Magnesium in PDB 4p0v: Crystal Structure of Human Farnesyl Diphosphoate Synthase in Complex with Zoledronate and Taxodione

All present enzymatic activity of Crystal Structure of Human Farnesyl Diphosphoate Synthase in Complex with Zoledronate and Taxodione:
2.5.1.1; 2.5.1.10;

The structure of Crystal Structure of Human Farnesyl Diphosphoate Synthase in Complex with Zoledronate and Taxodione, PDB code: 4p0v 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)	79.30 / 2.40
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	112.143, 112.143, 67.053, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 29.3

The binding sites of Magnesium atom in the Crystal Structure of Human Farnesyl Diphosphoate Synthase in Complex with Zoledronate and Taxodione (pdb code 4p0v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Human Farnesyl Diphosphoate Synthase in Complex with Zoledronate and Taxodione, PDB code: 4p0v:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Human Farnesyl Diphosphoate Synthase in Complex with Zoledronate and Taxodione


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Farnesyl Diphosphoate Synthase in Complex with Zoledronate and Taxodione within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:44.6 occ:1.00 OD2 A:ASP103 2.1 34.2 1.0 O A:HOH530 2.1 36.3 1.0 O16 A:ZOL401 2.1 38.8 1.0 OD2 A:ASP107 2.3 39.0 1.0 O12 A:ZOL401 2.3 36.2 1.0 CG A:ASP103 3.1 46.1 1.0 CG A:ASP107 3.2 41.3 1.0 CB A:ASP107 3.4 40.6 1.0 P14 A:ZOL401 3.5 41.4 1.0 MG A:MG405 3.5 30.4 1.0 OD1 A:ASP103 3.6 44.3 1.0 O A:HOH513 3.6 34.9 1.0 P9 A:ZOL401 3.7 38.0 1.0 NH2 A:ARG112 4.0 43.1 1.0 C8 A:ZOL401 4.0 41.5 1.0 OG A:SER109 4.0 44.7 1.0 O A:ASP103 4.1 38.2 1.0 O17 A:ZOL401 4.1 39.5 1.0 O11 A:ZOL401 4.2 43.4 1.0 C7 A:ZOL401 4.3 41.9 1.0 OD1 A:ASP107 4.3 46.3 1.0 OD1 A:ASP104 4.4 44.2 1.0 O A:HOH509 4.4 33.5 1.0 C A:ASP103 4.4 40.3 1.0 CB A:ASP103 4.4 43.1 1.0 O A:HOH516 4.5 35.7 1.0 O15 A:ZOL401 4.5 39.6 1.0 O10 A:ZOL401 4.9 39.8 1.0 O A:HOH523 4.9 39.3 1.0 N A:ASP104 4.9 39.5 1.0 CA A:ASP107 5.0 42.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Human Farnesyl Diphosphoate Synthase in Complex with Zoledronate and Taxodione


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Farnesyl Diphosphoate Synthase in Complex with Zoledronate and Taxodione within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:53.2 occ:1.00 O17 A:ZOL401 2.2 39.5 1.0 O11 A:ZOL401 2.2 43.4 1.0 O A:HOH509 2.3 33.5 1.0 OD2 A:ASP243 2.3 44.6 1.0 CG A:ASP243 3.2 40.8 1.0 P9 A:ZOL401 3.5 38.0 1.0 P14 A:ZOL401 3.6 41.4 1.0 O13 A:ZOL401 3.6 40.3 1.0 OD1 A:ASP243 3.7 45.9 1.0 O A:HOH510 3.8 43.8 1.0 OD2 A:ASP261 3.8 52.4 1.0 C8 A:ZOL401 3.8 41.5 1.0 O A:ASP243 3.9 45.8 1.0 OD1 A:ASP261 4.1 51.1 1.0 OD1 A:ASP244 4.1 47.3 1.0 NE2 A:GLN240 4.2 44.8 1.0 OD1 A:ASP247 4.2 46.8 1.0 C A:ASP243 4.2 43.0 1.0 CB A:ASP247 4.2 50.7 1.0 O16 A:ZOL401 4.3 38.8 1.0 O A:HOH530 4.3 36.3 1.0 CB A:ASP243 4.4 42.5 1.0 CG A:ASP261 4.4 51.2 1.0 O12 A:ZOL401 4.4 36.2 1.0 NZ A:LYS257 4.5 46.9 1.0 CG A:ASP247 4.6 55.0 1.0 O10 A:ZOL401 4.6 39.8 1.0 N A:ASP244 4.6 41.7 1.0 O15 A:ZOL401 4.7 39.6 1.0 CA A:ASP244 4.8 40.6 1.0 CA A:ASP243 4.9 42.5 1.0 O A:HOH513 4.9 34.9 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Human Farnesyl Diphosphoate Synthase in Complex with Zoledronate and Taxodione


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Farnesyl Diphosphoate Synthase in Complex with Zoledronate and Taxodione within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:30.4 occ:1.00 OD1 A:ASP103 2.0 44.3 1.0 OD2 A:ASP107 2.1 39.0 1.0 O12 A:ZOL401 2.2 36.2 1.0 CG A:ASP107 3.0 41.3 1.0 CG A:ASP103 3.0 46.1 1.0 OD1 A:ASP107 3.2 46.3 1.0 P9 A:ZOL401 3.3 38.0 1.0 O10 A:ZOL401 3.3 39.8 1.0 OD2 A:ASP103 3.4 34.2 1.0 MG A:MG403 3.5 44.6 1.0 OD1 A:ASP174 3.8 37.9 1.0 NE2 A:GLN171 4.1 33.4 1.0 OE1 A:GLN171 4.1 43.2 1.0 O A:HOH510 4.2 43.8 1.0 OD2 A:ASP174 4.2 39.8 1.0 O11 A:ZOL401 4.2 43.4 1.0 CG A:ASP174 4.3 37.2 1.0 O A:HOH530 4.3 36.3 1.0 C19 A:ZOL401 4.4 36.7 1.0 CB A:ASP103 4.4 43.1 1.0 NZ A:LYS266 4.4 53.8 1.0 CB A:ASP107 4.5 40.6 1.0 CD A:GLN171 4.6 41.1 1.0 C8 A:ZOL401 4.6 41.5 1.0 NZ A:LYS200 4.7 35.2 1.0 O16 A:ZOL401 4.7 38.8 1.0 C7 A:ZOL401 4.7 41.9 1.0 N15 A:ZOL401 4.8 40.0 1.0 O A:ASP103 4.8 38.2 1.0 CE A:LYS266 4.9 43.0 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