Magnesium in PDB 4rxe: T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-14

The structure of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-14, PDB code: 4rxe was solved by R.Cao, Y.-L.Liu, E.Oldfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.07 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	134.149, 119.149, 62.824, 90.00, 112.24, 90.00
R / Rfree (%)	19.7 / 25.5

The binding sites of Magnesium atom in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-14 (pdb code 4rxe). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-14, PDB code: 4rxe:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-14


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3002 b:51.1 occ:1.00 O5 A:3YQ3001 2.1 28.4 1.0 OD2 A:ASP103 2.2 51.5 1.0 O A:HOH3166 2.2 36.3 1.0 OD2 A:ASP107 2.4 27.7 1.0 O4 A:3YQ3001 2.9 31.9 1.0 CG A:ASP107 3.2 36.6 1.0 CG A:ASP103 3.3 43.3 1.0 CB A:ASP107 3.3 40.8 1.0 OD1 A:ASP104 3.5 33.3 1.0 OG A:SER109 3.5 42.7 1.0 P1 A:3YQ3001 3.6 36.3 1.0 OD1 A:ASP103 3.8 42.3 1.0 O A:HOH3144 3.9 47.3 1.0 O A:ASP103 4.0 39.9 1.0 NH2 A:ARG112 4.0 30.1 1.0 MG A:MG3004 4.1 36.5 1.0 P2 A:3YQ3001 4.2 34.5 1.0 C A:ASP103 4.3 40.2 1.0 C6 A:3YQ3001 4.3 31.4 1.0 N1 A:3YQ3001 4.3 30.8 1.0 CB A:ASP103 4.4 40.7 1.0 OD1 A:ASP107 4.4 40.9 1.0 O6 A:3YQ3001 4.5 33.3 1.0 CA A:ASP104 4.5 36.2 1.0 CB A:SER109 4.5 43.4 1.0 O2 A:3YQ3001 4.6 31.7 1.0 N A:ASP104 4.6 35.8 1.0 O A:HOH3165 4.7 25.1 1.0 O A:HOH3164 4.7 39.1 1.0 O A:HOH3139 4.7 40.7 1.0 CG A:ASP104 4.7 31.0 1.0 O3 A:3YQ3001 4.7 37.2 1.0 CA A:ASP107 4.8 43.3 1.0 CA A:ASP103 5.0 37.4 1.0

Magnesium binding site 2 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-14


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3003 b:34.6 occ:1.00 OD2 A:ASP255 2.1 41.7 1.0 O A:HOH3165 2.2 25.1 1.0 O A:HOH3130 2.2 31.1 1.0 O3 A:3YQ3001 2.3 37.2 1.0 O6 A:3YQ3001 2.4 33.3 1.0 CG A:ASP255 3.2 47.1 1.0 P2 A:3YQ3001 3.6 34.5 1.0 OD2 A:ASP273 3.7 58.8 1.0 P1 A:3YQ3001 3.8 36.3 1.0 OD1 A:ASP255 3.9 53.6 1.0 C6 A:3YQ3001 3.9 31.4 1.0 OD1 A:ASP273 4.0 57.2 1.0 NE2 A:GLN252 4.1 46.6 1.0 OD1 A:ASP259 4.3 42.8 1.0 CG A:ASP273 4.3 60.3 1.0 CB A:ASP255 4.3 49.2 1.0 OD1 A:ASP256 4.3 43.6 1.0 O A:ASP255 4.3 47.4 1.0 NZ A:LYS269 4.3 62.4 1.0 C A:ASP255 4.5 43.9 1.0 O1 A:3YQ3001 4.5 32.6 1.0 O5 A:3YQ3001 4.6 28.4 1.0 CG A:ASP259 4.6 48.5 1.0 O4 A:3YQ3001 4.6 31.9 1.0 O A:HOH3166 4.6 36.3 1.0 CB A:ASP259 4.6 44.2 1.0 N A:ASP256 4.8 44.0 1.0 O2 A:3YQ3001 4.8 31.7 1.0 CA A:ASP255 5.0 47.2 1.0

Magnesium binding site 3 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-14


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3004 b:36.5 occ:1.00 OD1 A:ASP103 2.1 42.3 1.0 O A:HOH3164 2.1 39.1 1.0 OD2 A:ASP107 2.3 27.7 1.0 O4 A:3YQ3001 2.4 31.9 1.0 OD1 A:ASP107 2.8 40.9 1.0 CG A:ASP107 2.9 36.6 1.0 CG A:ASP103 3.1 43.3 1.0 P2 A:3YQ3001 3.4 34.5 1.0 OD2 A:ASP103 3.4 51.5 1.0 O1 A:3YQ3001 3.5 32.6 1.0 OD1 A:ASP175 3.7 31.4 1.0 NE2 A:GLN172 3.9 32.2 1.0 MG A:MG3002 4.1 51.1 1.0 CG A:ASP175 4.2 35.7 1.0 OE1 A:GLN172 4.2 39.4 1.0 O A:HOH3166 4.3 36.3 1.0 OD2 A:ASP175 4.4 35.5 1.0 CB A:ASP107 4.4 40.8 1.0 CB A:ASP103 4.4 40.7 1.0 N1 A:3YQ3001 4.4 30.8 1.0 O3 A:3YQ3001 4.5 37.2 1.0 CD A:GLN172 4.5 34.6 1.0 C6 A:3YQ3001 4.6 31.4 1.0 C1 A:3YQ3001 4.7 35.6 1.0 O5 A:3YQ3001 4.8 28.4 1.0 NZ A:LYS212 4.8 30.9 1.0 O A:ASP103 4.9 39.9 1.0 N2 A:3YQ3001 5.0 36.7 1.0

