Zinc in PDB 2f9k: Crystal Structure of Human Fpps in Complex with Zoledronate and ZN2+

All present enzymatic activity of Crystal Structure of Human Fpps in Complex with Zoledronate and ZN2+:
2.5.1.1; 2.5.1.10;

The structure of Crystal Structure of Human Fpps in Complex with Zoledronate and ZN2+, PDB code: 2f9k 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)	49.76 / 2.06
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	111.270, 111.270, 69.029, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 25.9

The binding sites of Zinc atom in the Crystal Structure of Human Fpps in Complex with Zoledronate and ZN2+ (pdb code 2f9k). 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 Zoledronate and ZN2+, PDB code: 2f9k:
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 Zoledronate and ZN2+


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 Zoledronate and ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1001 b:30.4 occ:1.00 O F:HOH9016 1.9 31.0 1.0 O17 F:ZOL9001 2.0 34.2 1.0 OD1 F:ASP103 2.0 31.3 1.0 O12 F:ZOL9001 2.1 31.8 1.0 OD2 F:ASP107 2.1 34.1 1.0 O F:HOH9006 2.2 23.1 1.0 CG F:ASP103 3.0 30.9 1.0 ZN F:ZN1003 3.2 32.5 1.0 P14 F:ZOL9001 3.2 31.3 1.0 P9 F:ZOL9001 3.3 30.0 1.0 CG F:ASP107 3.3 34.3 1.0 OD2 F:ASP103 3.4 27.9 1.0 C8 F:ZOL9001 3.7 30.9 1.0 CB F:ASP107 3.8 33.4 1.0 O F:HOH9003 3.8 22.0 1.0 C7 F:ZOL9001 4.0 32.6 1.0 O16 F:ZOL9001 4.0 24.2 1.0 O11 F:ZOL9001 4.0 31.8 1.0 O F:HOH9014 4.2 34.0 1.0 NH2 F:ARG112 4.3 28.4 1.0 OD1 F:ASP107 4.3 30.9 1.0 O F:HOH9022 4.4 34.3 1.0 CB F:ASP103 4.4 27.5 1.0 O F:ASP103 4.4 25.7 1.0 OG F:SER109 4.4 35.0 1.0 O15 F:ZOL9001 4.5 26.9 1.0 O F:HOH9007 4.5 24.6 1.0 OD1 F:ASP104 4.6 23.2 1.0 O10 F:ZOL9001 4.6 28.3 1.0 C F:ASP103 4.7 26.6 1.0 O F:HOH9027 4.7 35.0 1.0 ZN F:ZN1002 4.8 31.4 1.0 O F:HOH9017 4.9 31.5 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Human Fpps in Complex with Zoledronate and ZN2+


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 Zoledronate and ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1002 b:31.4 occ:1.00 O11 F:ZOL9001 2.0 31.8 1.0 O16 F:ZOL9001 2.0 24.2 1.0 O F:HOH9014 2.1 34.0 1.0 OD2 F:ASP243 2.2 31.6 1.0 O F:HOH9005 2.2 23.8 1.0 O F:HOH9020 2.3 30.5 1.0 CG F:ASP243 3.2 33.5 1.0 P14 F:ZOL9001 3.2 31.3 1.0 P9 F:ZOL9001 3.3 30.0 1.0 O13 F:ZOL9001 3.4 34.1 1.0 C8 F:ZOL9001 3.5 30.9 1.0 OD1 F:ASP243 3.6 32.2 1.0 OD2 F:ASP247 3.9 38.4 1.0 O F:HOH9004 4.0 21.9 1.0 O17 F:ZOL9001 4.0 34.2 1.0 O12 F:ZOL9001 4.1 31.8 1.0 O F:ASP243 4.1 31.9 1.0 OD2 F:ASP261 4.2 36.9 1.0 NE2 F:GLN240 4.3 32.1 1.0 OD1 F:ASP261 4.3 37.1 1.0 O F:HOH9016 4.3 31.0 1.0 O F:HOH9155 4.4 59.1 1.0 O10 F:ZOL9001 4.4 28.3 1.0 O15 F:ZOL9001 4.4 26.9 1.0 CB F:ASP243 4.4 32.4 1.0 NZ F:LYS257 4.5 35.7 1.0 OD1 F:ASP244 4.5 28.3 1.0 CG F:ASP247 4.5 37.5 1.0 C F:ASP243 4.5 32.9 1.0 CE F:LYS257 4.6 33.3 1.0 CB F:ASP247 4.6 37.2 1.0 CG F:ASP261 4.7 35.6 1.0 ZN F:ZN1001 4.8 30.4 1.0 O F:HOH9003 4.8 22.0 1.0 N F:ASP244 5.0 29.7 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Human Fpps in Complex with Zoledronate and ZN2+


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 Zoledronate and ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn1003 b:32.5 occ:1.00 OD2 F:ASP103 2.1 27.9 1.0 O12 F:ZOL9001 2.2 31.8 1.0 O F:HOH9017 2.2 31.5 1.0 OD2 F:ASP107 2.3 34.1 1.0 O F:HOH9007 2.3 24.6 1.0 O F:HOH9008 2.3 25.5 1.0 CG F:ASP103 3.0 30.9 1.0 CG F:ASP107 3.0 34.3 1.0 OD1 F:ASP107 3.1 30.9 1.0 ZN F:ZN1001 3.2 30.4 1.0 OD1 F:ASP103 3.2 31.3 1.0 P9 F:ZOL9001 3.3 30.0 1.0 O10 F:ZOL9001 3.6 28.3 1.0 OD2 F:ASP174 3.8 33.7 1.0 OE1 F:GLN171 4.2 31.1 1.0 NE2 F:GLN171 4.2 26.7 1.0 O F:HOH9016 4.2 31.0 1.0 NZ F:LYS266 4.2 32.4 1.0 O F:HOH9004 4.3 21.9 1.0 C19 F:ZOL9001 4.4 32.7 1.0 CG F:ASP174 4.4 36.6 1.0 CB F:ASP103 4.4 27.5 1.0 O11 F:ZOL9001 4.5 31.8 1.0 CB F:ASP107 4.5 33.4 1.0 CD F:GLN171 4.6 32.1 1.0 C7 F:ZOL9001 4.6 32.6 1.0 OD1 F:ASP174 4.6 35.6 1.0 C8 F:ZOL9001 4.6 30.9 1.0 O17 F:ZOL9001 4.7 34.2 1.0 N15 F:ZOL9001 4.8 32.6 1.0 O F:ASP103 4.8 25.7 1.0 O F:HOH9022 4.9 34.3 1.0 NZ F:LYS200 4.9 23.4 1.0 O F:HOH9006 4.9 23.1 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