Zinc in PDB 2f94: Crystal Structure of Human Fpps in Complex with Ibandronate

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

The structure of Crystal Structure of Human Fpps in Complex with Ibandronate, PDB code: 2f94 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)	40.36 / 1.94
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	111.349, 111.349, 68.893, 90.00, 90.00, 90.00
R / Rfree (%)	32.8 / 34.4

The binding sites of Zinc atom in the Crystal Structure of Human Fpps in Complex with Ibandronate (pdb code 2f94). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Human Fpps in Complex with Ibandronate, PDB code: 2f94:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Human Fpps in Complex with Ibandronate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human Fpps in Complex with Ibandronate within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1001 b:28.4 occ:1.00 O F:HOH9032 2.0 34.3 1.0 O2 F:BFQ9001 2.0 28.8 0.5 O2 F:BFQ9001 2.0 28.4 0.5 OD1 F:ASP103 2.0 28.4 1.0 O F:HOH9003 2.1 24.3 1.0 O9 F:BFQ9001 2.2 28.3 0.5 O9 F:BFQ9001 2.2 28.5 0.5 OD2 F:ASP107 2.2 28.1 1.0 CG F:ASP103 3.0 27.1 1.0 ZN F:ZN1003 3.1 29.3 1.0 P1 F:BFQ9001 3.2 29.6 0.5 P1 F:BFQ9001 3.2 29.1 0.5 P8 F:BFQ9001 3.3 26.9 0.5 P8 F:BFQ9001 3.3 27.3 0.5 CG F:ASP107 3.3 28.7 1.0 OD2 F:ASP103 3.4 26.1 1.0 C7 F:BFQ9001 3.7 29.3 0.5 C7 F:BFQ9001 3.7 28.7 0.5 CB F:ASP107 3.8 27.6 1.0 O F:HOH9010 3.9 27.7 1.0 C16 F:BFQ9001 3.9 30.8 0.5 C16 F:BFQ9001 4.0 30.1 0.5 O3 F:BFQ9001 4.0 26.0 0.5 O3 F:BFQ9001 4.1 26.9 0.5 O12 F:BFQ9001 4.1 28.7 0.5 O12 F:BFQ9001 4.2 29.2 0.5 O F:HOH9011 4.2 27.4 1.0 NH2 F:ARG112 4.2 23.7 1.0 O F:HOH9005 4.3 26.1 1.0 O F:ASP103 4.3 24.5 1.0 CB F:ASP103 4.4 26.5 1.0 OD1 F:ASP107 4.4 27.4 1.0 O5 F:BFQ9001 4.4 28.4 0.5 OG F:SER109 4.4 34.5 1.0 O5 F:BFQ9001 4.5 27.8 0.5 OD1 F:ASP104 4.5 25.6 1.0 O F:HOH9019 4.6 31.6 1.0 C F:ASP103 4.6 25.6 1.0 O10 F:BFQ9001 4.6 28.8 0.5 O10 F:BFQ9001 4.6 28.5 0.5 O F:HOH9027 4.8 32.8 1.0 ZN F:ZN1002 4.9 28.2 1.0 O F:HOH9015 4.9 29.1 1.0 O F:HOH9012 5.0 28.4 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Human Fpps in Complex with Ibandronate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human Fpps in Complex with Ibandronate within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1002 b:28.2 occ:1.00 O3 F:BFQ9001 2.0 26.0 0.5 O3 F:BFQ9001 2.0 26.9 0.5 O F:HOH9011 2.0 27.4 1.0 O12 F:BFQ9001 2.0 28.7 0.5 O12 