Magnesium binding site 4 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-14


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-14 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg4002 b:47.2 occ:1.00 O B:HOH4191 1.9 37.8 1.0 O2 B:3YQ4001 2.1 27.5 1.0 OD2 B:ASP103 2.3 43.4 1.0 OD2 B:ASP107 2.4 36.3 1.0 O4 B:3YQ4001 2.6 31.4 1.0 CG B:ASP107 3.2 41.7 1.0 CG B:ASP103 3.3 38.8 1.0 CB B:ASP107 3.4 40.7 1.0 O B:HOH4109 3.4 38.6 1.0 P1 B:3YQ4001 3.5 32.7 1.0 OG B:SER109 3.6 48.3 1.0 OD1 B:ASP103 3.7 39.0 1.0 O B:ASP103 3.8 34.4 1.0 P2 B:3YQ4001 3.9 33.0 1.0 OD1 B:ASP104 3.9 30.6 1.0 MG B:MG4004 4.0 33.0 1.0 C6 B:3YQ4001 4.1 33.0 1.0 NH1 B:ARG112 4.2 38.6 1.0 N1 B:3YQ4001 4.2 31.9 1.0 C B:ASP103 4.3 33.4 1.0 O5 B:3YQ4001 4.3 38.7 1.0 OD1 B:ASP107 4.4 41.3 1.0 CB B:ASP103 4.5 34.9 1.0 O1 B:3YQ4001 4.5 39.0 1.0 O B:HOH4129 4.6 29.3 1.0 CA B:ASP104 4.6 31.3 1.0 O6 B:3YQ4001 4.7 28.8 1.0 N B:ASP104 4.7 33.2 1.0 CB B:SER109 4.8 42.0 1.0 CA B:ASP107 4.9 43.0 1.0 O B:HOH4192 5.0 31.2 1.0

Magnesium binding site 5 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-14


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-14 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg4003 b:43.7 occ:1.00 O1 B:3YQ4001 2.1 39.0 1.0 O5 B:3YQ4001 2.3 38.7 1.0 OD2 B:ASP255 2.6 41.2 1.0 P2 B:3YQ4001 3.5 33.0 1.0 OD2 B:ASP273 3.5 71.1 1.0 OD1 B:ASP259 3.6 58.1 1.0 P1 B:3YQ4001 3.7 32.7 1.0 OD1 B:ASP273 3.7 61.0 1.0 CG B:ASP255 3.8 43.8 1.0 C6 B:3YQ4001 4.0 33.0 1.0 CG B:ASP273 4.1 67.3 1.0 O4 B:3YQ4001 4.2 31.4 1.0 O B:HOH4191 4.2 37.8 1.0 O2 B:3YQ4001 4.2 27.5 1.0 NZ B:LYS269 4.2 46.6 1.0 CG B:ASP259 4.3 55.9 1.0 OD1 B:ASP255 4.3 47.3 1.0 O3 B:3YQ4001 4.6 31.9 1.0 CB B:ASP259 4.6 49.3 1.0 O6 B:3YQ4001 4.8 28.8 1.0 O B:HOH4157 4.8 46.1 1.0 O B:ASP255 4.8 42.4 1.0 NE2 B:GLN252 4.8 38.9 1.0 OD1 B:ASP256 4.8 36.7 1.0 CB B:ASP255 4.9 44.4 1.0 O B:HOH4109 5.0 38.6 1.0

Magnesium binding site 6 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-14


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-14 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg4004 b:33.0 occ:1.00 O B:HOH4192 2.2 31.2 1.0 O4 B:3YQ4001 2.2 31.4 1.0 OD1 B:ASP103 2.3 39.0 1.0 OD2 B:ASP107 2.5 36.3 1.0 O3 B:3YQ4001 3.0 31.9 1.0 P2 B:3YQ4001 3.0 33.0 1.0 CG B:ASP103 3.2 38.8 1.0 CG B:ASP107 3.5 41.7 1.0 OD2 B:ASP103 3.5 43.4 1.0 OD1 B:ASP107 3.7 41.3 1.0 OD1 B:ASP175 3.8 34.9 1.0 MG B:MG4002 4.0 47.2 1.0 OD2 B:ASP175 4.1 34.6 1.0 NE2 B:GLN172 4.1 31.9 1.0 OE1 B:GLN172 4.1 36.6 1.0 CG B:ASP175 4.1 34.0 1.0 O1 B:3YQ4001 4.2 39.0 1.0 N1 B:3YQ4001 4.2 31.9 1.0 C6 B:3YQ4001 4.3 33.0 1.0 NZ B:LYS212 4.4 31.0 1.0 C1 B:3YQ4001 4.5 34.3 1.0 CD B:GLN172 4.5 30.5 1.0 O B:HOH4191 4.5 37.8 1.0 CB B:ASP103 4.5 34.9 1.0 N2 B:3YQ4001 4.5 35.1 1.0 O2 B:3YQ4001 4.7 27.5 1.0 CB B:ASP107 4.9 40.7 1.0

Y.L.Liu, R.Cao, Y.Wang, E.Oldfield. Farnesyl Diphosphate Synthase Inhibitors with Unique Ligand-Binding Geometries. Acs Med Chem Lett V. 6 349 2015.
PubMed: 25815158
DOI: 10.1021/ML500528X