI93001 2.4 18.6 1.0
CD A:GLN172 3.0 20.8 1.0
NE2 A:GLN172 3.1 15.9 1.0
OE1 A:GLN172 3.2 20.5 1.0
CG A:GLN172 3.5 15.2 1.0
CB A:TYR99 3.6 12.1 1.0
N A:NI93001 3.6 22.8 1.0
C6 A:NI93001 3.7 17.5 1.0
CD1 A:TYR99 3.9 12.6 1.0
CG A:TYR99 4.0 12.3 1.0
O A:TYR99 4.1 20.7 1.0
C5 A:NI93001 4.1 19.4 1.0
CG2 A:THR168 4.2 15.6 1.0
OD1 A:ASP103 4.3 16.8 1.0
CB A:ASP103 4.3 17.7 1.0
C A:TYR99 4.4 14.5 1.0
CG A:ASP103 4.5 16.7 1.0
CA A:TYR99 4.5 13.5 1.0
O A:HOH5055 4.6 18.5 1.0
O A:HOH5014 4.6 16.0 1.0
C2 A:NI93001 4.8 19.4 1.0
CE1 A:TYR99 4.9 13.0 1.0
O A:LYS212 5.0 18.9 1.0

Fluorine binding site 2 out of 2 in 3dyg

Go back to Fluorine Binding Sites List in 3dyg
Fluorine binding site 2 out of 2 in the T. Brucei 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 2 of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-461 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F4001

b:24.5
occ:1.00
F B:NI94001 0.0 24.5 1.0
C7 B:NI94001 1.3 22.5 1.0
C3 B:NI94001 2.4 20.0 1.0
C4 B:NI94001 2.4 20.6 1.0
CD B:GLN172 2.9 23.5 1.0
NE2 B:GLN172 3.0 19.9 1.0
OE1 B:GLN172 3.2 23.1 1.0
CG B:GLN172 3.5 15.0 1.0
N B:NI94001 3.6 22.9 1.0
CB B:TYR99 3.6 12.3 1.0
C6 B:NI94001 3.6 20.2 1.0
CD1 B:TYR99 3.9 15.2 1.0
CG B:TYR99 3.9 14.8 1.0
C5 B:NI94001 4.1 20.8 1.0
CB B:ASP103 4.3 16.7 1.0
O B:TYR99 4.3 20.8 1.0
CG2 B:THR168 4.3 17.6 1.0
OD1 B:ASP103 4.4 19.3 1.0
C B:TYR99 4.4 15.5 1.0
CA B:TYR99 4.5 16.2 1.0
CG B:ASP103 4.6 16.1 1.0
O B:HOH5009 4.6 19.5 1.0
O A:HOH5090 4.7 22.5 1.0
C2 B:NI94001 4.8 20.3 1.0
O B:LYS212 4.8 17.2 1.0
CE1 B:TYR99 4.9 16.1 1.0
CD2 B:TYR99 5.0 13.0 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: Sun Dec 13 11:45:13 2020

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