Magnesium in PDB 5afx: T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-1238

The structure of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-1238, PDB code: 5afx was solved by G.Yang, E.Oldfield, J.H.No, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	85.34 / 2.39
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	132.471, 119.026, 63.470, 90.00, 112.47, 90.00
R / Rfree (%)	25.9 / 33.4

The binding sites of Magnesium atom in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-1238 (pdb code 5afx). 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-1238, PDB code: 5afx:
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-1238


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-1238 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1368 b:55.5 occ:1.00 O20 A:PVZ1371 2.6 60.2 1.0 O23 A:PVZ1371 2.9 62.1 1.0 OD2 A:ASP255 2.9 70.1 1.0 OD2 A:ASP259 3.0 0.1 1.0 CG A:ASP255 3.6 71.9 1.0 OD1 A:ASP273 3.7 0.1 1.0 OD1 A:ASP255 3.7 73.3 1.0 P22 A:PVZ1371 3.8 60.6 1.0 CG A:ASP259 3.9 99.7 1.0 O24 A:PVZ1371 3.9 54.3 1.0 P18 A:PVZ1371 3.9 66.4 1.0 OD2 A:ASP273 3.9 97.9 1.0 CB A:ASP259 4.2 88.6 1.0 CG A:ASP273 4.2 0.9 1.0 O17 A:PVZ1371 4.3 63.6 1.0 C16 A:PVZ1371 4.3 58.8 1.0 O19 A:PVZ1371 4.4 55.0 1.0 NZ A:LYS269 4.4 0.7 1.0 OD1 A:ASP256 4.7 86.4 1.0 NE2 A:GLN252 4.7 53.6 1.0 O A:ASP255 4.7 59.7 1.0 OD1 A:ASP259 4.9 92.8 1.0 CB A:ASP255 4.9 73.8 1.0 MG A:MG1369 5.0 57.9 1.0

Magnesium binding site 2 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-1238


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-1238 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1369 b:57.9 occ:1.00 O24 A:PVZ1371 1.9 54.3 1.0 OD2 A:ASP103 2.1 79.0 1.0 O19 A:PVZ1371 2.4 55.0 1.0 OD2 A:ASP107 2.5 63.6 1.0 CG A:ASP103 3.2 67.4 1.0 P22 A:PVZ1371 3.2 60.6 1.0 CG A:ASP107 3.4 67.6 1.0 P18 A:PVZ1371 3.6 66.4 1.0 CB A:ASP107 3.6 65.2 1.0 OD1 A:ASP103 3.7 72.1 1.0 C16 A:PVZ1371 3.8 58.8 1.0 MG A:MG1370 4.0 54.6 1.0 O25 A:PVZ1371 4.0 75.5 1.0 OG A:SER109 4.1 71.5 1.0 OD1 A:ASP104 4.1 66.4 1.0 O20 A:PVZ1371 4.2 60.2 1.0 O23 A:PVZ1371 4.3 62.1 1.0 C15 A:PVZ1371 4.3 58.6 1.0 CB A:ASP103 4.4 64.3 1.0 OD1 A:ASP107 4.5 66.3 1.0 NH2 A:ARG112 4.6 61.8 1.0 O A:ASP103 4.6 56.3 1.0 C A:ASP103 4.7 55.6 1.0 O21 A:PVZ1371 4.8 60.5 1.0 N A:ASP104 4.9 56.1 1.0 OG1 A:THR272 4.9 1.0 1.0 MG A:MG1368 5.0 55.5 1.0

Magnesium binding site 3 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-1238


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-1238 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1370 b:54.6 occ:1.00 OD1 A:ASP103 2.2 72.1 1.0 OD2 A:ASP107 2.3 63.6 1.0 O19 A:PVZ1371 2.6 55.0 1.0 OD1 A:ASP107 3.1 66.3 1.0 CG A:ASP107 3.1 67.6 1.0 CG A:ASP103 3.2 67.4 1.0 NE2 A:GLN172 3.5 70.8 1.0 OD2 A:ASP103 3.5 79.0 1.0 O21 A:PVZ1371 3.5 60.5 1.0 P18 A:PVZ1371 3.6 66.4 1.0 MG A:MG1369 4.0 57.9 1.0 OD1 A:ASP175 4.1 48.6 1.0 NZ A:LYS278 4.2 93.9 1.0 OD2 A:ASP175 4.3 63.1 1.0 CG A:ASP175 4.4 56.1 1.0 CD A:GLN172 4.5 66.7 1.0 CB A:ASP103 4.6 64.3 1.0 CB A:ASP107 4.6 65.2 1.0 O20 A:PVZ1371 4.7 60.2 1.0 C14 A:PVZ1371 4.7 60.6 1.0 OE1 A:GLN172 4.8 62.0 1.0

Magnesium binding site 4 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-1238


