Magnesium in PDB 3b7l: Human Farnesyl Diphosphate Synthase Complexed with Mg and Minodronate

All present enzymatic activity of Human Farnesyl Diphosphate Synthase Complexed with Mg and Minodronate:
2.5.1.10;

The structure of Human Farnesyl Diphosphate Synthase Complexed with Mg and Minodronate, PDB code: 3b7l was solved by E.S.Pilka, J.E.Dunford, K.Guo, A.C.W.Pike, K.L.Kavanagh, F.Von Delft, F.H.Ebetino, C.H.Arrowsmith, A.M.Edwards, R.G.G.Russell, U.Oppermann, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.21 / 1.95
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	110.922, 110.922, 67.308, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 20.2

The binding sites of Magnesium atom in the Human Farnesyl Diphosphate Synthase Complexed with Mg and Minodronate (pdb code 3b7l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Human Farnesyl Diphosphate Synthase Complexed with Mg and Minodronate, PDB code: 3b7l:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Human Farnesyl Diphosphate Synthase Complexed with Mg and Minodronate


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 Mg and Minodronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg907 b:23.6 occ:1.00 O A:HOH1131 2.1 20.4 1.0 O4 A:M0N901 2.1 29.5 1.0 O3 A:M0N901 2.1 32.9 1.0 O A:HOH1136 2.1 20.3 1.0 OD2 A:ASP103 2.2 30.2 1.0 OD2 A:ASP107 2.3 31.8 1.0 CG A:ASP103 3.1 27.6 1.0 MG A:MG909 3.2 23.0 1.0 CG A:ASP107 3.3 28.9 1.0 P1 A:M0N901 3.3 32.3 1.0 P2 A:M0N901 3.3 31.2 1.0 OD1 A:ASP103 3.4 32.1 1.0 CB A:ASP107 3.7 29.4 1.0 C9 A:M0N901 3.7 33.2 1.0 O A:HOH1059 3.8 22.0 1.0 O1 A:M0N901 3.9 32.9 1.0 O5 A:M0N901 4.0 33.1 1.0 C8 A:M0N901 4.2 30.8 1.0 NH2 A:ARG112 4.2 32.4 1.0 O A:HOH1134 4.2 19.9 1.0 O A:HOH1132 4.3 22.6 1.0 OG A:SER109 4.3 34.3 1.0 OD1 A:ASP107 4.4 28.8 1.0 MG A:MG910 4.4 31.0 1.0 O A:ASP103 4.4 29.8 1.0 CB A:ASP103 4.5 36.7 1.0 O6 A:M0N901 4.5 32.4 1.0 O2 A:M0N901 4.6 31.7 1.0 OD1 A:ASP104 4.6 33.1 1.0 C A:ASP103 4.7 29.9 1.0 O A:HOH1135 4.8 20.9 1.0 O A:HOH1008 4.8 23.9 1.0 MG A:MG908 4.9 24.6 1.0 O A:HOH1128 4.9 20.8 1.0

Magnesium binding site 2 out of 4 in the Human Farnesyl Diphosphate Synthase Complexed with Mg and Minodronate


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 Mg and Minodronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg908 b:24.6 occ:1.00 O5 A:M0N901 2.0 33.1 1.0 O1 A:M0N901 2.1 32.9 1.0 O A:HOH1129 2.1 22.5 1.0 O A:HOH1132 2.2 22.6 1.0 OD2 A:ASP243 2.2 28.6 1.0 O A:HOH1130 2.3 22.8 1.0 CG A:ASP243 3.1 35.0 1.0 P2 A:M0N901 3.3 31.2 1.0 P1 A:M0N901 3.3 32.3 1.0 O A:M0N901 3.5 30.1 1.0 OD1 A:ASP243 3.5 32.7 1.0 C9 A:M0N901 3.6 33.2 1.0 O A:HOH937 4.0 21.4 1.0 OD1 A:ASP247 4.0 33.5 1.0 O A:HOH1084 4.1 42.4 1.0 O4 A:M0N901 4.1 29.5 1.0 O A:HOH1131 4.1 20.4 1.0 O A:ASP243 4.2 31.9 1.0 OD2 A:ASP261 4.2 29.6 1.0 NE2 A:GLN240 4.2 29.0 1.0 OD1 A:ASP261 4.2 34.0 1.0 O3 A:M0N901 4.3 32.9 1.0 OD1 A:ASP244 4.4 29.4 1.0 CB A:ASP243 4.4 33.9 1.0 O6 A:M0N901 4.4 32.4 1.0 O2 A:M0N901 4.4 31.7 1.0 C A:ASP243 4.4 29.2 1.0 CG A:ASP247 4.6 36.9 1.0 NZ A:LYS257 4.6 50.6 1.0 CB A:ASP247 4.6 31.9 1.0 CG A:ASP261 4.7 35.2 1.0 O A:HOH1059 4.7 22.0 1.0 CE A:LYS257 4.7 29.6 1.0 N A:ASP244 4.8 33.4 1.0 MG A:MG907 4.9 23.6 1.0

