Magnesium in PDB 2vf6: Human Fdps Synthase in Complex with Minodronate

All present enzymatic activity of Human Fdps Synthase in Complex with Minodronate:
2.5.1.1;

The structure of Human Fdps Synthase in Complex with Minodronate, PDB code: 2vf6 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)	78.57 / 2.10
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	111.207, 111.207, 69.059, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 25.9

The binding sites of Magnesium atom in the Human Fdps Synthase in Complex with Minodronate (pdb code 2vf6). 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 Minodronate, PDB code: 2vf6:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Human Fdps Synthase in Complex with Minodronate


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 Minodronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1352 b:36.2 occ:1.00 O4 A:M0N1351 1.9 30.9 1.0 O A:HOH2119 2.1 30.9 1.0 O A:HOH2122 2.1 37.7 1.0 O1 A:M0N1351 2.1 32.2 1.0 OD2 A:ASP243 2.2 34.2 1.0 O A:HOH2117 2.3 34.5 1.0 P2 A:M0N1351 3.2 32.3 1.0 CG A:ASP243 3.2 32.6 1.0 P1 A:M0N1351 3.3 33.4 1.0 C9 A:M0N1351 3.5 34.1 1.0 O A:M0N1351 3.5 31.8 1.0 OD1 A:ASP243 3.6 36.8 1.0 NZ A:LYS257 3.8 50.9 1.0 O A:HOH2171 3.9 30.4 1.0 O5 A:M0N1351 4.0 26.6 1.0 O A:HOH2129 4.0 50.7 1.0 O A:ASP243 4.1 36.5 1.0 OD1 A:ASP247 4.1 36.4 1.0 O2 A:M0N1351 4.2 37.9 1.0 OD2 A:ASP261 4.3 33.1 1.0 OD1 A:ASP261 4.3 33.2 1.0 O A:HOH2049 4.3 29.6 1.0 NE2 A:GLN240 4.3 32.9 1.0 OD1 A:ASP244 4.4 31.4 1.0 O6 A:M0N1351 4.4 27.1 1.0 O3 A:M0N1351 4.4 28.9 1.0 C A:ASP243 4.5 36.0 1.0 CB A:ASP243 4.5 36.0 1.0 CB A:ASP247 4.6 41.0 1.0 CG A:ASP247 4.6 41.7 1.0 CG A:ASP261 4.7 35.8 1.0 O A:HOH2168 4.7 29.4 1.0 MG A:MG1353 4.8 27.6 1.0 N A:ASP244 5.0 30.9 1.0

Magnesium binding site 2 out of 3 in the Human Fdps Synthase in Complex with Minodronate


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 Minodronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1353 b:27.6 occ:1.00 O A:HOH2049 2.0 29.6 1.0 O A:HOH2044 2.0 28.5 1.0 O2 A:M0N1351 2.0 37.9 1.0 O5 A:M0N1351 2.0 26.6 1.0 OD2 A:ASP103 2.2 30.0 1.0 OD2 A:ASP107 2.2 34.6 1.0 CG A:ASP103 3.1 35.0 1.0 MG A:MG1354 3.2 33.5 1.0 P1 A:M0N1351 3.2 33.4 1.0 CG A:ASP107 3.3 39.6 1.0 P2 A:M0N1351 3.3 32.3 1.0 OD1 A:ASP103 3.4 30.7 1.0 C9 A:M0N1351 3.7 34.1 1.0 CB A:ASP107 3.7 26.5 1.0 O1 A:M0N1351 3.8 32.2 1.0 O A:HOH2168 3.9 29.4 1.0 O4 A:M0N1351 4.0 30.9 1.0 C8 A:M0N1351 4.0 29.2 1.0 NH2 A:ARG112 4.1 30.9 1.0 O A:HOH2170 4.1 28.2 1.0 O6 A:M0N1351 4.4 27.1 1.0 OD1 A:ASP107 4.4 30.2 1.0 O A:HOH2122 4.4 37.7 1.0 O A:HOH2135 4.4 32.0 1.0 O A:ASP103 4.4 26.0 1.0 OG A:SER109 4.4 31.5 1.0 O3 A:M0N1351 4.5 28.9 1.0 CB A:ASP103 4.5 26.9 1.0 OD1 A:ASP104 4.6 27.5 1.0 O A:HOH2169 4.7 32.3 1.0 C A:ASP103 4.7 29.9 1.0 MG A:MG1352 4.8 36.2 1.0 O A:HOH2136 4.8 31.9 1.0 O A:HOH2171 4.9 30.4 1.0 O A:HOH2050 4.9 25.9 1.0

Magnesium binding site 3 out of 3 in the Human Fdps Synthase in Complex with Minodronate


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 Minodronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1354 b:33.5 occ:1.00 O A:HOH2170 2.0 28.2 1.0 O A:HOH2050 2.0 25.9 1.0 OD1 A:ASP103 2.1 30.7 1.0 O A:HOH2169 2.1 32.3 1.0 OD2 A:ASP107 2.1 34.6 1.0 O2 A:M0N1351 2.2 37.9 1.0 CG A:ASP107 3.0 39.6 1.0 CG A:ASP103 3.1 35.0 1.0 OD1 A:ASP107 3.1 30.2 1.0 MG A:MG1353 3.2 27.6 1.0 P1 A:M0N1351 3.4 33.4 1.0 OD2 A:ASP103 3.4 30.0 1.0 O3 A:M0N1351 3.5 28.9 1.0 OD1 A:ASP174 3.7 38.0 1.0 NE2 A:GLN171 3.9 30.6 1.0 NZ A:LYS266 4.1 44.9 1.0 CG A:ASP174 4.2 39.3 1.0 OE1 A:GLN171 4.3 32.5 1.0 OD2 A:ASP174 4.3 33.5 1.0 O1 A:M0N1351 4.3 32.2 1.0 O A:HOH2049 4.3 29.6 1.0 O A:HOH2171 4.4 30.4 1.0 CB A:ASP107 4.4 26.5 1.0 CB A:ASP103 4.4 26.9 1.0 CD A:GLN171 4.5 35.0 1.0 NZ A:LYS200 4.6 30.9 1.0 C8 A:M0N1351 4.6 29.2 1.0 C9 A:M0N1351 4.7 34.1 1.0 C2 A:M0N1351 4.8 30.4 1.0 O5 A:M0N1351 4.8 26.6 1.0 O A:HOH2044 4.8 28.5 1.0 O A:ASP103 4.8 26.0 1.0 C3 A:M0N1351 5.0 23.8 1.0 N2 A:M0N1351 5.0 28.1 1.0

A.G.Evdokimov, B.L.Barnett, F.H.Ebetino, M.Pokross. Human Fdps Synthase in Complex with Novel Inhibitor To Be Published.