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-1238 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1368 b:75.0 occ:1.00 O23 B:PVZ1371 1.9 69.3 1.0 O20 B:PVZ1371 2.2 56.6 1.0 O B:HOH2062 2.5 43.7 1.0 OD2 B:ASP255 2.7 70.8 1.0 P22 B:PVZ1371 3.3 56.6 1.0 OD1 B:ASP259 3.3 87.6 1.0 P18 B:PVZ1371 3.5 62.0 1.0 CG B:ASP255 3.5 69.4 1.0 C16 B:PVZ1371 3.9 62.3 1.0 OD1 B:ASP255 3.9 65.6 1.0 CG B:ASP259 3.9 79.0 1.0 OD2 B:ASP273 4.0 85.8 1.0 O17 B:PVZ1371 4.0 60.6 1.0 OD1 B:ASP273 4.1 96.5 1.0 O24 B:PVZ1371 4.1 51.0 1.0 CB B:ASP259 4.2 79.9 1.0 O B:HOH2069 4.2 49.0 1.0 O19 B:PVZ1371 4.3 53.7 1.0 O25 B:PVZ1371 4.3 70.6 1.0 CG B:ASP273 4.4 93.0 1.0 NZ B:LYS269 4.6 0.8 1.0 NE2 B:GLN252 4.6 56.3 1.0 O21 B:PVZ1371 4.6 67.0 1.0 CB B:ASP255 4.7 73.4 1.0 OD1 B:ASP256 4.7 75.2 1.0 O B:ASP255 4.8 75.8 1.0 OD2 B:ASP259 4.8 72.5 1.0 C B:ASP255 5.0 72.3 1.0

Magnesium binding site 5 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-1238


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-1238 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1369 b:65.0 occ:1.00 OD2 B:ASP103 2.2 70.2 1.0 OD2 B:ASP107 2.3 66.5 1.0 O24 B:PVZ1371 2.4 51.0 1.0 O19 B:PVZ1371 3.1 53.7 1.0 CG B:ASP107 3.2 66.5 1.0 CG B:ASP103 3.3 65.5 1.0 CB B:ASP107 3.4 64.9 1.0 P22 B:PVZ1371 3.8 56.6 1.0 OG B:SER109 3.8 77.1 1.0 OD1 B:ASP103 3.9 56.5 1.0 OD1 B:ASP104 4.1 71.1 1.0 O B:HOH2069 4.2 49.0 1.0 NH2 B:ARG112 4.2 57.2 1.0 MG B:MG1370 4.3 44.5 1.0 P18 B:PVZ1371 4.3 62.0 1.0 OD1 B:ASP107 4.3 68.6 1.0 O B:ASP103 4.4 65.5 1.0 CB B:ASP103 4.4 59.2 1.0 O23 B:PVZ1371 4.4 69.3 1.0 C B:ASP103 4.5 61.3 1.0 C16 B:PVZ1371 4.5 62.3 1.0 C15 B:PVZ1371 4.6 60.2 1.0 N B:ASP104 4.7 60.2 1.0 CA B:ASP104 4.7 61.5 1.0 OG1 B:THR272 4.8 0.8 1.0 CB B:SER109 4.8 69.5 1.0 O20 B:PVZ1371 4.8 56.6 1.0 O25 B:PVZ1371 4.8 70.6 1.0 CA B:ASP107 4.9 66.6 1.0

Magnesium binding site 6 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-1238


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-1238 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1370 b:44.5 occ:1.00 OD1 B:ASP103 2.3 56.5 1.0 O B:HOH2032 2.3 53.3 1.0 OD2 B:ASP107 2.7 66.5 1.0 O19 B:PVZ1371 2.8 53.7 1.0 NE2 B:GLN172 3.0 73.8 1.0 OD1 B:ASP107 3.2 68.6 1.0 CG B:ASP103 3.3 65.5 1.0 CG B:ASP107 3.3 66.5 1.0 OD2 B:ASP103 3.6 70.2 1.0 OD1 B:ASP175 3.6 62.7 1.0 NZ B:LYS278 3.8 0.8 1.0 P18 B:PVZ1371 4.0 62.0 1.0 CD B:GLN172 4.0 69.0 1.0 O21 B:PVZ1371 4.1 67.0 1.0 CG B:ASP175 4.2 56.0 1.0 MG B:MG1369 4.3 65.0 1.0 OD2 B:ASP175 4.4 57.2 1.0 OE1 B:GLN172 4.5 71.1 1.0 CB B:ASP103 4.7 59.2 1.0 NZ B:LYS212 4.7 71.9 1.0 CB B:ASP107 4.8 64.9 1.0 C14 B:PVZ1371 4.9 63.3 1.0 CE B:LYS278 4.9 0.9 1.0 O20 B:PVZ1371 4.9 56.6 1.0

G.Yang, W.Zhu, K.Kim, S.Y.Byun, G.Choi, K.Wang, J.S.Cha, H.Cho, E.Oldfield, J.H.No. Inhibition of Trypanosoma Brucei Cell Growth By Lipophilic Bisphosphonates: An in Vitro and in Vivo Investigation. Antimicrob.Agents Chemother. V. 59 7530 2015.
ISSN: ISSN 0066-4804
PubMed: 26392508
DOI: 10.1128/AAC.01873-15