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Magnesium in PDB 5ahu: T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-1326

Enzymatic activity of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-1326

All present enzymatic activity of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-1326:
2.5.1.10;

Protein crystallography data

The structure of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-1326, PDB code: 5ahu 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) 32.84 / 2.69
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 63.010, 117.860, 123.724, 90.00, 95.80, 90.00
R / Rfree (%) 18.1 / 23.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-1326 (pdb code 5ahu). 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-1326, PDB code: 5ahu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5ahu

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Magnesium binding site 1 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-1326


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-1326 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1369

b:30.8
occ:1.00
 O B:HOH2008 2.1 40.3 1.0
OD1 B:ASP103 2.1 28.7 1.0
O B:HOH2007 2.3 41.0 1.0
O16 B:G761368 2.4 28.2 1.0
OD2 B:ASP107 2.4 31.0 1.0
OD1 B:ASP107 2.6 28.5 1.0
CG B:ASP107 2.8 32.0 1.0
CG B:ASP103 3.2 27.0 1.0
NE2 B:GLN172 3.4 41.0 1.0
OD2 B:ASP103 3.6 29.6 1.0
NZ B:LYS278 3.6 58.5 1.0
MG B:MG1370 3.6 41.7 1.0
P15 B:G761368 3.7 33.5 1.0
OD1 B:ASP175 3.9 51.2 1.0
O18 B:G761368 3.9 32.3 1.0
OD2 B:ASP175 4.0 44.6 1.0
CG B:ASP175 4.2 42.8 1.0
CB B:ASP107 4.3 34.9 1.0
O17 B:G761368 4.5 36.3 1.0
CE B:LYS278 4.5 55.9 1.0
CB B:ASP103 4.6 25.7 1.0
CD B:GLN172 4.6 37.5 1.0
O B:HOH2009 4.8 45.7 1.0
NZ B:LYS212 4.8 34.1 1.0
O B:ASP103 4.8 25.3 1.0

Magnesium binding site 2 out of 6 in 5ahu

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Magnesium binding site 2 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-1326


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-1326 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1370

b:41.7
occ:1.00
 OD2 B:ASP107 2.0 31.0 1.0
O20 B:G761368 2.0 28.7 1.0
OD2 B:ASP103 2.0 29.6 1.0
O16 B:G761368 2.2 28.2 1.0
O B:HOH2009 2.3 45.7 1.0
CG B:ASP103 3.1 27.0 1.0
CG B:ASP107 3.1 32.0 1.0
P19 B:G761368 3.2 32.0 1.0
P15 B:G761368 3.3 33.5 1.0
OD1 B:ASP103 3.4 28.7 1.0
MG B:MG1369 3.6 30.8 1.0
O22 B:G761368 3.6 35.5 1.0
C14 B:G761368 3.7 32.1 1.0
CB B:ASP107 3.7 34.9 1.0
O17 B:G761368 3.9 36.3 1.0
C13 B:G761368 4.1 33.0 1.0
OD1 B:ASP107 4.1 28.5 1.0
OG B:SER109 4.1 44.6 1.0
OD1 B:ASP104 4.2 37.8 1.0
NH2 B:ARG112 4.2 31.7 1.0
CB B:ASP103 4.4 25.7 1.0
O21 B:G761368 4.5 31.1 1.0
O B:ASP103 4.6 25.3 1.0
O18 B:G761368 4.7 32.3 1.0
O B:HOH2008 4.7 40.3 1.0
MG B:MG1371 4.8 40.1 1.0
C B:ASP103 4.8 25.6 1.0

Magnesium binding site 3 out of 6 in 5ahu

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Magnesium binding site 3 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-1326


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-1326 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1371

b:40.1
occ:1.00
 OD2 B:ASP255 2.1 38.5 1.0
O17 B:G761368 2.2 36.3 1.0
O22 B:G761368 2.5 35.5 1.0
CG B:ASP255 3.3 39.7 1.0
P15 B:G761368 3.6 33.5 1.0
OD2 B:ASP273 3.6 56.4 1.0
OD1 B:ASP259 3.7 60.3 1.0
P19 B:G761368 3.8 32.0 1.0
O B:HOH2009 3.8 45.7 1.0
C14 B:G761368 4.0 32.1 1.0
OD1 B:ASP255 4.0 41.0 1.0
OD1 B:ASP273 4.0 55.7 1.0
CG B:ASP259 4.1 54.9 1.0
CB B:ASP259 4.1 50.1 1.0
O B:ASP255 4.1 34.4 1.0
CG B:ASP273 4.2 55.9 1.0
O16 B:G761368 4.3 28.2 1.0
CB B:ASP255 4.4 37.0 1.0
OD1 B:ASP256 4.4 49.0 1.0
NZ B:LYS269 4.5 44.8 1.0
C B:ASP255 4.6 34.3 1.0
O20 B:G761368 4.6 28.7 1.0
O18 B:G761368 4.6 32.3 1.0
NE2 B:GLN252 4.6 30.1 1.0
O21 B:G761368 4.8 31.1 1.0
MG B:MG1370 4.8 41.7 1.0
CE B:LYS269 4.9 46.2 1.0
OD2 B:ASP259 5.0 46.8 1.0

Magnesium binding site 4 out of 6 in 5ahu

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Magnesium binding site 4 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-1326


