Manganese in PDB 2f89: Crystal Structure of Human Fpps in Complex with Pamidronate

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

The structure of Crystal Structure of Human Fpps in Complex with Pamidronate, PDB code: 2f89 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)	57.11 / 2.60
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	111.569, 111.569, 66.482, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 26.7

The binding sites of Manganese atom in the Crystal Structure of Human Fpps in Complex with Pamidronate (pdb code 2f89). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of Human Fpps in Complex with Pamidronate, PDB code: 2f89:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of Human Fpps in Complex with Pamidronate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Human Fpps in Complex with Pamidronate within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn5001 b:60.1 occ:1.00 O F:HOH9005 2.1 49.5 1.0 O2 F:2109001 2.2 61.1 1.0 OD2 F:ASP107 2.2 52.3 1.0 OD1 F:ASP103 2.3 52.7 1.0 O F:HOH9028 2.4 48.5 1.0 O9 F:2109001 2.6 60.1 1.0 CG F:ASP107 3.3 56.2 1.0 MN F:MN5003 3.3 56.1 1.0 CG F:ASP103 3.4 55.4 1.0 P1 F:2109001 3.4 59.7 1.0 P8 F:2109001 3.5 63.7 1.0 O F:HOH9019 3.7 62.8 1.0 CB F:ASP107 3.8 56.3 1.0 OD2 F:ASP103 3.8 59.4 1.0 O10 F:2109001 3.9 51.6 1.0 C7 F:2109001 3.9 61.2 1.0 O F:HOH9004 4.1 37.6 1.0 O3 F:2109001 4.1 60.8 1.0 NH2 F:ARG112 4.2 53.1 1.0 OG F:SER109 4.2 65.7 1.0 OD1 F:ASP107 4.3 53.3 1.0 O F:ASP103 4.4 56.0 1.0 C16 F:2109001 4.5 62.4 1.0 CB F:ASP103 4.6 53.6 1.0 OD1 F:ASP104 4.6 60.0 1.0 O F:HOH9009 4.7 44.3 1.0 O F:HOH9045 4.8 62.1 1.0 O F:HOH9025 4.8 48.8 1.0 O5 F:2109001 4.8 64.2 1.0 C F:ASP103 4.8 54.0 1.0 MN F:MN5002 4.9 60.7 1.0 O12 F:2109001 4.9 59.5 1.0 O F:HOH9033 4.9 50.3 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of Human Fpps in Complex with Pamidronate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Human Fpps in Complex with Pamidronate within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn5002 b:60.7 occ:1.00 O10 F:2109001 1.9 51.6 1.0 O F:HOH9034 2.0 61.8 1.0 O F:HOH9004 2.0 37.6 1.0 OD2 F:ASP243 2.2 52.5 1.0 O3 F:2109001 2.3 60.8 1.0 O F:HOH9003 2.6 41.5 1.0 O14 F:2109001 3.2 64.0 1.0 P1 F:2109001 3.3 59.7 1.0 P8 F:2109001 3.3 63.7 1.0 CG F:ASP243 3.4 60.9 1.0 C7 F:2109001 3.4 61.2 1.0 OD1 F:ASP243 3.9 65.5 1.0 O F:HOH9025 4.0 48.8 1.0 OD2 F:ASP247 4.1 72.5 1.0 O F:ASP243 4.1 62.8 1.0 O2 F:2109001 4.1 61.1 1.0 O12 F:2109001 4.3 59.5 1.0 O5 F:2109001 4.3 64.2 1.0 NE2 F:GLN240 4.3 65.4 1.0 NZ F:LYS257 4.4 53.0 1.0 O9 F:2109001 4.4 60.1 1.0 O F:HOH9028 4.5 48.5 1.0 OD2 F:ASP261 4.5 61.2 1.0 O F:HOH9019 4.5 62.8 1.0 OD1 F:ASP244 4.5 64.7 1.0 CB F:ASP243 4.5 62.2 1.0 C F:ASP243 4.5 61.1 1.0 OD1 F:ASP261 4.6 64.3 1.0 CB F:ASP247 4.6 68.7 1.0 CG F:ASP247 4.7 71.7 1.0 MN F:MN5001 4.9 60.1 1.0 CG F:ASP261 5.0 63.9 1.0 N F:ASP244 5.0 61.0 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of Human Fpps in Complex with Pamidronate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Human Fpps in Complex with Pamidronate within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn5003 b:56.1 occ:1.00 O F:HOH9009 1.9 44.3 1.0 O9 F:2109001 2.0 60.1 1.0 O F:HOH9012 2.2 50.5 1.0 OD2 F:ASP107 2.4 52.3 1.0 OD2 F:ASP103 2.4 59.4 1.0 O F:HOH9033 2.5 50.3 1.0 CG F:ASP107 3.2 56.2 1.0 CG F:ASP103 3.2 55.4 1.0 OD1 F:ASP107 3.3 53.3 1.0 OD1 F:ASP103 3.3 52.7 1.0 MN F:MN5001 3.3 60.1 1.0 P8 F:2109001 3.4 63.7 1.0 O12 F:2109001 3.8 59.5 1.0 O F:HOH9025 4.1 48.8 1.0 OD2 F:ASP174 4.1 55.0 1.0 NE2 F:GLN171 4.1 73.1 1.0 NZ F:LYS266 4.3 55.8 1.0 OE1 F:GLN171 4.4 72.1 1.0 O10 F:2109001 4.4 51.6 1.0 OD1 F:ASP174 4.4 50.5 1.0 CG F:ASP174 4.5 51.8 1.0 O F:HOH9028 4.6 48.5 1.0 CB F:ASP103 4.7 53.6 1.0 CB F:ASP107 4.7 56.3 1.0 NZ F:LYS200 4.7 44.9 1.0 CD F:GLN171 4.7 72.0 1.0 CE F:LYS266 4.7 52.3 1.0 C7 F:2109001 4.8 61.2 1.0 O2 F:2109001 4.9 61.1 1.0 C16 F:2109001 4.9 62.4 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