Magnesium in PDB 4nfi: Crystal Structure of Human Fpps in Complex with Magnesium and JDS05120

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

The structure of Crystal Structure of Human Fpps in Complex with Magnesium and JDS05120, PDB code: 4nfi 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)	50.85 / 1.85
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	110.510, 110.510, 66.970, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 19.6

The binding sites of Magnesium atom in the Crystal Structure of Human Fpps in Complex with Magnesium and JDS05120 (pdb code 4nfi). 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 Magnesium and JDS05120, PDB code: 4nfi:
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 Magnesium and JDS05120


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 Magnesium and JDS05120 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:22.2 occ:1.00 OAK F:JD5401 2.0 20.4 1.0 O F:HOH505 2.0 23.3 1.0 O F:HOH502 2.1 21.3 1.0 OD2 F:ASP107 2.1 23.6 1.0 OD2 F:ASP103 2.1 22.0 1.0 O F:HOH503 2.2 21.1 1.0 CG F:ASP107 3.0 22.6 1.0 CG F:ASP103 3.1 24.6 1.0 MG F:MG404 3.1 24.0 1.0 OD1 F:ASP107 3.2 26.1 1.0 OD1 F:ASP103 3.3 22.3 1.0 PAI F:JD5401 3.3 23.2 1.0 OAJ F:JD5401 3.4 22.2 1.0 OD2 F:ASP174 4.1 30.1 1.0 NE2 F:GLN171 4.1 32.1 1.0 O F:HOH506 4.2 23.9 1.0 OE1 F:GLN171 4.2 30.8 1.0 NZ F:LYS266 4.3 29.8 1.0 NAG F:JD5401 4.3 23.9 1.0 OD1 F:ASP174 4.3 28.3 1.0 OAL F:JD5401 4.4 23.1 1.0 CAE F:JD5401 4.4 26.0 1.0 O F:HOH507 4.4 22.5 1.0 CB F:ASP103 4.4 20.9 1.0 CB F:ASP107 4.4 21.7 1.0 CG F:ASP174 4.5 28.6 1.0 CAD F:JD5401 4.5 24.8 1.0 CAH F:JD5401 4.5 23.5 1.0 CD F:GLN171 4.6 29.5 1.0 OAP F:JD5401 4.7 21.0 1.0 O F:HOH532 4.8 23.5 1.0 NZ F:LYS200 4.8 22.0 1.0 O F:HOH509 4.8 22.8 1.0 O F:ASP103 4.8 20.7 1.0 CAV F:JD5401 4.9 33.5 1.0

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


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 Magnesium and JDS05120 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg403 b:23.0 occ:1.00 OAL F:JD5401 2.0 23.1 1.0 OAO F:JD5401 2.0 23.7 1.0 OD2 F:ASP243 2.1 23.8 1.0 O F:HOH501 2.1 21.9 1.0 O F:HOH504 2.1 22.5 1.0 O F:HOH508 2.2 26.1 1.0 CG F:ASP243 3.1 25.7 1.0 PAM F:JD5401 3.2 24.4 1.0 PAI F:JD5401 3.2 23.2 1.0 OD1 F:ASP243 3.5 25.9 1.0 CAH F:JD5401 3.5 23.5 1.0 NZ F:LYS257 3.9 28.6 0.5 OAP F:JD5401 3.9 21.0 1.0 OD2 F:ASP247 4.0 29.8 1.0 O F:HOH507 4.0 22.5 1.0 NE2 F:GLN240 4.1 25.5 1.0 OAK F:JD5401 4.2 20.4 1.0 O F:HOH506 4.2 23.9 1.0 O F:ASP243 4.3 26.7 1.0 OD1 F:ASP261 4.3 28.7 1.0 OD2 F:ASP261 4.3 26.9 1.0 NZ F:LYS257 4.3 31.5 0.5 OAN F:JD5401 4.4 23.1 1.0 OAJ F:JD5401 4.4 22.2 1.0 CB F:ASP243 4.4 24.5 1.0 CE F:LYS257 4.5 32.2 0.5 OD1 F:ASP244 4.6 23.8 1.0 O F:HOH581 4.6 40.9 1.0 C F:ASP243 4.6 26.1 1.0 CG F:ASP247 4.7 31.7 1.0 O F:HOH520 4.7 21.1 1.0 MG F:MG404 4.8 24.0 1.0 CG F:ASP261 4.8 26.5 1.0 CB F:ASP247 4.8 29.0 1.0 NAG F:JD5401 4.9 23.9 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Human Fpps in Complex with Magnesium and JDS05120


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 Magnesium and JDS05120 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg404 b:24.0 occ:1.00 O F:HOH506 2.1 23.9 1.0 OAP F:JD5401 2.1 21.0 1.0 OD1 F:ASP103 2.1 22.3 1.0 OAK F:JD5401 2.1 20.4 1.0 OD2 F:ASP107 2.2 23.6 1.0 O F:HOH509 2.2 22.8 1.0 CG F:ASP103 3.0 24.6 1.0 MG F:MG402 3.1 22.2 1.0 PAI F:JD5401 3.3 23.2 1.0 PAM F:JD5401 3.3 24.4 1.0 CG F:ASP107 3.3 22.6 1.0 OD2 F:ASP103 3.3 22.0 1.0 CAH F:JD5401 3.7 23.5 1.0 NAG F:JD5401 3.8 23.9 1.0 CB F:ASP107 3.8 21.7 1.0 O F:HOH520 3.9 21.1 1.0 OAL F:JD5401 3.9 23.1 1.0 OAO F:JD5401 4.0 23.7 1.0 O F:HOH501 4.2 21.9 1.0 O F:HOH503 4.3 21.1 1.0 NH2 F:ARG112 4.3 25.6 1.0 CB F:ASP103 4.4 20.9 1.0 O F:HOH532 4.4 23.5 1.0 OD1 F:ASP107 4.4 26.1 1.0 O F:ASP103 4.4 20.7 1.0 OAN F:JD5401 4.4 23.1 1.0 OAJ F:JD5401 4.5 22.2 1.0 OG F:SER109 4.5 24.4 1.0 OD1 F:ASP104 4.6 22.1 1.0 O F:HOH505 4.6 23.3 1.0 C F:ASP103 4.7 20.5 1.0 O F:HOH549 4.8 28.3 1.0 CAD F:JD5401 4.8 24.8 1.0 MG F:MG403 4.8 23.0 1.0 O F:HOH502 4.9 21.3 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.