Magnesium in PDB 4rxc: T. Brucei Farnesyl Diphosphate Synthase Complexed with Homorisedronate Bph-6

The structure of T. Brucei Farnesyl Diphosphate Synthase Complexed with Homorisedronate Bph-6, PDB code: 4rxc 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)	40.99 / 2.31
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	133.012, 120.919, 63.340, 90.00, 118.33, 90.00
R / Rfree (%)	19.7 / 25.4

The binding sites of Magnesium atom in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Homorisedronate Bph-6 (pdb code 4rxc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Homorisedronate Bph-6, PDB code: 4rxc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Homorisedronate Bph-6


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 Homorisedronate Bph-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:39.9 occ:1.00 O11 A:HRX401 1.9 24.8 1.0 OD2 A:ASP103 2.1 41.8 1.0 O15 A:HRX401 2.1 36.3 1.0 OD2 A:ASP107 2.3 36.0 1.0 CG A:ASP103 3.1 43.7 1.0 P14 A:HRX401 3.1 37.7 1.0 P9 A:HRX401 3.3 40.2 1.0 OD1 A:ASP103 3.4 42.1 1.0 CG A:ASP107 3.4 36.7 1.0 O16 A:HRX401 3.4 38.6 1.0 MG A:MG403 3.4 39.8 1.0 O A:HOH577 3.5 31.2 1.0 C8 A:HRX401 3.6 33.2 1.0 CB A:ASP107 3.8 38.2 1.0 C7 A:HRX401 3.9 32.7 1.0 NH2 A:ARG112 4.1 34.5 1.0 OG A:SER109 4.2 41.7 1.0 O10 A:HRX401 4.2 34.0 1.0 O12 A:HRX401 4.3 37.2 1.0 OD1 A:ASP104 4.4 36.7 1.0 CB A:ASP103 4.4 34.0 1.0 O A:ASP103 4.4 42.3 1.0 OD1 A:ASP107 4.5 34.6 1.0 O17 A:HRX401 4.5 38.5 1.0 C9 A:HRX401 4.6 41.7 1.0 C A:ASP103 4.7 39.4 1.0 MG A:MG404 4.8 49.4 1.0

Magnesium binding site 2 out of 8 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Homorisedronate Bph-6


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 Homorisedronate Bph-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:39.8 occ:1.00 OD2 A:ASP107 2.2 36.0 1.0 OD1 A:ASP103 2.2 42.1 1.0 O15 A:HRX401 2.2 36.3 1.0 CG A:ASP107 2.9 36.7 1.0 OD1 A:ASP107 3.0 34.6 1.0 CG A:ASP103 3.3 43.7 1.0 P14 A:HRX401 3.3 37.7 1.0 MG A:MG402 3.4 39.9 1.0 OD2 A:ASP103 3.6 41.8 1.0 O17 A:HRX401 3.7 38.5 1.0 C9 A:HRX401 4.1 41.7 1.0 OD1 A:ASP175 4.1 54.8 1.0 NE2 A:GLN172 4.2 39.0 1.0 OE1 A:GLN172 4.3 36.9 1.0 O16 A:HRX401 4.3 38.6 1.0 CB A:ASP107 4.4 38.2 1.0 C7 A:HRX401 4.5 32.7 1.0 CB A:ASP103 4.6 34.0 1.0 C8 A:HRX401 4.6 33.2 1.0 CD A:GLN172 4.7 30.8 1.0 O11 A:HRX401 4.8 24.8 1.0 O A:ASP103 4.8 42.3 1.0 CG A:ASP175 4.8 40.6 1.0 NE2 B:GLN127 5.0 46.7 1.0

Magnesium binding site 3 out of 8 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Homorisedronate Bph-6


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 Homorisedronate Bph-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:49.4 occ:1.00 O10 A:HRX401 2.1 34.0 1.0 O17 A:HRX405 2.1 62.2 1.0 O16 A:HRX401 2.2 38.6 1.0 O11 A:HRX405 2.7 35.2 1.0 P14 A:HRX405 3.1 37.1 1.0 P9 A:HRX401 3.3 40.2 1.0 O16 A:HRX405 3.3 74.5 1.0 P9 A:HRX405 3.5 42.0 1.0 P14 A:HRX401 3.5 37.7 1.0 O12 A:HRX405 3.5 59.0 1.0 C8 A:HRX405 3.7 46.3 1.0 O11 A:HRX401 3.7 24.8 1.0 C8 A:HRX401 3.7 33.2 1.0 O13 A:HRX405 3.8 39.6 1.0 O13 A:HRX401 3.8 31.4 1.0 O A:HOH556 4.1 33.6 1.0 O17 A:HRX401 4.4 38.5 1.0 O15 A:HRX405 4.5 44.4 1.0 O12 A:HRX401 4.5 37.2 1.0 O15 A:HRX401 4.6 36.3 1.0 O A:HOH577 4.6 31.2 1.0 MG A:MG406 4.7 46.4 1.0 MG A:MG402 4.8 39.9 1.0 O10 A:HRX405 4.9 56.1 1.0