F:BFQ9001 2.0 29.2 0.5 OD2 F:ASP243 2.1 27.6 1.0 O F:HOH9002 2.2 21.6 1.0 O F:HOH9020 2.2 30.4 1.0 CG F:ASP243 3.1 28.7 1.0 P1 F:BFQ9001 3.2 29.6 0.5 P1 F:BFQ9001 3.3 29.1 0.5 P8 F:BFQ9001 3.3 27.3 0.5 P8 F:BFQ9001 3.3 26.9 0.5 O14 F:BFQ9001 3.5 29.2 0.5 OD1 F:ASP243 3.5 29.5 1.0 C7 F:BFQ9001 3.6 28.7 0.5 C7 F:BFQ9001 3.6 29.3 0.5 O14 F:BFQ9001 3.6 29.6 0.5 OD2 F:ASP247 3.8 34.2 1.0 O F:HOH9012 3.9 28.4 1.0 O2 F:BFQ9001 3.9 28.8 0.5 O2 F:BFQ9001 4.0 28.4 0.5 O9 F:BFQ9001 4.1 28.5 0.5 O9 F:BFQ9001 4.1 28.3 0.5 NE2 F:GLN240 4.2 27.3 1.0 OD2 F:ASP261 4.2 32.8 1.0 O F:HOH9032 4.2 34.3 1.0 O F:ASP243 4.3 29.3 1.0 OD1 F:ASP261 4.3 31.5 1.0 CB F:ASP243 4.4 29.2 1.0 O5 F:BFQ9001 4.4 27.8 0.5 O5 F:BFQ9001 4.4 28.4 0.5 O10 F:BFQ9001 4.5 28.5 0.5 O10 F:BFQ9001 4.5 28.8 0.5 CG F:ASP247 4.5 32.9 1.0 OD1 F:ASP244 4.5 26.0 1.0 C F:ASP243 4.5 29.5 1.0 O F:HOH9187 4.7 56.0 1.0 CB F:ASP247 4.7 32.6 1.0 CG F:ASP261 4.7 32.1 1.0 CE F:LYS257 4.7 40.6 1.0 NZ F:LYS257 4.7 41.7 1.0 ZN F:ZN1001 4.9 28.4 1.0 O F:HOH9010 4.9 27.7 1.0 N F:ASP244 5.0 29.0 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Human Fpps in Complex with Ibandronate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human Fpps in Complex with Ibandronate within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1003 b:29.3 occ:1.00 OD2 F:ASP103 2.0 26.1 1.0 OD2 F:ASP107 2.1 28.1 1.0 O9 F:BFQ9001 2.1 28.5 0.5 O9 F:BFQ9001 2.1 28.3 0.5 O F:HOH9005 2.1 26.1 1.0 O F:HOH9015 2.2 29.1 1.0 O F:HOH9004 2.2 24.2 1.0 CG F:ASP107 2.9 28.7 1.0 CG F:ASP103 3.0 27.1 1.0 OD1 F:ASP107 3.1 27.4 1.0 ZN F:ZN1001 3.1 28.4 1.0 OD1 F:ASP103 3.2 28.4 1.0 P8 F:BFQ9001 3.3 27.3 0.5 P8 F:BFQ9001 3.3 26.9 0.5 O10 F:BFQ9001 3.6 28.8 0.5 O10 F:BFQ9001 3.6 28.5 0.5 OD2 F:ASP174 4.0 34.7 1.0 NZ F:LYS266 4.1 34.4 1.0 NE2 F:GLN171 4.1 35.3 1.0 OE1 F:GLN171 4.1 34.2 1.0 O F:HOH9032 4.1 34.3 1.0 O F:HOH9012 4.2 28.4 1.0 CB F:ASP103 4.4 26.5 1.0 O12 F:BFQ9001 4.4 28.7 0.5 CB F:ASP107 4.4 27.6 1.0 OD1 F:ASP174 4.4 33.5 1.0 O12 F:BFQ9001 4.4 29.2 0.5 CG F:ASP174 4.5 34.2 1.0 CD F:GLN171 4.5 34.9 1.0 C16 F:BFQ9001 4.5 30.8 0.5 C7 F:BFQ9001 4.6 29.3 0.5 C7 F:BFQ9001 4.7 28.7 0.5 O2 F:BFQ9001 4.7 28.8 0.5 O F:ASP103 4.7 24.5 1.0 C16 F:BFQ9001 4.7 30.1 0.5 O2 F:BFQ9001 4.7 28.4 0.5 NZ F:LYS200 4.8 24.3 1.0 C23 F:BFQ9001 4.8 34.2 0.5 C23 F:BFQ9001 4.8 35.0 0.5 O F:HOH9003 4.8 24.3 1.0 O F:HOH9019 4.9 31.6 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