Magnesium in PDB 4p0w: Human Farnesyl Diphosphate Synthase in Complex with Arenarone and Zoledronate

All present enzymatic activity of Human Farnesyl Diphosphate Synthase in Complex with Arenarone and Zoledronate:
2.5.1.1; 2.5.1.10;

The structure of Human Farnesyl Diphosphate Synthase in Complex with Arenarone and Zoledronate, PDB code: 4p0w was solved by Y.L.Liu, E.Oldfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.58 / 2.41
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	111.239, 111.239, 67.292, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 28.9

The binding sites of Magnesium atom in the Human Farnesyl Diphosphate Synthase in Complex with Arenarone and Zoledronate (pdb code 4p0w). 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 in Complex with Arenarone and Zoledronate, PDB code: 4p0w:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Human Farnesyl Diphosphate Synthase in Complex with Arenarone and Zoledronate


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 in Complex with Arenarone and Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:32.1 occ:1.00 O16 A:ZOL501 2.0 31.0 1.0 OD2 A:ASP103 2.0 30.9 1.0 O A:HOH643 2.0 28.7 1.0 OD2 A:ASP107 2.1 29.9 1.0 O A:HOH644 2.1 26.1 1.0 O12 A:ZOL501 2.1 27.9 1.0 CG A:ASP103 3.0 36.0 1.0 MG A:MG504 3.1 14.7 1.0 CG A:ASP107 3.1 32.7 1.0 P14 A:ZOL501 3.3 33.6 1.0 OD1 A:ASP103 3.3 35.0 1.0 P9 A:ZOL501 3.4 31.4 1.0 CB A:ASP107 3.6 34.4 1.0 O A:HOH630 3.7 24.8 1.0 C8 A:ZOL501 3.8 33.2 1.0 O11 A:ZOL501 3.8 33.5 1.0 C7 A:ZOL501 4.0 35.6 1.0 O17 A:ZOL501 4.1 28.1 1.0 NH2 A:ARG112 4.1 39.7 1.0 OD1 A:ASP107 4.1 33.4 1.0 O A:HOH647 4.2 19.8 1.0 O A:ASP103 4.2 30.4 1.0 CB A:ASP103 4.3 34.5 1.0 O15 A:ZOL501 4.3 32.6 1.0 O A:HOH620 4.4 29.9 1.0 O A:HOH628 4.4 29.8 1.0 OG A:SER109 4.4 32.3 1.0 O10 A:ZOL501 4.5 33.6 1.0 O A:HOH642 4.6 31.9 1.0 C A:ASP103 4.6 34.8 1.0 OD1 A:ASP104 4.6 30.8 1.0 O A:HOH641 4.6 26.8 1.0 MG A:MG503 4.8 34.4 1.0 O A:HOH646 4.8 40.0 1.0

Magnesium binding site 2 out of 3 in the Human Farnesyl Diphosphate Synthase in Complex with Arenarone and Zoledronate


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 in Complex with Arenarone and Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:34.4 occ:1.00 O11 A:ZOL501 1.9 33.5 1.0 O A:HOH620 2.0 29.9 1.0 O A:HOH622 2.0 37.1 1.0 O17 A:ZOL501 2.1 28.1 1.0 O A:HOH629 2.1 37.6 1.0 OD2 A:ASP243 2.2 30.9 1.0 CG A:ASP243 3.2 36.5 1.0 P9 A:ZOL501 3.3 31.4 1.0 P14 A:ZOL501 3.3 33.6 1.0 O13 A:ZOL501 3.5 33.9 1.0 C8 A:ZOL501 3.6 33.2 1.0 OD1 A:ASP243 3.7 37.1 1.0 O A:HOH646 3.7 40.0 1.0 O16 A:ZOL501 3.9 31.0 1.0 OD1 A:ASP247 4.1 36.3 1.0 OD2 A:ASP261 4.1 40.0 1.0 OD1 A:ASP261 4.1 42.6 1.0 O A:ASP243 4.2 40.8 1.0 O A:HOH643 4.2 28.7 1.0 O12 A:ZOL501 4.3 27.9 1.0 O10 A:ZOL501 4.4 33.6 1.0 NE2 A:GLN240 4.4 41.6 1.0 O15 A:ZOL501 4.5 32.6 1.0 O A:HOH630 4.5 24.8 1.0 CB A:ASP243 4.5 34.5 1.0 C A:ASP243 4.5 37.7 1.0 NZ A:LYS257 4.5 40.5 1.0 CB A:ASP247 4.5 43.9 1.0 OD1 A:ASP244 4.5 35.4 1.0 CG A:ASP261 4.6 41.4 1.0 CG A:ASP247 4.6 46.0 1.0 MG A:MG502 4.8 32.1 1.0 N A:ASP244 4.9 38.7 1.0

Magnesium binding site 3 out of 3 in the Human Farnesyl Diphosphate Synthase in Complex with Arenarone and Zoledronate


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 in Complex with Arenarone and Zoledronate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:14.7 occ:1.00 O A:HOH642 1.8 31.9 1.0 O12 A:ZOL501 1.9 27.9 1.0 O A:HOH641 1.9 26.8 1.0 O A:HOH647 1.9 19.8 1.0 OD1 A:ASP103 2.0 35.0 1.0 OD2 A:ASP107 2.0 29.9 1.0 CG A:ASP103 2.9 36.0 1.0 CG A:ASP107 2.9 32.7 1.0 MG A:MG502 3.1 32.1 1.0 OD1 A:ASP107 3.1 33.4 1.0 OD2 A:ASP103 3.2 30.9 1.0 P9 A:ZOL501 3.3 31.4 1.0 O10 A:ZOL501 3.4 33.6 1.0 OD1 A:ASP174 3.9 30.0 1.0 O A:HOH643 4.1 28.7 1.0 O A:HOH646 4.1 40.0 1.0 NZ A:LYS266 4.2 44.3 1.0 OE1 A:GLN171 4.2 32.6 1.0 O11 A:ZOL501 4.3 33.5 1.0 NE2 A:GLN171 4.3 34.1 1.0 CB A:ASP103 4.3 34.5 1.0 OD2 A:ASP174 4.3 36.1 1.0 CG A:ASP174 4.3 33.7 1.0 CB A:ASP107 4.4 34.4 1.0 C19 A:ZOL501 4.4 30.9 1.0 O16 A:ZOL501 4.5 31.0 1.0 C7 A:ZOL501 4.5 35.6 1.0 C8 A:ZOL501 4.6 33.2 1.0 CD A:GLN171 4.7 37.3 1.0 O A:ASP103 4.7 30.4 1.0 N15 A:ZOL501 4.8 33.1 1.0 O A:HOH644 4.8 26.1 1.0 CA A:ASP103 4.9 34.8 1.0

Y.L.Liu, S.Lindert, W.Zhu, K.Wang, J.A.Mccammon, E.Oldfield. Taxodione and Arenarone Inhibit Farnesyl Diphosphate Synthase By Binding to the Isopentenyl Diphosphate Site. Proc.Natl.Acad.Sci.Usa V. 111 E2530 2014.
ISSN: ESSN 1091-6490
PubMed: 24927548
DOI: 10.1073/PNAS.1409061111