Magnesium in PDB 4l2x: Crystal Structure of Human Fpps in Complex with Magnesium, CL02134, and Inorganic Pyrophosphate

All present enzymatic activity of Crystal Structure of Human Fpps in Complex with Magnesium, CL02134, and Inorganic Pyrophosphate:
2.5.1.1; 2.5.1.10;

The structure of Crystal Structure of Human Fpps in Complex with Magnesium, CL02134, and Inorganic Pyrophosphate, PDB code: 4l2x was solved by J.Park, C.-Y.Leung, 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)	35.23 / 2.55
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	111.340, 111.340, 68.770, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 25.7

The binding sites of Magnesium atom in the Crystal Structure of Human Fpps in Complex with Magnesium, CL02134, and Inorganic Pyrophosphate (pdb code 4l2x). 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, CL02134, and Inorganic Pyrophosphate, PDB code: 4l2x:
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, CL02134, and Inorganic Pyrophosphate


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, CL02134, and Inorganic Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg403 b:43.6 occ:1.00 O F:HOH507 2.0 41.9 1.0 OD2 F:ASP107 2.1 51.6 1.0 OD1 F:ASP103 2.1 45.7 1.0 O F:HOH508 2.3 28.4 1.0 OAV F:YL2401 2.3 50.2 1.0 OAZ F:YL2401 2.3 57.6 1.0 CG F:ASP107 3.0 50.8 1.0 CG F:ASP103 3.1 45.8 1.0 MG F:MG404 3.2 34.1 1.0 CB F:ASP107 3.3 54.6 1.0 PAT F:YL2401 3.5 51.2 1.0 OD2 F:ASP103 3.6 39.2 1.0 PAS F:YL2401 3.6 55.0 1.0 O F:ASP103 4.0 44.5 1.0 NH2 F:ARG112 4.1 37.3 1.0 OAY F:YL2401 4.1 46.1 1.0 CAR F:YL2401 4.1 51.6 1.0 OD1 F:ASP107 4.1 54.0 1.0 OG F:SER109 4.1 43.7 1.0 O F:HOH506 4.2 31.9 1.0 OAW F:YL2401 4.3 53.2 1.0 CB F:ASP103 4.4 42.9 1.0 C F:ASP103 4.4 47.8 1.0 OD1 F:ASP104 4.5 37.4 1.0 NAJ F:YL2401 4.6 56.6 1.0 OAX F:YL2401 4.6 35.1 1.0 O F:HOH503 4.7 31.0 1.0 O F:HOH501 4.8 39.6 1.0 CA F:ASP107 4.8 52.0 1.0 OAU F:YL2401 4.9 48.2 1.0 MG F:MG405 5.0 42.1 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Human Fpps in Complex with Magnesium, CL02134, and Inorganic Pyrophosphate


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, CL02134, and Inorganic Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg404 b:34.1 occ:1.00 O F:HOH501 1.9 39.6 1.0 OD2 F:ASP103 2.0 39.2 1.0 OD2 F:ASP107 2.1 51.6 1.0 OAV F:YL2401 2.1 50.2 1.0 O F:HOH503 2.2 31.0 1.0 O F:HOH502 2.2 48.5 1.0 CG F:ASP103 2.9 45.8 1.0 CG F:ASP107 3.0 50.8 1.0 OD1 F:ASP103 3.1 45.7 1.0 PAS F:YL2401 3.1 55.0 1.0 MG F:MG403 3.2 43.6 1.0 OD1 F:ASP107 3.2 54.0 1.0 OAU F:YL2401 3.4 48.2 1.0 OD2 F:ASP174 3.6 52.5 1.0 NZ F:LYS266 3.8 48.6 1.0 OAW F:YL2401 4.0 53.2 1.0 OE1 F:GLN171 4.1 55.9 1.0 O F:HOH507 4.2 41.9 1.0 NE2 F:GLN171 4.3 61.3 1.0 CB F:ASP103 4.4 42.9 1.0 CB F:ASP107 4.4 54.6 1.0 CAR F:YL2401 4.5 51.6 1.0 CG F:ASP174 4.6 60.8 1.0 O F:HOH513 4.6 49.6 1.0 CD F:GLN171 4.6 57.2 1.0 OAZ F:YL2401 4.7 57.6 1.0 NAJ F:YL2401 4.7 56.6 1.0 NZ F:LYS200 4.8 52.4 1.0 O F:ASP103 4.8 44.5 1.0 CAC F:YL2401 4.9 62.6 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Human Fpps in Complex with Magnesium, CL02134, and Inorganic Pyrophosphate


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, CL02134, and Inorganic Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg405 b:42.1 occ:1.00 OAY F:YL2401 1.7 46.1 1.0 OAW F:YL2401 2.1 53.2 1.0 O F:HOH505 2.1 35.2 1.0 O F:HOH504 2.2 40.8 1.0 OD2 F:ASP243 2.2 53.6 1.0 O F:HOH506 2.3 31.9 1.0 PAT F:YL2401 3.1 51.2 1.0 CG F:ASP243 3.1 51.7 1.0 PAS F:YL2401 3.1 55.0 1.0 OD1 F:ASP243 3.3 40.0 1.0 CAR F:YL2401 3.3 51.6 1.0 O F:HOH507 3.9 41.9 1.0 OAV F:YL2401 4.0 50.2 1.0 O F:ASP243 4.0 48.4 1.0 OAZ F:YL2401 4.0 57.6 1.0 OAU F:YL2401 4.1 48.2 1.0 NE2 F:GLN240 4.2 58.1 1.0 OAX F:YL2401 4.3 35.1 1.0 NZ F:LYS257 4.3 55.9 1.0 OD1 F:ASP261 4.4 50.3 1.0 OD1 F:ASP244 4.4 41.5 1.0 OD2 F:ASP247 4.4 47.7 1.0 CB F:ASP243 4.4 46.5 1.0 O F:HOH513 4.4 49.6 1.0 C F:ASP243 4.5 50.8 1.0 NAJ F:YL2401 4.8 56.6 1.0 CE F:LYS257 4.8 57.6 1.0 OD2 F:ASP261 4.9 62.2 1.0 MG F:MG403 5.0 43.6 1.0 CB F:ASP247 5.0 65.3 1.0

C.Y.Leung, J.Park, J.W.De Schutter, M.Sebag, A.M.Berghuis, Y.S.Tsantrizos. Thienopyrimidine Bisphosphonate (Thpbp) Inhibitors of the Human Farnesyl Pyrophosphate Synthase: Optimization and Characterization of the Mode of Inhibition. J.Med.Chem. V. 56 7939 2013.
ISSN: ISSN 0022-2623
PubMed: 23998921
DOI: 10.1021/JM400946F