Magnesium in PDB 4dem: Crystal Structure of Human Fpps in Complex with YS_04_70

All present enzymatic activity of Crystal Structure of Human Fpps in Complex with YS_04_70:
2.5.1.1; 2.5.1.10;

The structure of Crystal Structure of Human Fpps in Complex with YS_04_70, PDB code: 4dem 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 / 1.85
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	111.230, 111.230, 67.724, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 20.2

The binding sites of Magnesium atom in the Crystal Structure of Human Fpps in Complex with YS_04_70 (pdb code 4dem). 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 Complex with YS_04_70, PDB code: 4dem:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Human Fpps in Complex with YS_04_70


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 Complex with YS_04_70 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:21.9 occ:1.00 O3 F:YS4401 2.1 24.9 1.0 O F:HOH505 2.1 24.1 1.0 O F:HOH546 2.2 24.6 1.0 O F:HOH520 2.2 25.6 1.0 OD2 F:ASP121 2.2 23.2 1.0 OD2 F:ASP117 2.2 23.9 1.0 CG F:ASP121 3.1 23.6 1.0 MG F:MG403 3.1 25.8 1.0 OD1 F:ASP121 3.2 21.9 1.0 CG F:ASP117 3.2 23.3 1.0 P1 F:YS4401 3.4 26.9 1.0 OD1 F:ASP117 3.4 24.6 1.0 O2 F:YS4401 3.5 24.3 1.0 NZ F:LYS280 3.8 37.3 1.0 NE2 F:GLN185 4.1 32.4 1.0 OD2 F:ASP188 4.2 34.0 1.0 OE1 F:GLN185 4.2 28.2 1.0 O F:HOH511 4.2 23.5 1.0 O F:HOH533 4.3 26.2 1.0 O4 F:YS4401 4.3 24.8 1.0 N1 F:YS4401 4.4 24.8 1.0 OD1 F:ASP188 4.4 31.8 1.0 CB F:ASP121 4.5 21.1 1.0 C11 F:YS4401 4.5 26.5 1.0 CD F:GLN185 4.5 34.1 1.0 C13 F:YS4401 4.6 25.6 1.0 CB F:ASP117 4.6 19.2 1.0 CG F:ASP188 4.6 31.9 1.0 C12 F:YS4401 4.7 21.9 1.0 O F:HOH516 4.8 26.5 1.0 NZ F:LYS214 4.8 21.1 1.0 O6 F:YS4401 4.8 23.6 1.0 O F:HOH502 4.9 21.4 1.0 CE F:LYS280 4.9 36.2 1.0 O F:ASP117 5.0 20.2 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Human Fpps in Complex with YS_04_70


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 Complex with YS_04_70 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg403 b:25.8 occ:1.00 O F:HOH511 2.1 23.5 1.0 O3 F:YS4401 2.1 24.9 1.0 OD1 F:ASP117 2.1 24.6 1.0 O6 F:YS4401 2.1 23.6 1.0 O F:HOH502 2.1 21.4 1.0 OD2 F:ASP121 2.2 23.2 1.0 CG F:ASP117 3.1 23.3 1.0 MG F:MG402 3.1 21.9 1.0 CG F:ASP121 3.3 23.6 1.0 P2 F:YS4401 3.3 25.8 1.0 P1 F:YS4401 3.4 26.9 1.0 OD2 F:ASP117 3.4 23.9 1.0 C13 F:YS4401 3.7 25.6 1.0 CB F:ASP121 3.7 21.1 1.0 N1 F:YS4401 3.8 24.8 1.0 O F:HOH514 3.9 25.6 1.0 O4 F:YS4401 4.0 24.8 1.0 O5 F:YS4401 4.0 24.7 1.0 O F:HOH506 4.2 24.1 1.0 NH2 F:ARG126 4.3 23.9 1.0 O F:HOH505 4.3 24.1 1.0 O F:HOH516 4.3 26.5 1.0 OD1 F:ASP121 4.4 21.9 1.0 CB F:ASP117 4.4 19.2 1.0 O7 F:YS4401 4.4 23.9 1.0 O F:ASP117 4.5 20.2 1.0 OG F:SER123 4.5 26.1 1.0 OD1 F:ASP118 4.5 20.5 1.0 O2 F:YS4401 4.6 24.3 1.0 O F:HOH552 4.8 26.2 1.0 C F:ASP117 4.8 19.6 1.0 O F:HOH546 4.8 24.6 1.0 C12 F:YS4401 4.8 21.9 1.0 MG F:MG404 4.9 27.0 1.0 O F:HOH520 5.0 25.6 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Human Fpps in Complex with YS_04_70


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 Complex with YS_04_70 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg404 b:27.0 occ:1.00 O F:HOH509 2.1 22.9 1.0 O5 F:YS4401 2.1 24.7 1.0 O4 F:YS4401 2.1 24.8 1.0 OD2 F:ASP257 2.2 20.9 1.0 O F:HOH526 2.2 23.6 1.0 O F:HOH506 2.3 24.1 1.0 P1 F:YS4401 3.2 26.9 1.0 CG F:ASP257 3.2 23.6 1.0 P2 F:YS4401 3.3 25.8 1.0 C13 F:YS4401 3.5 25.6 1.0 OD1 F:ASP257 3.6 25.1 1.0 O F:HOH533 3.9 26.2 1.0 OD2 F:ASP261 4.0 30.0 1.0 O F:HOH632 4.1 38.8 1.0 O6 F:YS4401 4.1 23.6 1.0 NE2 F:GLN254 4.1 22.2 1.0 NZ F:LYS271 4.2 49.0 1.0 O3 F:YS4401 4.2 24.9 1.0 OD2 F:ASP275 4.2 23.7 1.0 O F:ASP257 4.3 25.6 1.0 O F:HOH511 4.3 23.5 1.0 OD1 F:ASP275 4.3 24.7 1.0 O2 F:YS4401 4.4 24.3 1.0 OD1 F:ASP258 4.4 23.8 1.0 CB F:ASP257 4.5 22.6 1.0 O7 F:YS4401 4.5 23.9 1.0 C F:ASP257 4.6 24.3 1.0 CG F:ASP261 4.6 28.2 1.0 O F:HOH646 4.7 39.2 1.0 CG F:ASP275 4.7 25.6 1.0 CB F:ASP261 4.8 26.1 1.0 O F:HOH514 4.8 25.6 1.0 MG F:MG403 4.9 25.8 1.0 CE F:LYS271 5.0 41.0 1.0 N1 F:YS4401 5.0 24.8 1.0

Y.S.Lin, J.Park, J.W.De Schutter, X.F.Huang, A.M.Berghuis, M.Sebag, Y.S.Tsantrizos. Design and Synthesis of Active Site Inhibitors of the Human Farnesyl Pyrophosphate Synthase: Apoptosis and Inhibition of Erk Phosphorylation in Multiple Myeloma Cells. J.Med.Chem. V. 55 3201 2012.
ISSN: ISSN 0022-2623
PubMed: 22390415
DOI: 10.1021/JM201657X