Magnesium in PDB 3rye: Human Fdps Synthase in Complex with A N-Methyl Pyridinum Bisphosphonate

All present enzymatic activity of Human Fdps Synthase in Complex with A N-Methyl Pyridinum Bisphosphonate:
2.5.1.1; 2.5.1.10;

The structure of Human Fdps Synthase in Complex with A N-Methyl Pyridinum Bisphosphonate, PDB code: 3rye was solved by A.G.Evdokimov, B.L.Barnett, F.H.Ebetino, M.Pokross, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.20 / 2.10
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	111.311, 111.311, 69.713, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 23.9

The binding sites of Magnesium atom in the Human Fdps Synthase in Complex with A N-Methyl Pyridinum Bisphosphonate (pdb code 3rye). 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 Fdps Synthase in Complex with A N-Methyl Pyridinum Bisphosphonate, PDB code: 3rye:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Human Fdps Synthase in Complex with A N-Methyl Pyridinum Bisphosphonate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Fdps Synthase in Complex with A N-Methyl Pyridinum Bisphosphonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg907 b:29.5 occ:1.00 O A:HOH500 2.0 33.6 1.0 O9 A:UNR901 2.0 29.9 1.0 O5 A:UNR901 2.1 35.1 1.0 OD1 A:ASP103 2.1 31.3 1.0 O A:HOH497 2.1 25.9 1.0 OD2 A:ASP107 2.2 30.9 1.0 CG A:ASP103 3.0 32.8 1.0 MG A:MG909 3.2 32.2 1.0 OD2 A:ASP103 3.3 30.9 1.0 CG A:ASP107 3.3 36.0 1.0 P1 A:UNR901 3.3 34.4 1.0 P4 A:UNR901 3.3 32.1 1.0 C1 A:UNR901 3.7 34.0 1.0 CB A:ASP107 3.7 30.0 1.0 O6 A:UNR901 3.9 29.3 1.0 C3 A:UNR901 3.9 37.9 1.0 O A:HOH417 4.0 33.9 1.0 O8 A:UNR901 4.0 27.6 1.0 NH2 A:ARG112 4.0 27.9 1.0 O A:HOH3 4.1 28.8 1.0 O A:ASP103 4.3 26.2 1.0 O10 A:UNR901 4.4 26.7 1.0 OD1 A:ASP107 4.4 31.6 1.0 O A:HOH381 4.4 36.3 1.0 O A:HOH476 4.4 32.0 1.0 CB A:ASP103 4.4 27.2 1.0 OG A:SER109 4.5 37.4 1.0 O7 A:UNR901 4.5 31.6 1.0 OD1 A:ASP104 4.5 26.7 1.0 O A:HOH501 4.7 26.8 1.0 C A:ASP103 4.7 28.8 1.0 O A:HOH433 4.9 24.8 1.0 O A:HOH392 4.9 31.5 1.0 MG A:MG908 4.9 29.5 1.0 C27 A:UNR901 4.9 38.4 1.0

Magnesium binding site 2 out of 3 in the Human Fdps Synthase in Complex with A N-Methyl Pyridinum Bisphosphonate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Fdps Synthase in Complex with A N-Methyl Pyridinum Bisphosphonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg908 b:29.5 occ:1.00 O8 A:UNR901 2.0 27.6 1.0 O6 A:UNR901 2.0 29.3 1.0 O A:HOH476 2.0 32.0 1.0 O A:HOH496 2.1 31.8 1.0 O A:HOH499 2.2 31.4 1.0 OD2 A:ASP243 2.3 35.0 1.0 CG A:ASP243 3.3 32.3 1.0 P1 A:UNR901 3.3 34.4 1.0 P4 A:UNR901 3.4 32.1 1.0 O2 A:UNR901 3.6 33.0 1.0 C1 A:UNR901 3.6 34.0 1.0 OD1 A:ASP243 3.7 33.9 1.0 O A:HOH373 3.9 34.8 1.0 OD1 A:ASP247 3.9 43.5 1.0 O9 A:UNR901 4.1 29.9 1.0 O A:HOH446 4.1 49.4 1.0 O A:ASP243 4.2 30.9 1.0 OD2 A:ASP261 4.2 30.4 1.0 O5 A:UNR901 4.2 35.1 1.0 NE2 A:GLN240 4.3 32.8 1.0 OD1 A:ASP261 4.3 35.0 1.0 O A:HOH500 4.3 33.6 1.0 OD1 A:ASP244 4.4 30.9 1.0 O7 A:UNR901 4.4 31.6 1.0 O10 A:UNR901 4.5 26.7 1.0 CB A:ASP243 4.5 31.4 1.0 C A:ASP243 4.5 31.3 1.0 CG A:ASP247 4.5 40.8 1.0 CB A:ASP247 4.6 34.1 1.0 CG A:ASP261 4.7 39.7 1.0 NZ A:LYS257 4.7 45.0 1.0 CE A:LYS257 4.7 38.5 1.0 O A:HOH417 4.8 33.9 1.0 MG A:MG907 4.9 29.5 1.0 N A:ASP244 4.9 28.9 1.0

Magnesium binding site 3 out of 3 in the Human Fdps Synthase in Complex with A N-Methyl Pyridinum Bisphosphonate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Fdps Synthase in Complex with A N-Methyl Pyridinum Bisphosphonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg909 b:32.2 occ:1.00 O A:HOH3 2.0 28.8 1.0 OD2 A:ASP103 2.0 30.9 1.0 O A:HOH433 2.1 24.8 1.0 O A:HOH501 2.1 26.8 1.0 OD2 A:ASP107 2.1 30.9 1.0 O5 A:UNR901 2.2 35.1 1.0 CG A:ASP107 3.0 36.0 1.0 CG A:ASP103 3.1 32.8 1.0 OD1 A:ASP107 3.2 31.6 1.0 MG A:MG907 3.2 29.5 1.0 P4 A:UNR901 3.4 32.1 1.0 OD1 A:ASP103 3.4 31.3 1.0 O7 A:UNR901 3.5 31.6 1.0 OD1 A:ASP174 4.0 43.7 1.0 OE1 A:GLN171 4.1 48.0 1.0 NE2 A:GLN171 4.1 43.9 1.0 O A:HOH500 4.3 33.6 1.0 CB A:ASP103 4.4 27.2 1.0 OD2 A:ASP174 4.4 34.1 1.0 O6 A:UNR901 4.4 29.3 1.0 O A:HOH373 4.4 34.8 1.0 NZ A:LYS266 4.4 46.6 1.0 CB A:ASP107 4.4 30.0 1.0 CG A:ASP174 4.4 44.1 1.0 CD A:GLN171 4.5 45.9 1.0 C1 A:UNR901 4.6 34.0 1.0 C23 A:UNR901 4.6 32.9 1.0 C3 A:UNR901 4.6 37.9 1.0 C27 A:UNR901 4.7 38.4 1.0 CE A:LYS266 4.7 39.5 1.0 NZ A:LYS200 4.8 36.0 1.0 O9 A:UNR901 4.8 29.9 1.0 O A:ASP103 4.8 26.2 1.0 O A:HOH497 4.9 25.9 1.0

A.G.Evdokimov, B.L.Barnett, F.H.Ebetino, M.Pokross. Human Fdps Synthase in Complex with A N-Methyl Pyridinum Bisphosphonate To Be Published.