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Magnesium in PDB 5ael: T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-597

Enzymatic activity of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-597

All present enzymatic activity of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-597:
2.5.1.10;

Protein crystallography data

The structure of T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-597, PDB code: 5ael 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) 85.49 / 2.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 133.835, 118.250, 62.424, 90.00, 112.39, 90.00
R / Rfree (%) 16.4 / 23

Magnesium Binding Sites:

The binding sites of Magnesium atom in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-597 (pdb code 5ael). 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-597, PDB code: 5ael:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5ael

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Magnesium binding site 1 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-597


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-597 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1369

b:38.0
occ:1.00
 OD2 A:ASP103 2.1 45.4 1.0
O17 A:QAF1368 2.1 52.9 1.0
OD2 A:ASP107 2.2 46.9 1.0
O20 A:QAF1368 2.3 33.5 1.0
O A:HOH2024 2.3 38.4 1.0
O A:HOH2028 2.4 42.2 1.0
P14 A:QAF1368 3.1 44.0 1.0
CG A:ASP103 3.2 39.6 1.0
P18 A:QAF1368 3.2 39.5 1.0
CG A:ASP107 3.3 45.2 1.0
C13 A:QAF1368 3.5 45.0 1.0
O15 A:QAF1368 3.5 55.0 1.0
OD1 A:ASP103 3.5 42.8 1.0
O19 A:QAF1368 3.7 40.7 1.0
CB A:ASP107 3.8 45.3 1.0
MG A:MG1371 3.8 32.1 1.0
C12 A:QAF1368 3.8 42.4 1.0
O A:HOH2025 4.2 64.6 1.0
NH2 A:ARG112 4.2 36.9 1.0
O A:HOH2050 4.3 60.9 1.0
O A:HOH2029 4.3 27.8 1.0
OG A:SER109 4.4 40.0 1.0
MG A:MG1370 4.4 47.9 1.0
OD1 A:ASP107 4.4 43.2 1.0
O16 A:QAF1368 4.4 57.1 1.0
O A:HOH2030 4.5 38.8 1.0
CB A:ASP103 4.5 37.3 1.0
O21 A:QAF1368 4.5 47.7 1.0
OD1 A:ASP104 4.6 46.3 1.0
N11 A:QAF1368 4.8 43.6 1.0
O A:ASP103 4.9 35.0 1.0
C A:ASP103 5.0 35.6 1.0

Magnesium binding site 2 out of 6 in 5ael

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Magnesium binding site 2 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-597


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-597 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1370

b:47.9
occ:1.00
 O19 A:QAF1368 2.2 40.7 1.0
OD2 A:ASP255 2.3 39.8 1.0
O17 A:QAF1368 2.9 52.9 1.0
O16 A:QAF1368 2.9 57.1 1.0
OD1 A:ASP259 3.3 52.9 1.0
P14 A:QAF1368 3.3 44.0 1.0
O A:HOH2028 3.3 42.2 1.0
CG A:ASP255 3.4 38.3 1.0
P18 A:QAF1368 3.5 39.5 1.0
OD1 A:ASP255 3.8 44.0 1.0
OD1 A:ASP273 3.9 43.4 1.0
C13 A:QAF1368 3.9 45.0 1.0
OD2 A:ASP273 4.0 41.9 1.0
CG A:ASP259 4.1 46.4 1.0
O A:HOH2050 4.3 60.9 1.0
CG A:ASP273 4.3 45.2 1.0
CB A:ASP259 4.4 45.2 1.0
MG A:MG1369 4.4 38.0 1.0
O20 A:QAF1368 4.4 33.5 1.0
O A:ASP255 4.5 40.4 1.0
NZ A:LYS269 4.5 68.7 1.0
CE A:LYS269 4.5 59.4 1.0
O A:HOH2084 4.6 67.4 1.0
O21 A:QAF1368 4.6 47.7 1.0
CB A:ASP255 4.6 36.9 1.0
O15 A:QAF1368 4.7 55.0 1.0
NE2 A:GLN252 4.7 37.9 1.0
C A:ASP255 4.8 37.3 1.0
OD1 A:ASP256 4.9 46.0 1.0
OD2 A:ASP259 5.0 40.8 1.0

Magnesium binding site 3 out of 6 in 5ael

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Magnesium binding site 3 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-597


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-597 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1371

b:32.1
occ:1.00
 O20 A:QAF1368 2.2 33.5 1.0
OD1 A:ASP103 2.2 42.8 1.0
OD2 A:ASP107 2.5 46.9 1.0
OD1 A:ASP107 3.1 43.2 1.0
O A:HOH2050 3.1 60.9 1.0
NE2 A:GLN172 3.1 39.8 1.0
CG A:ASP107 3.2 45.2 1.0
CG A:ASP103 3.3 39.6 1.0
P18 A:QAF1368 3.4 39.5 1.0
O21 A:QAF1368 3.4 47.7 1.0
OD2 A:ASP175 3.5 52.7 1.0
OD1 A:ASP175 3.6 43.3 1.0
OD2 A:ASP103 3.6 45.4 1.0
CG A:ASP175 3.7 43.5 1.0
MG A:MG1369 3.8 38.0 1.0
NZ A:LYS278 4.0 52.9 1.0
CD A:GLN172 4.3 38.2 1.0
NZ A:LYS212 4.3 36.3 1.0
O19 A:QAF1368 4.4 40.7 1.0
C22 A:QAF1368 4.4 38.1 1.0
N11 A:QAF1368 4.6 43.6 1.0
CB A:ASP103 4.6 37.3 1.0
CB A:ASP107 4.7 45.3 1.0
C13 A:QAF1368 4.7 45.0 1.0
C12 A:QAF1368 4.8 42.4 1.0
CB A:ASP175 4.8 38.3 1.0
O A:HOH2028 4.8 42.2 1.0
OE1 A:GLN172 4.9 47.0 1.0
CE A:LYS278 4.9 52.0 1.0
C07 A:QAF1368 4.9 35.6 1.0

