Fluorine in PDB 2z78: S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Bph-806

All present enzymatic activity of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Bph-806:
2.5.1.1; 2.5.1.10; 2.5.1.29; 2.5.1.30;

The structure of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Bph-806, PDB code: 2z78 was solved by C.K.-M.Chen, R.T.Guo, M.Hudock, R.Cao, E.Oldfield, A.H.-J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.80 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.330, 116.639, 129.780, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 23.7

The binding sites of Fluorine atom in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Bph-806 (pdb code 2z78). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Bph-806, PDB code: 2z78:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Bph-806


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Bph-806 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1300 b:46.1 occ:1.00 FAH A:H861300 0.0 46.1 1.0 CBA A:H861300 1.3 44.6 1.0 CAK A:H861300 2.4 44.2 1.0 CAJ A:H861300 2.4 45.8 1.0 O A:SER76 3.0 19.6 1.0 CB A:ILE79 3.5 19.8 1.0 CG2 A:ILE79 3.5 21.5 1.0 OE2 A:GLU83 3.6 22.9 1.0 O B:HOH394 3.6 21.4 1.0 N A:ASP80 3.6 20.4 1.0 NE2 A:GLN147 3.6 24.4 1.0 CBD A:H861300 3.6 43.7 1.0 CBB A:H861300 3.6 46.0 1.0 CA A:ASP80 4.0 19.1 1.0 C A:SER76 4.0 21.0 1.0 C A:ILE79 4.1 18.4 1.0 CA A:SER76 4.1 20.8 1.0 CD A:GLN147 4.1 28.4 1.0 CAL A:H861300 4.1 44.4 1.0 CB A:ASP80 4.2 23.9 1.0 O B:HOH393 4.2 17.0 1.0 CD A:GLU83 4.3 21.3 1.0 OH A:TYR112 4.3 28.0 1.0 CA A:ILE79 4.4 18.8 1.0 CG A:GLN147 4.4 22.4 1.0 CB A:SER76 4.5 18.3 1.0 OE1 A:GLU83 4.5 20.0 1.0 CG1 A:ILE79 4.6 20.2 1.0 O A:ILE79 4.7 20.3 1.0 FAI A:H861300 4.7 53.2 1.0 CBE A:H861300 4.8 43.6 1.0 OG A:SER76 4.8 24.2 1.0 OE1 A:GLN147 4.9 29.4 1.0 OD1 A:ASP80 4.9 28.0 1.0 N A:ILE79 5.0 18.9 1.0

Fluorine binding site 2 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Bph-806


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Bph-806 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1300 b:53.2 occ:1.00 FAI A:H861300 0.0 53.2 1.0 CBB A:H861300 1.3 46.0 1.0 CAJ A:H861300 2.4 45.8 1.0 CAL A:H861300 2.4 44.4 1.0 O A:LEU143 2.7 16.4 1.0 C A:LEU143 2.9 17.6 1.0 CB A:LEU143 3.2 24.9 1.0 CG A:LEU143 3.3 29.7 1.0 CA A:LEU143 3.5 21.1 1.0 N A:HIS144 3.5 16.1 1.0 CBA A:H861300 3.6 44.6 1.0 CBD A:H861300 3.6 43.7 1.0 CB A:GLN147 3.7 18.9 1.0 CD1 A:LEU143 3.8 31.2 1.0 CA A:HIS144 4.0 16.8 1.0 CAK A:H861300 4.1 44.2 1.0 CG A:GLN147 4.4 22.4 1.0 O A:LYS174 4.6 24.6 1.0 CD2 A:LEU143 4.7 28.8 1.0 CG A:HIS144 4.7 17.4 1.0 FAH A:H861300 4.7 46.1 1.0 CD2 A:HIS144 4.7 16.1 1.0 CG A:LYS174 4.8 24.2 1.0 CBE A:H861300 4.8 43.6 1.0 N A:GLN147 4.8 18.4 1.0 CA A:GLN147 4.8 17.9 1.0 CD A:GLN147 4.9 28.4 1.0 N A:LEU143 4.9 18.1 1.0 ND1 A:HIS144 4.9 20.8 1.0 OE1 A:GLN147 5.0 29.4 1.0 NE2 A:HIS144 5.0 21.6 1.0 C A:HIS144 5.0 15.9 1.0 CB A:HIS144 5.0 15.2 1.0