Magnesium binding site 4 out of 8 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Homorisedronate Bph-6


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 Homorisedronate Bph-6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:46.4 occ:1.00 O12 A:HRX405 2.1 59.0 1.0 OD2 A:ASP255 2.4 35.1 1.0 O15 A:HRX405 2.7 44.4 1.0 O17 A:HRX405 2.8 62.2 1.0 P14 A:HRX405 3.2 37.1 1.0 P9 A:HRX405 3.4 42.0 1.0 CG A:ASP255 3.6 40.8 1.0 C8 A:HRX405 3.7 46.3 1.0 NZ A:LYS269 3.8 40.8 1.0 C7 A:HRX405 3.9 53.0 1.0 OD1 A:ASP273 3.9 53.7 1.0 OD2 A:ASP273 4.0 39.1 1.0 O10 A:HRX405 4.1 56.1 1.0 OD2 A:ASP259 4.2 44.8 1.0 OD1 A:ASP255 4.3 40.9 1.0 CG A:ASP273 4.4 40.1 1.0 O A:HOH512 4.4 41.3 1.0 NE2 A:GLN252 4.4 44.8 1.0 O11 A:HRX405 4.5 35.2 1.0 CB A:ASP255 4.7 40.4 1.0 O16 A:HRX405 4.7 74.5 1.0 MG A:MG404 4.7 49.4 1.0 O A:ASP255 4.8 33.7 1.0 CB A:ASP259 4.8 34.9 1.0 CG A:ASP259 4.9 41.6 1.0 OD1 A:ASP256 4.9 37.4 1.0 CE A:LYS278 4.9 70.9 1.0 CE A:LYS269 4.9 55.5 1.0

Magnesium binding site 5 out of 8 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Homorisedronate Bph-6


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 Homorisedronate Bph-6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:56.0 occ:1.00 O B:HOH548 1.2 60.3 1.0 O15 B:HRX401 1.8 41.6 1.0 O11 B:HRX401 2.1 26.9 1.0 OD2 B:ASP107 2.2 39.4 1.0 OD2 B:ASP103 2.2 37.7 1.0 CG B:ASP103 3.2 44.8 1.0 CG B:ASP107 3.2 35.2 1.0 P14 B:HRX401 3.3 37.6 1.0 MG B:MG403 3.3 39.9 1.0 P9 B:HRX401 3.5 38.0 1.0 OD1 B:ASP103 3.5 42.1 1.0 CB B:ASP107 3.6 39.8 1.0 O B:HOH522 3.7 35.4 1.0 C8 B:HRX401 3.8 35.5 1.0 OG B:SER109 4.0 38.1 1.0 C7 B:HRX401 4.1 36.7 1.0 O17 B:HRX401 4.2 50.8 1.0 O16 B:HRX401 4.3 53.4 1.0 NH2 B:ARG112 4.3 34.7 1.0 O B:HOH568 4.3 23.3 1.0 O B:ASP103 4.3 44.6 1.0 OD1 B:ASP107 4.3 35.4 1.0 O10 B:HRX401 4.4 30.9 1.0 O12 B:HRX401 4.4 45.8 1.0 OD1 B:ASP104 4.5 37.2 1.0 CB B:ASP103 4.5 35.7 1.0 C B:ASP103 4.6 35.5 1.0 MG B:MG404 4.8 53.1 1.0

Magnesium binding site 6 out of 8 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Homorisedronate Bph-6


