Magnesium in PDB 2f8z: Crystal Structure of Human Fpps in Complex with Zoledronate and Isopentenyl Diphosphate

All present enzymatic activity of Crystal Structure of Human Fpps in Complex with Zoledronate and Isopentenyl Diphosphate:
2.5.1.1; 2.5.1.10;

The structure of Crystal Structure of Human Fpps in Complex with Zoledronate and Isopentenyl Diphosphate, PDB code: 2f8z was solved by J.-M.Rondeau, F.Bitsch, E.Bourgier, M.Geiser, R.Hemmig, M.Kroemer, S.Lehmann, P.Ramage, S.Rieffel, A.Strauss, J.R.Green, W.Jahnke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.71 / 2.60
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	112.155, 112.155, 65.725, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 28

The binding sites of Magnesium atom in the Crystal Structure of Human Fpps in Complex with Zoledronate and Isopentenyl Diphosphate (pdb code 2f8z). 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 Zoledronate and Isopentenyl Diphosphate, PDB code: 2f8z:
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 Zoledronate and Isopentenyl Diphosphate


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 Zoledronate and Isopentenyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1001 b:53.6 occ:1.00 O F:HOH9018 1.9 37.0 1.0 O17 F:ZOL5001 1.9 48.0 1.0 O F:HOH9022 2.1 40.0 1.0 OD1 F:ASP103 2.2 43.9 1.0 OD2 F:ASP107 2.3 34.8 1.0 O12 F:ZOL5001 2.4 55.3 1.0 P14 F:ZOL5001 3.2 38.9 1.0 CG F:ASP107 3.2 46.0 1.0 O F:HOH9006 3.3 30.6 1.0 MG F:MG1003 3.4 25.3 1.0 CG F:ASP103 3.4 49.3 1.0 CB F:ASP107 3.5 43.6 1.0 P9 F:ZOL5001 3.6 50.7 1.0 C8 F:ZOL5001 3.9 46.0 1.0 OG F:SER109 3.9 54.0 1.0 O16 F:ZOL5001 4.0 54.3 1.0 OD2 F:ASP103 4.1 43.1 1.0 NH2 F:ARG112 4.1 25.2 1.0 O F:ASP103 4.1 40.6 1.0 O F:HOH9005 4.2 22.3 1.0 OD1 F:ASP104 4.2 50.1 1.0 O11 F:ZOL5001 4.2 33.4 1.0 C7 F:ZOL5001 4.3 49.5 1.0 OD1 F:ASP107 4.4 40.2 1.0 CB F:ASP103 4.5 47.2 1.0 C F:ASP103 4.5 43.9 1.0 O15 F:ZOL5001 4.5 46.7 1.0 O F:HOH9042 4.6 50.3 1.0 O F:HOH9004 4.7 22.4 1.0 O F:HOH9038 4.8 57.8 1.0 O10 F:ZOL5001 4.9 44.1 1.0 N F:ASP104 5.0 41.6 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Human Fpps in Complex with Zoledronate and Isopentenyl Diphosphate


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 Zoledronate and Isopentenyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1002 b:38.8 occ:1.00 O11 F:ZOL5001 1.9 33.4 1.0 O F:HOH9009 1.9 39.5 1.0 OD2 F:ASP243 2.0 51.6 1.0 O F:HOH9005 2.1 22.3 1.0 O16 F:ZOL5001 2.1 54.3 1.0 O F:HOH9007 2.5 31.1 1.0 CG F:ASP243 2.9 54.9 1.0 O13 F:ZOL5001 3.1 42.2 1.0 P14 F:ZOL5001 3.2 38.9 1.0 P9 F:ZOL5001 3.2 50.7 1.0 OD1 F:ASP243 3.3 51.3 1.0 C8 F:ZOL5001 3.3 46.0 1.0 O F:ASP243 4.0 55.7 1.0 O17 F:ZOL5001 4.1 48.0 1.0 O12 F:ZOL5001 4.1 55.3 1.0 O15 F:ZOL5001 4.1 46.7 1.0 O F:HOH9013 4.2 38.6 1.0 CB F:ASP243 4.2 53.6 1.0 NE2 F:GLN240 4.3 43.4 1.0 O10 F:ZOL5001 4.3 44.1 1.0 C F:ASP243 4.3 55.1 1.0 OD2 F:ASP247 4.3 64.7 1.0 O F:HOH9006 4.5 30.6 1.0 OD1 F:ASP244 4.5 53.4 1.0 O F:HOH9022 4.5 40.0 1.0 OD2 F:ASP261 4.5 46.3 1.0 OD1 F:ASP261 4.6 49.6 1.0 NZ F:LYS257 4.7 44.3 1.0 CB F:ASP247 4.8 57.9 1.0 N F:ASP244 4.8 52.5 1.0 CA F:ASP243 4.9 53.7 1.0 C7 F:ZOL5001 4.9 49.5 1.0 CE F:LYS257 5.0 48.1 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Human Fpps in Complex with Zoledronate and Isopentenyl Diphosphate


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 Zoledronate and Isopentenyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1003 b:25.3 occ:1.00 O12 F:ZOL5001 1.8 55.3 1.0 O F:HOH9003 2.0 24.0 1.0 O F:HOH9004 2.1 22.4 1.0 OD2 F:ASP107 2.2 34.8 1.0 OD2 F:ASP103 2.4 43.1 1.0 O F:HOH9002 2.5 20.2 1.0 OD1 F:ASP103 2.9 43.9 1.0 P9 F:ZOL5001 2.9 50.7 1.0 CG F:ASP103 3.0 49.3 1.0 O10 F:ZOL5001 3.1 44.1 1.0 CG F:ASP107 3.2 46.0 1.0 MG F:MG1001 3.4 53.6 1.0 OD1 F:ASP107 3.5 40.2 1.0 O F:HOH9022 3.8 40.0 1.0 O F:HOH9013 3.9 38.6 1.0 O11 F:ZOL5001 4.1 33.4 1.0 C8 F:ZOL5001 4.2 46.0 1.0 OD2 F:ASP174 4.2 37.4 1.0 C19 F:ZOL5001 4.2 48.5 1.0 OD1 F:ASP174 4.3 39.9 1.0 C7 F:ZOL5001 4.4 49.5 1.0 OE1 F:GLN171 4.4 43.9 1.0 O17 F:ZOL5001 4.5 48.0 1.0 CB F:ASP103 4.5 47.2 1.0 CG F:ASP174 4.5 42.3 1.0 NE2 F:GLN171 4.5 32.9 1.0 N15 F:ZOL5001 4.5 53.0 1.0 NZ F:LYS200 4.6 38.8 1.0 NZ F:LYS266 4.6 45.6 1.0 CB F:ASP107 4.6 43.6 1.0 CE F:LYS266 4.8 47.0 1.0 CD F:GLN171 4.9 45.2 1.0 O F:HOH9018 4.9 37.0 1.0 O F:ASP103 5.0 40.6 1.0

J.M.Rondeau, F.Bitsch, E.Bourgier, M.Geiser, R.Hemmig, M.Kroemer, S.Lehmann, P.Ramage, S.Rieffel, A.Strauss, J.R.Green, W.Jahnke. Structural Basis For the Exceptional in Vivo Efficacy of Bisphosphonate Drugs. Chemmedchem V. 1 267 2006.
ISSN: ISSN 1860-7179
PubMed: 16892359
DOI: 10.1002/CMDC.200500059