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Magnesium in PDB 3icn: Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with Isopentenyl Pyrophosphate and 3-Fluoro-1-(2-Hydroxy-2,2-Bis- Phosphono-Ethyl)-Pyridinium

Enzymatic activity of Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with Isopentenyl Pyrophosphate and 3-Fluoro-1-(2-Hydroxy-2,2-Bis- Phosphono-Ethyl)-Pyridinium

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

Protein crystallography data

The structure of Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with Isopentenyl Pyrophosphate and 3-Fluoro-1-(2-Hydroxy-2,2-Bis- Phosphono-Ethyl)-Pyridinium, PDB code: 3icn 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) 34.97 / 2.40
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 57.976, 57.976, 389.756, 90.00, 90.00, 120.00
R / Rfree (%) 17.5 / 24.3

Other elements in 3icn:

The structure of Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with Isopentenyl Pyrophosphate and 3-Fluoro-1-(2-Hydroxy-2,2-Bis- Phosphono-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 Isopentenyl Pyrophosphate and 3-Fluoro-1-(2-Hydroxy-2,2-Bis- Phosphono-Ethyl)-Pyridinium (pdb code 3icn). 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 Isopentenyl Pyrophosphate and 3-Fluoro-1-(2-Hydroxy-2,2-Bis- Phosphono-Ethyl)-Pyridinium, PDB code: 3icn:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3icn

Go back to Magnesium Binding Sites List in 3icn
Magnesium binding site 1 out of 3 in the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with Isopentenyl Pyrophosphate and 3-Fluoro-1-(2-Hydroxy-2,2-Bis- Phosphono-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 Isopentenyl Pyrophosphate and 3-Fluoro-1-(2-Hydroxy-2,2-Bis- Phosphono-Ethyl)-Pyridinium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:25.6
occ:1.00
 O5 A:NI9363 2.0 28.2 1.0
O6 A:NI9363 2.0 30.3 1.0
O A:HOH554 2.1 16.8 1.0
OD2 A:ASP102 2.1 23.9 1.0
O A:HOH564 2.1 24.2 1.0
OD2 A:ASP98 2.2 23.4 1.0
MG A:MG403 2.9 27.5 1.0
CG A:ASP98 3.0 27.0 1.0
OD1 A:ASP98 3.1 21.0 1.0
CG A:ASP102 3.3 27.8 1.0
P2 A:NI9363 3.3 29.0 1.0
P1 A:NI9363 3.4 27.4 1.0
C1 A:NI9363 3.6 28.0 1.0
C2 A:NI9363 3.8 28.2 1.0
CB A:ASP102 3.9 28.2 1.0
O3 A:NI9363 4.1 23.6 1.0
O4 A:NI9363 4.2 27.2 1.0
O A:HOH617 4.2 59.1 1.0
O A:HOH579 4.2 36.6 1.0
O A:ASP98 4.2 28.3 1.0
NH2 A:ARG107 4.3 30.7 1.0
OD1 A:ASP102 4.3 23.5 1.0
O1 A:NI9363 4.4 28.1 1.0
CB A:ASP98 4.4 26.7 1.0
OD1 A:ASP99 4.4 26.5 1.0
O7 A:NI9363 4.5 23.9 1.0
OG A:SER104 4.5 30.9 1.0
C A:ASP98 4.6 27.5 1.0
O A:HOH440 4.6 22.6 1.0
O A:HOH364 4.7 29.8 1.0
O A:HOH365 4.8 20.4 1.0
N A:NI9363 4.8 29.2 1.0
O A:HOH567 4.9 34.5 1.0

