Magnesium in PDB 4h5d: Crystal Structure of Human Fpps in Ternary Complex with YS0470 and Inorganic Pyrophosphate

All present enzymatic activity of Crystal Structure of Human Fpps in Ternary Complex with YS0470 and Inorganic Pyrophosphate:
2.5.1.1; 2.5.1.10;

The structure of Crystal Structure of Human Fpps in Ternary Complex with YS0470 and Inorganic Pyrophosphate, PDB code: 4h5d was solved by J.Park, Y.-S.Lin, Y.S.Tsantrizos, A.M.Berghuis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.02
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	111.527, 111.527, 66.242, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 20.3

The binding sites of Magnesium atom in the Crystal Structure of Human Fpps in Ternary Complex with YS0470 and Inorganic Pyrophosphate (pdb code 4h5d). 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 Fpps in Ternary Complex with YS0470 and Inorganic Pyrophosphate, PDB code: 4h5d:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Human Fpps in Ternary Complex with YS0470 and Inorganic Pyrophosphate


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 Fpps in Ternary Complex with YS0470 and Inorganic Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg403 b:26.1 occ:1.00 O F:HOH510 2.0 25.9 1.0 O F:HOH508 2.1 28.5 1.0 O F:HOH509 2.1 30.7 1.0 OD2 F:ASP107 2.1 30.0 1.0 O3 F:YS4401 2.1 30.3 1.0 OD2 F:ASP103 2.2 28.4 1.0 CG F:ASP107 3.0 29.8 1.0 OD1 F:ASP107 3.2 30.0 1.0 CG F:ASP103 3.2 28.1 1.0 MG F:MG404 3.2 31.2 1.0 P1 F:YS4401 3.4 29.9 1.0 OD1 F:ASP103 3.4 26.2 1.0 O2 F:YS4401 3.5 26.5 1.0 NZ F:LYS266 3.8 30.9 0.6 NE2 F:GLN171 4.0 35.4 1.0 OE1 F:GLN171 4.2 36.0 1.0 O F:HOH601 4.2 25.7 1.0 OD2 F:ASP174 4.2 39.8 1.0 OD1 F:ASP174 4.2 37.7 1.0 O F:HOH530 4.3 29.1 1.0 NZ F:LYS266 4.3 28.7 0.4 O4 F:YS4401 4.4 32.3 1.0 N1 F:YS4401 4.4 27.3 1.0 CB F:ASP107 4.5 30.5 1.0 CG F:ASP174 4.5 39.0 1.0 CD F:GLN171 4.5 36.4 1.0 C13 F:YS4401 4.6 31.6 1.0 CB F:ASP103 4.6 22.9 1.0 C11 F:YS4401 4.6 28.3 1.0 CE F:LYS266 4.6 29.6 0.4 C12 F:YS4401 4.7 29.1 1.0 NZ F:LYS200 4.8 29.4 1.0 O F:HOH522 4.8 31.0 1.0 CE F:LYS266 4.9 31.0 0.6 O F:HOH506 4.9 24.2 1.0 O F:ASP103 5.0 24.4 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Human Fpps in Ternary Complex with YS0470 and Inorganic Pyrophosphate