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-1326 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1369

b:39.0
occ:1.00
 OD2 D:ASP103 1.9 40.2 1.0
O22 D:G761368 2.2 31.1 1.0
OD2 D:ASP107 2.2 38.2 1.0
O18 D:G761368 2.6 25.6 1.0
CG D:ASP103 3.1 34.1 1.0
CG D:ASP107 3.1 34.9 1.0
CB D:ASP107 3.3 34.1 1.0
OD1 D:ASP103 3.6 36.8 1.0
OD1 D:ASP104 3.7 35.0 1.0
P19 D:G761368 3.7 32.7 1.0
OG D:SER109 3.7 40.8 1.0
O D:HOH2036 3.7 50.9 1.0
P15 D:G761368 4.0 31.5 1.0
O D:ASP103 4.0 28.6 1.0
NH2 D:ARG112 4.1 26.6 1.0
O D:HOH2009 4.2 39.9 1.0
OD1 D:ASP107 4.2 36.2 1.0
MG D:MG1371 4.3 28.5 1.0
CB D:ASP103 4.3 29.7 1.0
C14 D:G761368 4.3 30.4 1.0
C D:ASP103 4.4 28.2 1.0
O21 D:G761368 4.4 32.7 1.0
O D:HOH2039 4.6 42.8 1.0
OG1 D:THR272 4.7 47.2 1.0
C13 D:G761368 4.7 31.7 1.0
O16 D:G761368 4.7 27.4 1.0
CA D:ASP107 4.8 32.0 1.0
CA D:ASP104 4.8 29.0 1.0
CB D:SER109 4.8 40.3 1.0
O20 D:G761368 4.8 31.3 1.0
N D:ASP104 4.8 28.6 1.0
CG D:ASP104 4.9 30.9 1.0
CA D:ASP103 5.0 27.8 1.0

Magnesium binding site 5 out of 6 in 5ahu

Go back to Magnesium Binding Sites List in 5ahu
Magnesium binding site 5 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-1326


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-1326 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1370

b:37.0
occ:1.00
 O21 D:G761368 2.1 32.7 1.0
OD2 D:ASP255 2.1 40.3 1.0
O D:HOH2036 2.2 50.9 1.0
O16 D:G761368 2.3 27.4 1.0
CG D:ASP255 3.3 37.5 1.0
P19 D:G761368 3.4 32.7 1.0
P15 D:G761368 3.5 31.5 1.0
OD1 D:ASP259 3.6 57.2 1.0
C14 D:G761368 3.7 30.4 1.0
OD1 D:ASP255 3.9 39.1 1.0
OD1 D:ASP273 4.0 45.2 1.0
O22 D:G761368 4.0 31.1 1.0
O18 D:G761368 4.2 25.6 1.0
OD2 D:ASP273 4.2 44.4 1.0
CG D:ASP259 4.2 49.3 1.0
O D:ASP255 4.2 31.2 1.0
NE2 D:GLN252 4.5 35.3 1.0
CB D:ASP255 4.5 36.0 1.0
NZ D:LYS269 4.5 55.0 1.0
O20 D:G761368 4.5 31.3 1.0
CG D:ASP273 4.5 46.8 1.0
CB D:ASP259 4.6 42.6 1.0
C D:ASP255 4.6 31.4 1.0
O17 D:G761368 4.7 29.9 1.0
OD1 D:ASP256 4.7 35.8 1.0
CE D:LYS269 5.0 55.9 1.0
OD2 D:ASP259 5.0 43.8 1.0

Magnesium binding site 6 out of 6 in 5ahu

Go back to Magnesium Binding Sites List in 5ahu
Magnesium binding site 6 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-1326


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-1326 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1371

b:28.5
occ:1.00
 OD1 D:ASP103 2.2 36.8 1.0
O D:HOH2008 2.4 52.5 1.0
OD2 D:ASP107 2.5 38.2 1.0
O18 D:G761368 2.6 25.6 1.0
NE2 D:GLN172 3.1 41.4 1.0
OD1 D:ASP107 3.1 36.2 1.0
CG D:ASP107 3.2 34.9 1.0
O17 D:G761368 3.3 29.9 1.0
CG D:ASP103 3.4 34.1 1.0
P15 D:G761368 3.4 31.5 1.0
OD1 D:ASP175 3.6 44.8 1.0
OD2 D:ASP103 3.7 40.2 1.0
OD2 D:ASP175 3.8 38.9 1.0
CG D:ASP175 3.9 36.4 1.0
MG D:MG1369 4.3 39.0 1.0
CD D:GLN172 4.3 37.3 1.0
NZ D:LYS278 4.3 42.0 1.0
O16 D:G761368 4.4 27.4 1.0
NZ D:LYS212 4.5 29.8 1.0
CB D:ASP103 4.7 29.7 1.0
CB D:ASP107 4.8 34.1 1.0
CE D:LYS278 4.8 40.9 1.0
C12 D:G761368 4.8 33.2 1.0
OE1 D:GLN172 4.8 40.8 1.0
C14 D:G761368 4.9 30.4 1.0
N11 D:G761368 5.0 33.6 1.0
CB D:ASP175 5.0 31.6 1.0

Reference:

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
Page generated: Sun Sep 29 00:32:04 2024

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