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Magnesium in PDB 3id0: Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Bisphosphono-Ethyl)Pyridinium

Enzymatic activity of Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Bisphosphono-Ethyl)Pyridinium

All present enzymatic activity of Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Bisphosphono-Ethyl)Pyridinium:
2.5.1.10;

Protein crystallography data

The structure of Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Bisphosphono-Ethyl)Pyridinium, PDB code: 3id0 was solved by L.M.Amzel, C.H.Huang, S.B.Gabelli, E.Oldfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.81
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 58.197, 58.197, 390.223, 90.00, 90.00, 120.00
R / Rfree (%) 21.7 / 28

Other elements in 3id0:

The structure of Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Bisphosphono-Ethyl)Pyridinium also contains other interesting chemical elements:

Fluorine (F) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Bisphosphono-Ethyl)Pyridinium (pdb code 3id0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Bisphosphono-Ethyl)Pyridinium, PDB code: 3id0:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3id0

Go back to Magnesium Binding Sites List in 3id0
Magnesium binding site 1 out of 3 in the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Bisphosphono-Ethyl)Pyridinium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Bisphosphono-Ethyl)Pyridinium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:19.6
occ:1.00
 OD2 A:ASP98 2.3 31.4 1.0
OD2 A:ASP102 2.3 58.5 1.0
O4 A:NI9363 2.5 24.6 1.0
O3 A:NI9363 2.9 15.8 1.0
CG A:ASP102 3.1 41.0 1.0
CG A:ASP98 3.2 29.1 1.0
CB A:ASP102 3.3 40.1 1.0
OD1 A:ASP98 3.6 9.5 1.0
OG A:SER104 3.8 41.0 1.0
O A:ASP98 3.9 33.3 1.0
P1 A:NI9363 3.9 44.4 1.0
OD1 A:ASP99 3.9 46.3 1.0
P2 A:NI9363 4.0 52.9 1.0
MG A:MG403 4.2 36.5 1.0
NH2 A:ARG107 4.2 45.0 1.0
OD1 A:ASP102 4.3 49.8 1.0
C A:ASP98 4.3 33.2 1.0
O5 A:NI9363 4.3 11.7 1.0
CB A:ASP98 4.4 31.6 1.0
C1 A:NI9363 4.5 28.5 1.0
O7 A:NI9363 4.6 32.1 1.0
C2 A:NI9363 4.7 28.0 1.0
N A:ASP99 4.7 33.8 1.0
CB A:SER104 4.7 40.9 1.0
CA A:ASP102 4.8 40.1 1.0
CA A:ASP99 4.8 34.2 1.0
CA A:ASP98 4.9 32.1 1.0
CG2 A:THR267 5.0 46.3 1.0
O6 A:NI9363 5.0 10.1 1.0

Magnesium binding site 2 out of 3 in 3id0

Go back to Magnesium Binding Sites List in 3id0
Magnesium binding site 2 out of 3 in the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Bisphosphono-Ethyl)Pyridinium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Bisphosphono-Ethyl)Pyridinium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:30.5
occ:1.00
 OD2 A:ASP250 2.7 34.3 1.0
O5 A:NI9363 2.7 11.7 1.0
O6 A:NI9363 2.9 10.1 1.0
OD2 A:ASP268 3.5 43.0 1.0
OD1 A:ASP251 3.6 18.9 1.0
O A:ASP250 3.6 42.2 1.0
CG A:ASP250 3.7 41.1 1.0
OD1 A:ASP268 3.8 43.1 1.0
NE2 A:GLN247 4.1 41.4 1.0
C A:ASP250 4.1 42.0 1.0
P1 A:NI9363 4.1 44.4 1.0
CG A:ASP268 4.1 46.3 1.0
P2 A:NI9363 4.1 52.9 1.0
O2 A:NI9363 4.2 24.9 1.0
OD1 A:ASP254 4.3 37.1 1.0
CB A:ASP254 4.3 47.0 1.0
O4 A:NI9363 4.4 24.6 1.0
CB A:ASP250 4.4 41.2 1.0
C1 A:NI9363 4.4 28.5 1.0
CA A:ASP251 4.5 42.6 1.0
N A:ASP251 4.5 42.2 1.0
OD1 A:ASP250 4.5 41.8 1.0
CG A:ASP254 4.7 49.1 1.0
CG A:ASP251 4.7 43.2 1.0
CA A:ASP250 4.9 41.5 1.0
O1 A:NI9363 4.9 49.8 1.0

Magnesium binding site 3 out of 3 in 3id0

Go back to Magnesium Binding Sites List in 3id0
Magnesium binding site 3 out of 3 in the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Bisphosphono-Ethyl)Pyridinium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 3-Fluoro-1-(2-Hydroxy-2,2-Bisphosphono-Ethyl)Pyridinium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:36.5
occ:1.00
 OD1 A:ASP98 2.3 9.5 1.0
O7 A:NI9363 2.4 32.1 1.0
OD2 A:ASP102 2.6 58.5 1.0
OD2 A:ASP170 2.9 59.3 1.0
O4 A:NI9363 3.0 24.6 1.0
P1 A:NI9363 3.2 44.4 1.0
OD1 A:ASP102 3.3 49.8 1.0
CG A:ASP102 3.3 41.0 1.0
CG A:ASP98 3.4 29.1 1.0
OD2 A:ASP98 3.8 31.4 1.0
OE1 A:GLN167 3.8 24.2 1.0
CG A:ASP170 4.1 42.0 1.0
O6 A:NI9363 4.1 10.1 1.0
MG A:MG401 4.2 19.6 1.0
C3 A:NI9363 4.6 39.6 1.0
NZ A:LYS273 4.6 57.5 1.0
CB A:ASP98 4.7 31.6 1.0
NZ A:LYS207 4.7 9.7 1.0
C1 A:NI9363 4.7 28.5 1.0
N A:NI9363 4.7 29.3 1.0
OD1 A:ASP170 4.8 46.4 1.0
CB A:ASP102 4.8 40.1 1.0
CD A:GLN167 4.8 33.8 1.0
C2 A:NI9363 4.9 28.0 1.0
NE2 A:GLN167 5.0 29.1 1.0
C7 A:NI9363 5.0 41.9 1.0

Reference:

C.H.Huang, S.B.Gabelli, E.Oldfield, L.M.Amzel. Binding of Nitrogen-Containing Bisphosphonates (N-Bps) to the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer. Proteins V. 78 888 2010.
ISSN: ISSN 0887-3585
PubMed: 19876942
DOI: 10.1002/PROT.22614
Page generated: Wed Aug 14 16:05:29 2024

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