Magnesium in PDB 2opm: 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;

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

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

Fluorine

(F)

1 atom

The binding sites of Magnesium 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 Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Human Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph- 461, PDB code: 2opm:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Human Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph- 461


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg907 b:73.1 occ:1.00 O A:HOH3092 2.0 66.9 1.0 O A:HOH3027 2.1 41.3 1.0 OD2 A:ASP117 2.2 54.1 1.0 O3 A:NI9901 2.2 77.1 1.0 OD2 A:ASP121 2.3 63.5 1.0 O7 A:NI9901 2.6 70.6 1.0 CG A:ASP117 3.2 54.1 1.0 CG A:ASP121 3.3 58.1 1.0 P2 A:NI9901 3.6 75.8 1.0 OD1 A:ASP117 3.6 59.5 1.0 P1 A:NI9901 3.7 77.8 1.0 CB A:ASP121 3.8 49.4 1.0 MG A:MG909 3.8 50.2 1.0 NH2 A:ARG126 4.0 41.6 1.0 O6 A:NI9901 4.1 79.7 1.0 O1 A:NI9901 4.2 77.9 1.0 C1 A:NI9901 4.2 74.5 1.0 OD1 A:ASP121 4.4 84.5 1.0 OG A:SER123 4.4 45.4 1.0 O A:ASP117 4.4 35.0 1.0 OD1 A:ASP118 4.5 25.5 1.0 O A:HOH3123 4.5 64.7 1.0 O A:HOH3084 4.5 68.9 1.0 CB A:ASP117 4.5 43.9 1.0 O5 A:NI9901 4.7 75.9 1.0 C2 A:NI9901 4.7 73.5 1.0 O A:HOH3080 4.7 47.1 1.0 C A:ASP117 4.8 40.5 1.0 MG A:MG908 4.8 70.7 1.0 NZ A:LYS280 5.0 72.9 1.0

Magnesium binding site 2 out of 3 in the Human Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph- 461


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph- 461 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg908 b:70.7 occ:1.00 O A:HOH3068 2.0 49.6 1.0 O5 A:NI9901 2.2 75.9 1.0 OD2 A:ASP257 2.3 52.5 1.0 O6 A:NI9901 2.6 79.7 1.0 P2 A:NI9901 2.9 75.8 1.0 O2 A:NI9901 2.9 65.8 1.0 C1 A:NI9901 3.1 74.5 1.0 O3 A:NI9901 3.2 77.1 1.0 CG A:ASP257 3.4 46.9 1.0 P1 A:NI9901 3.5 77.8 1.0 O A:HOH3120 3.5 69.6 1.0 O A:HOH3092 3.6 66.9 1.0 O A:HOH3121 3.8 62.0 1.0 OD1 A:ASP257 3.9 62.0 1.0 O A:HOH3070 4.0 73.0 1.0 NE2 A:GLN254 4.1 40.9 1.0 OD1 A:ASP261 4.1 42.8 1.0 O1 A:NI9901 4.3 77.9 1.0 OD2 A:ASP275 4.4 41.1 1.0 O7 A:NI9901 4.4 70.6 1.0 O A:ASP257 4.5 56.9 1.0 OD1 A:ASP275 4.6 49.7 1.0 C2 A:NI9901 4.6 73.5 1.0 CB A:ASP257 4.6 41.8 1.0 O4 A:NI9901 4.7 65.6 1.0 OD1 A:ASP258 4.7 34.0 1.0 CG A:ASP261 4.7 50.0 1.0 NZ A:LYS271 4.7 49.1 1.0 C A:ASP257 4.8 47.3 1.0 MG A:MG907 4.8 73.1 1.0 CB A:ASP261 4.9 44.4 1.0 CG A:ASP275 4.9 45.5 1.0

Magnesium binding site 3 out of 3 in the Human Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph- 461


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph- 461 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg909 b:50.2 occ:1.00 O7 A:NI9901 2.1 70.6 1.0 O A:HOH3072 2.5 53.4 1.0 OD1 A:ASP117 2.6 59.5 1.0 OD2 A:ASP121 2.8 63.5 1.0 NZ A:LYS280 3.1 72.9 1.0 NE2 A:GLN185 3.1 82.9 1.0 P1 A:NI9901 3.1 77.8 1.0 OD1 A:ASP188 3.3 52.2 1.0 O4 A:NI9901 3.3 65.6 1.0 OD1 A:ASP121 3.5 84.5 1.0 CG A:ASP121 3.5 58.1 1.0 CG A:ASP117 3.6 54.1 1.0 O6 A:NI9901 3.8 79.7 1.0 MG A:MG907 3.8 73.1 1.0 OD2 A:ASP117 3.9 54.1 1.0 CD A:GLN185 4.0 72.5 1.0 CE A:LYS280 4.4 50.4 1.0 OE1 A:GLN185 4.4 87.0 1.0 O A:HOH3070 4.4 73.0 1.0 O A:HOH3092 4.4 66.9 1.0 CG A:ASP188 4.5 44.5 1.0 C3 A:NI9901 4.6 72.3 1.0 C1 A:NI9901 4.8 74.5 1.0 NZ A:LYS214 4.9 50.5 1.0 O3 A:NI9901 4.9 77.1 1.0 CB A:ASP117 4.9 43.9 1.0 N A:NI9901 4.9 73.7 1.0 C7 A:NI9901 5.0 68.1 1.0 CG A:GLN185 5.0 61.1 1.0 CE A:LYS214 5.0 54.4 1.0 CB A:ASP121 5.0 49.4 1.0 CD A:LYS214 5.0 49.1 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