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 Homorisedronate Bph-6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:39.9 occ:1.00 O B:HOH568 2.3 23.3 1.0 OD1 B:ASP103 2.3 42.1 1.0 OD2 B:ASP107 2.3 39.4 1.0 O15 B:HRX401 2.7 41.6 1.0 O17 B:HRX401 2.8 50.8 1.0 CG B:ASP107 3.1 35.2 1.0 P14 B:HRX401 3.2 37.6 1.0 CG B:ASP103 3.2 44.8 1.0 OD1 B:ASP107 3.3 35.4 1.0 MG B:MG402 3.3 56.0 1.0 OD2 B:ASP103 3.5 37.7 1.0 OD2 B:ASP175 4.1 49.4 1.0 C7 B:HRX401 4.1 36.7 1.0 NE2 B:GLN172 4.2 35.4 1.0 O B:HOH548 4.3 60.3 1.0 C8 B:HRX401 4.4 35.5 1.0 OE1 B:GLN172 4.5 40.9 1.0 O16 B:HRX401 4.5 53.4 1.0 CB B:ASP107 4.6 39.8 1.0 O11 B:HRX401 4.6 26.9 1.0 CB B:ASP103 4.6 35.7 1.0 CD B:GLN172 4.8 29.2 1.0 CG B:ASP175 4.8 38.7 1.0 O B:ASP103 4.9 44.6 1.0

Magnesium binding site 7 out of 8 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Homorisedronate Bph-6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of T. Brucei Farnesyl Diphosphate Synthase Complexed with Homorisedronate Bph-6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:53.1 occ:1.00 O16 B:HRX401 2.2 53.4 1.0 O10 B:HRX401 2.3 30.9 1.0 O10 B:HRX405 2.4 31.0 1.0 O16 B:HRX405 2.4 64.7 1.0 P9 B:HRX401 3.3 38.0 1.0 P14 B:HRX401 3.3 37.6 1.0 P14 B:HRX405 3.4 40.7 1.0 O17 B:HRX405 3.5 57.6 1.0 P9 B:HRX405 3.5 38.2 1.0 C8 B:HRX401 3.6 35.5 1.0 O13 B:HRX401 3.7 30.0 1.0 O11 B:HRX401 3.7 26.9 1.0 O15 B:HRX401 3.7 41.6 1.0 C8 B:HRX405 3.8 43.6 1.0 O13 B:HRX405 3.8 39.7 1.0 O11 B:HRX405 3.9 35.7 1.0 CE B:LYS278 4.3 77.4 1.0 O B:HOH522 4.5 35.4 1.0 O17 B:HRX401 4.6 50.8 1.0 O12 B:HRX401 4.7 45.8 1.0 O15 B:HRX405 4.8 45.7 1.0 MG B:MG402 4.8 56.0 1.0 O12 B:HRX405 4.8 44.4 1.0 NZ B:LYS278 4.9 86.1 1.0

Magnesium binding site 8 out of 8 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Homorisedronate Bph-6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of T. Brucei Farnesyl Diphosphate Synthase Complexed with Homorisedronate Bph-6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg406 b:47.2 occ:1.00 O11 B:HRX405 2.3 35.7 1.0 OD2 B:ASP255 2.3 38.7 1.0 O B:HOH565 2.5 30.5 1.0 O15 B:HRX405 2.7 45.7 1.0 O16 B:HRX405 2.7 64.7 1.0 P14 B:HRX405 3.2 40.7 1.0 CG B:ASP255 3.5 38.1 1.0 P9 B:HRX405 3.6 38.2 1.0 O B:HOH560 3.7 38.8 1.0 C8 B:HRX405 3.7 43.6 1.0 NZ B:LYS269 3.8 39.7 1.0 C7 B:HRX405 3.9 49.6 1.0 OD2 B:ASP273 3.9 30.4 1.0 OD1 B:ASP273 4.0 57.7 1.0 OD1 B:ASP255 4.1 37.8 1.0 O B:HOH547 4.3 37.3 1.0 OD2 B:ASP259 4.4 49.5 1.0 NE2 B:GLN252 4.4 53.1 1.0 CG B:ASP273 4.4 52.0 1.0 O10 B:HRX405 4.5 31.0 1.0 O12 B:HRX405 4.5 44.4 1.0 O17 B:HRX405 4.6 57.6 1.0 CB B:ASP255 4.6 35.2 1.0 O B:ASP255 4.7 34.6 1.0 CB B:ASP259 4.7 36.7 1.0 OD1 B:ASP256 4.8 32.5 1.0 CE B:LYS269 4.9 51.6 1.0 CG B:ASP259 4.9 42.9 1.0 C B:ASP255 5.0 40.2 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