Magnesium binding site 3 out of 4 in the Human Farnesyl Diphosphate Synthase Complexed with Mg and Minodronate


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 Mg and Minodronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg909 b:23.0 occ:1.00 O A:HOH1134 2.0 19.9 1.0 O A:HOH1135 2.1 20.9 1.0 O3 A:M0N901 2.1 32.9 1.0 O A:HOH1128 2.1 20.8 1.0 OD1 A:ASP103 2.2 32.1 1.0 OD2 A:ASP107 2.2 31.8 1.0 CG A:ASP107 3.1 28.9 1.0 CG A:ASP103 3.2 27.6 1.0 MG A:MG907 3.2 23.6 1.0 OD1 A:ASP107 3.3 28.8 1.0 P1 A:M0N901 3.3 32.3 1.0 O2 A:M0N901 3.5 31.7 1.0 OD2 A:ASP103 3.5 30.2 1.0 OD1 A:ASP174 3.9 41.1 1.0 NE2 A:GLN171 4.1 28.3 1.0 O1 A:M0N901 4.2 32.9 1.0 O A:HOH1131 4.2 20.4 1.0 OE1 A:GLN171 4.2 34.3 1.0 OD2 A:ASP174 4.2 38.4 1.0 O A:HOH937 4.3 21.4 1.0 CG A:ASP174 4.3 34.7 1.0 CB A:ASP107 4.5 29.4 1.0 CB A:ASP103 4.5 36.7 1.0 C9 A:M0N901 4.6 33.2 1.0 NZ A:LYS266 4.6 43.2 1.0 CD A:GLN171 4.6 33.6 1.0 CE A:LYS266 4.7 36.0 1.0 NZ A:LYS200 4.7 32.2 1.0 C8 A:M0N901 4.7 30.8 1.0 O4 A:M0N901 4.8 29.5 1.0 C2 A:M0N901 4.8 32.0 1.0 N2 A:M0N901 4.9 31.3 1.0 C3 A:M0N901 5.0 34.2 1.0 MG A:MG910 5.0 31.0 1.0 O A:HOH1136 5.0 20.3 1.0

Magnesium binding site 4 out of 4 in the Human Farnesyl Diphosphate Synthase Complexed with Mg and Minodronate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Farnesyl Diphosphate Synthase Complexed with Mg and Minodronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg910 b:31.0 occ:1.00 OD1 A:ASP261 2.7 34.0 1.0 O A:HOH1131 2.8 20.4 1.0 OG1 A:THR260 2.8 33.1 1.0 OD2 A:ASP264 3.2 32.0 1.0 CE A:LYS266 3.6 36.0 1.0 O A:HOH1132 3.7 22.6 1.0 O A:HOH937 3.8 21.4 1.0 OD2 A:ASP107 3.8 31.8 1.0 CG A:LYS266 3.8 30.1 1.0 C A:THR260 3.8 31.8 1.0 N A:ASP261 3.8 26.1 1.0 CA A:ASP261 3.8 28.6 1.0 CG A:ASP107 3.8 28.9 1.0 CB A:ASP107 3.9 29.4 1.0 CB A:THR260 3.9 34.7 1.0 CG A:ASP261 3.9 35.2 1.0 CG A:ASP264 3.9 35.6 1.0 O A:THR260 4.0 29.7 1.0 O A:HOH1134 4.0 19.9 1.0 CB A:ASP264 4.0 31.6 1.0 CD A:LYS266 4.3 31.3 1.0 CA A:THR260 4.4 31.9 1.0 MG A:MG907 4.4 23.6 1.0 CB A:ASP261 4.5 29.7 1.0 OD1 A:ASP107 4.5 28.8 1.0 O A:HOH1008 4.6 23.9 1.0 N A:THR260 4.7 32.7 1.0 O A:ASP107 4.7 30.3 1.0 NZ A:LYS266 4.8 43.2 1.0 O3 A:M0N901 4.8 32.9 1.0 CA A:ASP107 4.8 33.7 1.0 O1 A:M0N901 4.9 32.9 1.0 OD2 A:ASP261 4.9 29.6 1.0 CB A:LYS266 5.0 29.9 1.0 MG A:MG909 5.0 23.0 1.0

E.S.Pilka, J.E.Dunford, K.Guo, A.C.W.Pike, K.L.Kavanagh, F.Von Delft, F.H.Ebetino, C.H.Arrowsmith, A.M.Edwards, R.G.G.Russell, U.Oppermann. Human Farnesyl Diphosphate Synthase Complexed with Mg and Minodronate. To Be Published.