Fluorine binding site 3 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Bph-806


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Bph-806 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1301 b:51.9 occ:1.00 FAH B:H861301 0.0 51.9 1.0 CBA B:H861301 1.3 50.2 1.0 CAJ B:H861301 2.4 51.0 1.0 CAK B:H861301 2.4 49.2 1.0 O B:SER76 3.0 19.1 1.0 NE2 B:GLN147 3.4 22.4 1.0 CBB B:H861301 3.6 50.8 1.0 CBD B:H861301 3.7 50.2 1.0 N B:ASP80 3.7 19.0 1.0 CG2 B:ILE79 3.7 17.3 1.0 OE2 B:GLU83 3.7 21.4 1.0 CB B:ASP80 3.9 21.7 1.0 C B:SER76 3.9 22.0 1.0 CD B:GLN147 3.9 24.5 1.0 O B:HOH345 4.0 19.2 1.0 CA B:ASP80 4.0 19.0 1.0 CA B:SER76 4.0 22.4 1.0 CB B:SER76 4.1 24.4 1.0 CB B:ILE79 4.1 16.4 1.0 CAL B:H861301 4.1 50.9 1.0 CG B:GLN147 4.3 20.9 1.0 C B:ILE79 4.4 17.5 1.0 OD2 B:ASP80 4.5 24.8 1.0 CD B:GLU83 4.6 21.1 1.0 OE1 B:GLN147 4.6 24.4 1.0 OH B:TYR112 4.7 28.9 1.0 O B:HOH346 4.7 24.4 1.0 CG B:ASP80 4.7 25.8 1.0 FAI B:H861301 4.7 55.3 1.0 OG B:SER76 4.7 33.4 1.0 CBE B:H861301 4.8 50.1 1.0 CA B:ILE79 4.8 16.3 1.0 OE1 B:GLU83 4.9 21.6 1.0

Fluorine binding site 4 out of 4 in the S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Bph-806


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of S. Cerevisiae Geranylgeranyl Pyrophosphate Synthase in Complex with Bph-806 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1301 b:55.3 occ:1.00 FAI B:H861301 0.0 55.3 1.0 CBB B:H861301 1.3 50.8 1.0 CAJ B:H861301 2.4 51.0 1.0 CAL B:H861301 2.4 50.9 1.0 O B:LEU143 2.5 16.4 1.0 CG B:LEU143 2.6 30.8 1.0 CD2 B:LEU143 2.8 31.7 1.0 C B:LEU143 3.0 18.4 1.0 CB B:GLN147 3.5 19.5 1.0 CB B:LEU143 3.5 24.3 1.0 CA B:LEU143 3.5 19.2 1.0 CBA B:H861301 3.6 50.2 1.0 CBD B:H861301 3.6 50.2 1.0 CD1 B:LEU143 3.7 34.4 1.0 N B:HIS144 3.9 15.2 1.0 O B:LYS174 4.0 24.2 1.0 CAK B:H861301 4.1 49.2 1.0 N B:GLN147 4.2 18.3 1.0 CG B:LYS174 4.2 26.6 1.0 CA B:GLN147 4.3 18.2 1.0 CA B:HIS144 4.3 17.4 1.0 CA B:LYS174 4.4 23.6 1.0 CG B:GLN147 4.5 20.9 1.0 OE1 B:GLN147 4.6 24.4 1.0 C B:LYS174 4.6 23.6 1.0 CD B:GLN147 4.7 24.5 1.0 FAH B:H861301 4.7 51.9 1.0 CB B:LYS174 4.8 24.2 1.0 CBE B:H861301 4.8 50.1 1.0 N B:LEU143 4.9 17.2 1.0

C.K.-M.Chen, M.P.Hudock, Y.Zhang, R.-T.Guo, R.Cao, J.H.No, P.-H.Liang, T.-P.Ko, T.-H.Chang, S.-C.Chang, Y.Song, J.Axelson, A.Kumar, A.H.-J.Wang, E.Oldfield. Inhibition of Geranylgeranyl Diphosphate Synthase By Bisphosphonates: A Crystallographic and Computational Investigation J.Med.Chem. V. 51 5594 2008.
ISSN: ISSN 0022-2623
PubMed: 18800762
DOI: 10.1021/JM800325Y