Magnesium binding site 2 out of 3 in 3icn

Go back to Magnesium Binding Sites List in 3icn
Magnesium binding site 2 out of 3 in the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with Isopentenyl Pyrophosphate and 3-Fluoro-1-(2-Hydroxy-2,2-Bis- Phosphono-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 Isopentenyl Pyrophosphate and 3-Fluoro-1-(2-Hydroxy-2,2-Bis- Phosphono-Ethyl)-Pyridinium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:33.7
occ:1.00
 O3 A:NI9363 1.9 23.6 1.0
O4 A:NI9363 2.1 27.2 1.0
O A:HOH555 2.1 24.9 1.0
O A:HOH364 2.3 29.8 1.0
OD2 A:ASP250 2.3 24.0 1.0
CG A:ASP250 3.3 29.3 1.0
P2 A:NI9363 3.3 29.0 1.0
P1 A:NI9363 3.4 27.4 1.0
O2 A:NI9363 3.6 27.6 1.0
C1 A:NI9363 3.7 28.0 1.0
OD1 A:ASP250 3.8 27.1 1.0
O A:HOH433 3.8 26.1 1.0
O6 A:NI9363 4.0 30.3 1.0
O5 A:NI9363 4.0 28.2 1.0
OD2 A:ASP268 4.0 29.1 1.0
O A:ASP250 4.1 29.6 1.0
OD1 A:ASP254 4.1 34.3 1.0
O A:HOH543 4.2 42.5 1.0
OD1 A:ASP268 4.2 28.1 1.0
NE2 A:GLN247 4.2 23.8 1.0
O A:HOH564 4.2 24.2 1.0
O1 A:NI9363 4.4 28.1 1.0
NZ A:LYS264 4.4 34.4 1.0
OD1 A:ASP251 4.4 29.0 1.0
CB A:ASP250 4.5 29.3 1.0
C A:ASP250 4.5 29.8 1.0
O A:HOH579 4.5 36.6 1.0
O7 A:NI9363 4.6 23.9 1.0
CG A:ASP268 4.6 29.8 1.0
CG A:ASP254 4.7 32.1 1.0
CB A:ASP254 4.7 31.4 1.0
CE A:LYS264 4.8 32.9 1.0
N A:ASP251 5.0 29.3 1.0

Magnesium binding site 3 out of 3 in 3icn

Go back to Magnesium Binding Sites List in 3icn
Magnesium binding site 3 out of 3 in the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with Isopentenyl Pyrophosphate and 3-Fluoro-1-(2-Hydroxy-2,2-Bis- Phosphono-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 Isopentenyl Pyrophosphate and 3-Fluoro-1-(2-Hydroxy-2,2-Bis- Phosphono-Ethyl)-Pyridinium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:27.5
occ:1.00
 O A:HOH617 1.3 59.1 1.0
OD1 A:ASP98 2.1 21.0 1.0
O6 A:NI9363 2.2 30.3 1.0
OD2 A:ASP102 2.3 23.9 1.0
O A:HOH567 2.4 34.5 1.0
O A:HOH365 2.4 20.4 1.0
MG A:MG401 2.9 25.6 1.0
CG A:ASP98 3.1 27.0 1.0
P1 A:NI9363 3.1 27.4 1.0
O7 A:NI9363 3.2 23.9 1.0
CG A:ASP102 3.2 27.8 1.0
OD1 A:ASP102 3.4 23.5 1.0
OD2 A:ASP98 3.5 23.4 1.0
O A:HOH564 3.7 24.2 1.0
OD2 A:ASP170 3.8 34.9 1.0
O A:HOH433 4.1 26.1 1.0
O4 A:NI9363 4.2 27.2 1.0
C1 A:NI9363 4.3 28.0 1.0
C2 A:NI9363 4.4 28.2 1.0
CG A:ASP170 4.4 30.0 1.0
NE2 A:GLN167 4.4 22.2 1.0
NZ A:LYS273 4.4 34.6 1.0
CB A:ASP98 4.4 26.7 1.0
C3 A:NI9363 4.4 30.6 1.0
O5 A:NI9363 4.4 28.2 1.0
OD1 A:ASP170 4.4 28.7 1.0
N A:NI9363 4.4 29.2 1.0
CB A:ASP102 4.6 28.2 1.0
OE1 A:GLN167 4.6 28.7 1.0
O A:HOH554 4.7 16.8 1.0
O A:HOH440 4.8 22.6 1.0
NZ A:LYS207 4.8 22.4 1.0
O A:ASP98 4.8 28.3 1.0
CD A:GLN167 5.0 25.7 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 16:04:34 2024

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