Nickel in PDB 4nfk: Crystal Structure of Human Fpps in Complex with Nickel, JDS05120, and Sulfate

All present enzymatic activity of Crystal Structure of Human Fpps in Complex with Nickel, JDS05120, and Sulfate:
2.5.1.1; 2.5.1.10;

The structure of Crystal Structure of Human Fpps in Complex with Nickel, JDS05120, and Sulfate, PDB code: 4nfk was solved by J.Park, J.W.De Schutter, 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)	51.58 / 1.85
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	110.940, 110.940, 68.460, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 18.2

The binding sites of Nickel atom in the Crystal Structure of Human Fpps in Complex with Nickel, JDS05120, and Sulfate (pdb code 4nfk). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure of Human Fpps in Complex with Nickel, JDS05120, and Sulfate, PDB code: 4nfk:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Crystal Structure of Human Fpps in Complex with Nickel, JDS05120, and Sulfate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Human Fpps in Complex with Nickel, JDS05120, and Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ F:Ni401 b:27.0 occ:1.00 OD2 F:ASP103 2.0 24.7 1.0 OD2 F:ASP107 2.1 24.0 1.0 OAK F:JD5404 2.1 24.6 1.0 O F:HOH520 2.1 25.2 1.0 O F:HOH521 2.1 24.2 1.0 O F:HOH519 2.2 26.0 1.0 CG F:ASP107 3.0 26.5 1.0 CG F:ASP103 3.0 25.3 1.0 NI F:NI403 3.1 26.1 1.0 OD1 F:ASP107 3.2 27.1 1.0 PAI F:JD5404 3.3 26.4 1.0 OD1 F:ASP103 3.3 24.7 1.0 OAJ F:JD5404 3.4 24.9 1.0 OE1 F:GLN171 4.1 37.8 1.0 NZ F:LYS266 4.1 40.2 1.0 OD2 F:ASP174 4.1 37.2 1.0 NE2 F:GLN171 4.1 38.1 1.0 O F:HOH525 4.2 24.6 1.0 OD1 F:ASP174 4.2 34.4 1.0 NAG F:JD5404 4.3 27.2 1.0 OAL F:JD5404 4.4 29.2 1.0 CB F:ASP103 4.4 23.7 1.0 CB F:ASP107 4.4 24.6 1.0 O F:HOH508 4.4 25.9 1.0 CAH F:JD5404 4.5 26.1 1.0 CAE F:JD5404 4.5 25.3 1.0 CG F:ASP174 4.5 35.6 1.0 CAD F:JD5404 4.5 24.5 1.0 CD F:GLN171 4.6 31.9 1.0 OAN F:JD5404 4.7 25.8 1.0 O F:HOH526 4.7 25.3 1.0 O F:HOH517 4.7 27.6 1.0 O F:ASP103 4.8 24.5 1.0 NZ F:LYS200 4.8 24.5 1.0 CAR F:JD5404 4.9 39.6 1.0

Nickel binding site 2 out of 3 in the Crystal Structure of Human Fpps in Complex with Nickel, JDS05120, and Sulfate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Human Fpps in Complex with Nickel, JDS05120, and Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ F:Ni402 b:27.6 occ:1.00 OAP F:JD5404 1.9 28.0 1.0 OAL F:JD5404 2.0 29.2 1.0 O F:HOH523 2.1 26.1 1.0 OD2 F:ASP243 2.1 27.7 1.0 O F:HOH522 2.1 27.2 1.0 O F:HOH524 2.2 27.7 1.0 CG F:ASP243 3.1 27.4 1.0 PAM F:JD5404 3.3 26.9 1.0 PAI F:JD5404 3.3 26.4 1.0 OD1 F:ASP243 3.4 29.0 1.0 CAH F:JD5404 3.6 26.1 1.0 OD2 F:ASP247 3.9 30.6 1.0 O F:HOH508 3.9 25.9 1.0 NE2 F:GLN240 4.1 28.3 1.0 OAN F:JD5404 4.1 25.8 1.0 OAK F:JD5404 4.1 24.6 1.0 O F:HOH525 4.2 24.6 1.0 O F:ASP243 4.2 26.1 1.0 OD1 F:ASP261 4.3 31.2 1.0 OD2 F:ASP261 4.3 30.4 1.0 CB F:ASP243 4.4 26.9 1.0 OAO F:JD5404 4.4 26.2 1.0 OD1 F:ASP244 4.4 25.7 1.0 NZ F:LYS257 4.4 45.8 1.0 C F:ASP243 4.5 29.0 1.0 OAJ F:JD5404 4.5 24.9 1.0 CG F:ASP247 4.6 33.3 1.0 CE F:LYS257 4.7 40.7 1.0 CG F:ASP261 4.7 29.5 1.0 CB F:ASP247 4.7 32.1 1.0 O F:HOH509 4.7 29.2 1.0 O F:HOH587 4.8 42.8 1.0 NI F:NI403 4.8 26.1 1.0 N F:ASP244 4.9 25.6 1.0

Nickel binding site 3 out of 3 in the Crystal Structure of Human Fpps in Complex with Nickel, JDS05120, and Sulfate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Human Fpps in Complex with Nickel, JDS05120, and Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ F:Ni403 b:26.1 occ:1.00 OD1 F:ASP103 2.0 24.7 1.0 OAK F:JD5404 2.0 24.6 1.0 OAN F:JD5404 2.0 25.8 1.0 O F:HOH526 2.1 25.3 1.0 OD2 F:ASP107 2.1 24.0 1.0 O F:HOH525 2.2 24.6 1.0 CG F:ASP103 3.0 25.3 1.0 NI F:NI401 3.1 27.0 1.0 CG F:ASP107 3.2 26.5 1.0 PAI F:JD5404 3.3 26.4 1.0 OD2 F:ASP103 3.3 24.7 1.0 PAM F:JD5404 3.3 26.9 1.0 CAH F:JD5404 3.6 26.1 1.0 CB F:ASP107 3.7 24.6 1.0 NAG F:JD5404 3.7 27.2 1.0 O F:HOH509 3.8 29.2 1.0 OAL F:JD5404 4.0 29.2 1.0 OAP F:JD5404 4.0 28.0 1.0 O F:HOH522 4.1 27.2 1.0 NH2 F:ARG112 4.3 26.8 1.0 O F:HOH519 4.3 26.0 1.0 O F:HOH517 4.3 27.6 1.0 CB F:ASP103 4.4 23.7 1.0 OD1 F:ASP107 4.4 27.1 1.0 O F:ASP103 4.4 24.5 1.0 OG F:SER109 4.5 30.2 1.0 OAO F:JD5404 4.5 26.2 1.0 OAJ F:JD5404 4.5 24.9 1.0 OD1 F:ASP104 4.6 27.4 1.0 C F:ASP103 4.7 23.9 1.0 O F:HOH520 4.7 25.2 1.0 O F:HOH530 4.8 31.7 1.0 CAD F:JD5404 4.8 24.5 1.0 NI F:NI402 4.8 27.6 1.0 O F:HOH521 4.9 24.2 1.0

J.Park, J.W.De Schutter, Y.S.Tsantrizos, A.M.Berghuis. Crystal Structure of Human Farnesyl Pyrophosphate Synthase in Complex with A Novel Bisphosphonate Reveals Unexpected Binding Interactions To Be Published.