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 Fpps in Ternary Complex with YS0470 and Inorganic Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg404 b:31.2 occ:1.00 O3 F:YS4401 2.0 30.3 1.0 O F:HOH506 2.1 24.2 1.0 O F:HOH601 2.1 25.7 1.0 OD2 F:ASP107 2.1 30.0 1.0 OD1 F:ASP103 2.2 26.2 1.0 O5 F:YS4401 2.3 28.5 1.0 CG F:ASP103 3.1 28.1 1.0 CG F:ASP107 3.1 29.8 1.0 MG F:MG403 3.2 26.1 1.0 OD2 F:ASP103 3.4 28.4 1.0 P1 F:YS4401 3.4 29.9 1.0 P2 F:YS4401 3.5 30.9 1.0 CB F:ASP107 3.6 30.5 1.0 C13 F:YS4401 3.7 31.6 1.0 N1 F:YS4401 3.8 27.3 1.0 O F:HOH520 3.9 28.9 1.0 O4 F:YS4401 4.1 32.3 1.0 O7 F:YS4401 4.2 31.1 1.0 NH2 F:ARG112 4.2 24.5 1.0 OD1 F:ASP107 4.3 30.0 1.0 O F:ASP103 4.3 24.4 1.0 O F:HOH508 4.3 28.5 1.0 O F:HOH522 4.4 31.0 1.0 OG F:SER109 4.4 32.9 1.0 O F:HOH511 4.4 27.7 1.0 CB F:ASP103 4.5 22.9 1.0 OD1 F:ASP104 4.5 27.0 1.0 O6 F:YS4401 4.6 28.8 1.0 O2 F:YS4401 4.6 26.5 1.0 C F:ASP103 4.7 24.9 1.0 O F:HOH510 4.7 25.9 1.0 O F:HOH507 4.7 28.8 1.0 C12 F:YS4401 4.9 29.1 1.0 MG F:MG405 4.9 32.5 1.0 O F:HOH509 5.0 30.7 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Human Fpps in Ternary Complex with YS0470 and Inorganic Pyrophosphate


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 Fpps in Ternary Complex with YS0470 and Inorganic Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg405 b:32.5 occ:1.00 O7 F:YS4401 1.9 31.1 1.0 O F:HOH512 2.0 31.2 1.0 O4 F:YS4401 2.0 32.3 1.0 OD2 F:ASP243 2.1 31.4 1.0 O F:HOH511 2.2 27.7 1.0 O F:HOH513 2.3 34.0 1.0 CG F:ASP243 3.1 32.3 1.0 P2 F:YS4401 3.2 30.9 1.0 P1 F:YS4401 3.2 29.9 1.0 OD1 F:ASP243 3.5 31.9 1.0 C13 F:YS4401 3.5 31.6 1.0 O F:HOH530 3.9 29.1 1.0 O5 F:YS4401 4.0 28.5 1.0 NZ F:LYS257 4.1 31.6 1.0 O F:HOH601 4.1 25.7 1.0 O F:HOH557 4.1 35.9 1.0 NE2 F:GLN240 4.2 29.9 1.0 O3 F:YS4401 4.2 30.3 1.0 O F:ASP243 4.2 35.0 1.0 OD1 F:ASP244 4.3 36.3 1.0 OD2 F:ASP261 4.3 34.7 1.0 CB F:ASP243 4.4 30.6 1.0 O2 F:YS4401 4.4 26.5 1.0 OD2 F:ASP247 4.4 35.4 1.0 OD1 F:ASP261 4.4 35.0 1.0 O6 F:YS4401 4.5 28.8 1.0 C F:ASP243 4.5 32.4 1.0 CB F:ASP247 4.7 34.9 1.0 CG F:ASP261 4.8 35.2 1.0 O F:HOH520 4.8 28.9 1.0 CE F:LYS257 4.8 35.4 1.0 CG F:ASP247 4.9 37.7 1.0 N F:ASP244 4.9 32.9 1.0 MG F:MG404 4.9 31.2 1.0 O F:HOH543 5.0 33.1 1.0 N1 F:YS4401 5.0 27.3 1.0

J.Park, Y.S.Lin, J.W.De Schutter, Y.S.Tsantrizos, A.M.Berghuis. Ternary Complex Structures of Human Farnesyl Pyrophosphate Synthase Bound with A Novel Inhibitor and Secondary Ligands Provide Insights Into the Molecular Details of the Enzyme'S Active Site Closure. Bmc Struct.Biol. V. 12 32 2012.
ISSN: ESSN 1472-6807
PubMed: 23234314
DOI: 10.1186/1472-6807-12-32