Magnesium in PDB 4n1z: Crystal Structure of Human Farnesyl Diphosphate Synthase in Complex with Bph-1222

All present enzymatic activity of Crystal Structure of Human Farnesyl Diphosphate Synthase in Complex with Bph-1222:
2.5.1.1; 2.5.1.10;

The structure of Crystal Structure of Human Farnesyl Diphosphate Synthase in Complex with Bph-1222, PDB code: 4n1z was solved by Y.L.Liu, Y.Xia, Y.Zhang, I.Verma, E.Oldfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.17 / 2.35
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	111.946, 111.946, 67.284, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 26.5

The binding sites of Magnesium atom in the Crystal Structure of Human Farnesyl Diphosphate Synthase in Complex with Bph-1222 (pdb code 4n1z). 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 Diphosphate Synthase in Complex with Bph-1222, PDB code: 4n1z:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Human Farnesyl Diphosphate Synthase in Complex with Bph-1222


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 Diphosphate Synthase in Complex with Bph-1222 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:39.3 occ:1.00 OAC F:N1Z406 2.2 34.5 1.0 OAE F:N1Z406 2.2 27.2 1.0 OD2 F:ASP243 2.3 34.7 1.0 CG F:ASP243 3.4 33.1 1.0 PAX F:N1Z406 3.4 36.2 1.0 O F:HOH533 3.5 29.8 1.0 PAW F:N1Z406 3.6 31.4 1.0 OD1 F:ASP261 3.8 47.4 1.0 OD2 F:ASP261 3.9 46.2 1.0 OD1 F:ASP243 3.9 34.8 1.0 CAV F:N1Z406 4.0 39.2 1.0 OD2 F:ASP247 4.0 54.2 1.0 OD1 F:ASP244 4.0 34.5 1.0 O F:ASP243 4.1 34.5 1.0 NE2 F:GLN240 4.2 36.0 1.0 CG F:ASP261 4.2 43.0 1.0 CB F:ASP247 4.3 48.0 1.0 OAH F:N1Z406 4.4 29.9 1.0 CG F:ASP247 4.4 54.3 1.0 OAB F:N1Z406 4.4 31.3 1.0 C F:ASP243 4.4 33.6 1.0 CB F:ASP243 4.6 34.7 1.0 OAD F:N1Z406 4.6 39.4 1.0 OAF F:N1Z406 4.7 37.9 1.0 N F:ASP244 4.8 36.2 1.0 CA F:ASP244 4.8 33.1 1.0 OAG F:N1Z406 4.9 33.9 1.0 NZ F:LYS257 4.9 43.0 1.0 MG F:MG403 5.0 51.5 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Human Farnesyl Diphosphate Synthase in Complex with Bph-1222


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 Diphosphate Synthase in Complex with Bph-1222 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg403 b:51.5 occ:1.00 OAD F:N1Z406 1.6 39.4 1.0 OD2 F:ASP107 2.4 35.7 1.0 OD1 F:ASP103 2.6 41.0 1.0 OAH F:N1Z406 2.9 29.9 1.0 OAF F:N1Z406 2.9 37.9 1.0 CAV F:N1Z406 3.0 39.2 1.0 CG F:ASP107 3.0 32.9 1.0 CB F:ASP107 3.2 32.2 1.0 PAW F:N1Z406 3.5 31.4 1.0 CG F:ASP103 3.6 39.0 1.0 O F:HOH505 3.7 28.4 1.0 PAX F:N1Z406 3.7 36.2 1.0 MG F:MG404 3.8 22.2 1.0 OG F:SER109 3.8 38.5 1.0 OD2 F:ASP103 4.0 37.6 1.0 O F:HOH513 4.0 39.4 1.0 OAE F:N1Z406 4.1 27.2 1.0 CAS F:N1Z406 4.2 41.9 1.0 OD1 F:ASP107 4.2 39.0 1.0 OAC F:N1Z406 4.3 34.5 1.0 O F:ASP103 4.3 30.1 1.0 NH2 F:ARG112 4.5 31.1 1.0 OD1 F:ASP104 4.6 39.0 1.0 OG1 F:THR260 4.6 42.7 1.0 OAG F:N1Z406 4.8 33.9 1.0 CA F:ASP107 4.8 34.1 1.0 C F:ASP103 4.8 33.1 1.0 CB F:ASP103 4.9 36.6 1.0 MG F:MG402 5.0 39.3 1.0 O F:HOH533 5.0 29.8 1.0 OAB F:N1Z406 5.0 31.3 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Human Farnesyl Diphosphate Synthase in Complex with Bph-1222


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 Diphosphate Synthase in Complex with Bph-1222 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg404 b:22.2 occ:1.00 OAF F:N1Z406 1.6 37.9 1.0 OD2 F:ASP103 2.0 37.6 1.0 OD2 F:ASP107 2.1 35.7 1.0 CG F:ASP107 3.0 32.9 1.0 CG F:ASP103 3.0 39.0 1.0 OD1 F:ASP107 3.2 39.0 1.0 PAW F:N1Z406 3.2 31.4 1.0 OD1 F:ASP103 3.4 41.0 1.0 OAB F:N1Z406 3.6 31.3 1.0 OAD F:N1Z406 3.6 39.4 1.0 OE1 F:GLN171 3.8 48.1 1.0 OD2 F:ASP174 3.8 44.3 1.0 MG F:MG403 3.8 51.5 1.0 OD1 F:ASP174 3.8 44.9 1.0 NE2 F:GLN171 4.1 41.9 1.0 CG F:ASP174 4.1 38.5 1.0 CAV F:N1Z406 4.1 39.2 1.0 OAE F:N1Z406 4.3 27.2 1.0 NZ F:LYS266 4.3 40.7 1.0 O F:HOH533 4.4 29.8 1.0 CD F:GLN171 4.4 45.5 1.0 CB F:ASP103 4.4 36.6 1.0 CAK F:N1Z406 4.4 36.6 1.0 CB F:ASP107 4.5 32.2 1.0 NZ F:LYS200 4.6 32.5 1.0 CE F:LYS266 4.7 34.4 1.0 NAT F:N1Z406 4.8 41.0 1.0 CAS F:N1Z406 4.8 41.9 1.0 O F:ASP103 4.8 30.1 1.0 O F:HOH513 4.9 39.4 1.0

Y.Xia, Y.L.Liu, Y.Xie, W.Zhu, F.Guerra, S.Shen, N.Yeddula, W.Fischer, W.Low, X.Zhou, Y.Zhang, E.Oldfield, I.M.Verma. A Combination Therapy For Kras-Driven Lung Adenocarcinomas Using Lipophilic Bisphosphonates and Rapamycin. Sci Transl Med V. 6 RA161 2014.
ISSN: ISSN 1946-6234
PubMed: 25411474
DOI: 10.1126/SCITRANSLMED.3010382