Magnesium binding site 4 out of 6 in 5ael

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Magnesium binding site 4 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-597


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-597 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1369

b:47.2
occ:1.00
 OD2 B:ASP107 2.1 37.0 1.0
OD2 B:ASP103 2.2 45.1 1.0
O16 B:QAF1368 2.2 43.6 1.0
O21 B:QAF1368 2.5 49.4 1.0
O B:HOH2079 2.9 55.7 1.0
CG B:ASP107 3.1 36.4 1.0
P18 B:QAF1368 3.1 45.5 1.0
CG B:ASP103 3.2 38.9 1.0
P14 B:QAF1368 3.3 41.1 1.0
O20 B:QAF1368 3.4 55.4 1.0
CB B:ASP107 3.5 37.6 1.0
C13 B:QAF1368 3.6 46.2 1.0
OD1 B:ASP103 3.6 43.8 1.0
MG B:MG1371 3.6 33.7 1.0
O15 B:QAF1368 4.1 53.5 1.0
OD1 B:ASP107 4.2 38.1 1.0
C12 B:QAF1368 4.2 39.9 1.0
OG B:SER109 4.2 50.7 1.0
NH2 B:ARG112 4.3 40.0 1.0
OD1 B:ASP104 4.5 44.1 1.0
O17 B:QAF1368 4.5 46.3 1.0
O19 B:QAF1368 4.6 46.5 1.0
CB B:ASP103 4.6 37.5 1.0
MG B:MG1370 4.7 50.2 1.0
O B:ASP103 4.7 40.2 1.0
C B:ASP103 4.9 38.3 1.0

Magnesium binding site 5 out of 6 in 5ael

Go back to Magnesium Binding Sites List in 5ael
Magnesium binding site 5 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-597


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-597 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1370

b:50.2
occ:1.00
 O20 B:QAF1368 2.1 55.4 1.0
OD2 B:ASP255 2.2 41.3 1.0
O15 B:QAF1368 2.3 53.5 1.0
O B:HOH2079 2.6 55.7 1.0
CG B:ASP255 3.2 39.6 1.0
P14 B:QAF1368 3.5 41.1 1.0
P18 B:QAF1368 3.5 45.5 1.0
OD1 B:ASP255 3.7 48.9 1.0
OD1 B:ASP259 3.8 52.2 1.0
C13 B:QAF1368 3.8 46.2 1.0
OD2 B:ASP273 3.9 54.8 1.0
O16 B:QAF1368 3.9 43.6 1.0
OD1 B:ASP273 4.1 57.4 1.0
O19 B:QAF1368 4.2 46.5 1.0
NZ B:LYS269 4.2 66.4 1.0
O B:ASP255 4.4 40.0 1.0
CB B:ASP255 4.4 38.8 1.0
CE B:LYS269 4.4 65.1 1.0
CG B:ASP273 4.4 54.2 1.0
CG B:ASP259 4.4 43.3 1.0
NE2 B:GLN252 4.5 40.8 1.0
CB B:ASP259 4.6 38.1 1.0
C B:ASP255 4.6 37.6 1.0
OD1 B:ASP256 4.6 49.3 1.0
O21 B:QAF1368 4.7 49.4 1.0
O17 B:QAF1368 4.7 46.3 1.0
MG B:MG1369 4.7 47.2 1.0
N B:ASP256 5.0 37.7 1.0

Magnesium binding site 6 out of 6 in 5ael

Go back to Magnesium Binding Sites List in 5ael
Magnesium binding site 6 out of 6 in the T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate Bph-597


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-597 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1371

b:33.7
occ:1.00
 O21 B:QAF1368 1.8 49.4 1.0
O B:HOH2034 2.0 46.2 1.0
OD2 B:ASP107 2.1 37.0 1.0
OD1 B:ASP103 2.2 43.8 1.0
CG B:ASP107 2.8 36.4 1.0
OD1 B:ASP107 2.9 38.1 1.0
P18 B:QAF1368 3.2 45.5 1.0
CG B:ASP103 3.2 38.9 1.0
NE2 B:GLN172 3.2 43.9 1.0
OD2 B:ASP103 3.5 45.1 1.0
OD2 B:ASP175 3.6 40.0 1.0
MG B:MG1369 3.6 47.2 1.0
O19 B:QAF1368 3.6 46.5 1.0
NZ B:LYS278 3.8 47.1 1.0
CG B:ASP175 4.0 39.0 1.0
OD1 B:ASP175 4.0 42.5 1.0
O20 B:QAF1368 4.1 55.4 1.0
CD B:GLN172 4.2 44.1 1.0
OE1 B:GLN172 4.3 40.1 1.0
CB B:ASP107 4.4 37.6 1.0
CB B:ASP103 4.6 37.5 1.0
C13 B:QAF1368 4.6 46.2 1.0
C22 B:QAF1368 4.6 39.1 1.0
NZ B:LYS212 4.6 39.2 1.0
N11 B:QAF1368 4.8 38.6 1.0
CE B:LYS278 4.8 47.3 1.0
C12 B:QAF1368 4.9 39.9 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 00:30:49 2024

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