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Magnesium in PDB 3ick: Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with Minodronate and Isopentenyl Disphosphate

Enzymatic activity of Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with Minodronate and Isopentenyl Disphosphate

All present enzymatic activity of Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with Minodronate and Isopentenyl Disphosphate:
2.5.1.10;

Protein crystallography data

The structure of Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with Minodronate and Isopentenyl Disphosphate, PDB code: 3ick 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) 39.81 / 2.40
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 58.100, 58.100, 390.567, 90.00, 90.00, 120.00
R / Rfree (%) 18.1 / 25.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with Minodronate and Isopentenyl Disphosphate (pdb code 3ick). 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 Minodronate and Isopentenyl Disphosphate, PDB code: 3ick:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3ick

Go back to Magnesium Binding Sites List in 3ick
Magnesium binding site 1 out of 3 in the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with Minodronate and Isopentenyl Disphosphate


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 Minodronate and Isopentenyl Disphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:25.9
occ:1.00
 O4 A:M0N363 2.1 28.3 1.0
OD2 A:ASP98 2.1 35.3 1.0
O1 A:M0N363 2.1 32.3 1.0
O A:HOH365 2.2 29.6 1.0
OD2 A:ASP102 2.2 32.7 1.0
O A:HOH366 2.2 30.4 1.0
CG A:ASP98 2.9 35.3 1.0
OD1 A:ASP98 3.1 35.3 1.0
MG A:MG403 3.2 30.5 1.0
CG A:ASP102 3.2 34.2 1.0
P2 A:M0N363 3.3 30.1 1.0
P1 A:M0N363 3.4 29.2 1.0
CB A:ASP102 3.6 35.2 1.0
C8 A:M0N363 3.7 27.4 1.0
O6 A:M0N363 3.8 33.8 1.0
C9 A:M0N363 3.8 29.6 1.0
O3 A:M0N363 4.0 32.0 1.0
O A:HOH453 4.0 28.8 1.0
OD1 A:ASP102 4.3 31.5 1.0
O A:ASP98 4.3 32.4 1.0
CB A:ASP98 4.3 32.6 1.0
O A:HOH364 4.3 37.0 1.0
O A:HOH376 4.4 30.4 1.0
OD1 A:ASP99 4.4 32.6 1.0
OG A:SER104 4.5 37.2 1.0
O5 A:M0N363 4.6 24.7 1.0
NH1 A:ARG107 4.6 44.6 1.0
NH2 A:ARG107 4.6 51.3 1.0
C A:ASP98 4.6 32.4 1.0
O2 A:M0N363 4.6 31.4 1.0
O A:HOH367 4.7 30.4 1.0
O A:HOH369 4.7 28.1 1.0
O A:HOH370 4.8 37.7 1.0
MG A:MG402 4.8 28.1 1.0
C2 A:M0N363 4.9 28.1 1.0
O A:HOH444 4.9 24.9 1.0

Magnesium binding site 2 out of 3 in 3ick

Go back to Magnesium Binding Sites List in 3ick
Magnesium binding site 2 out of 3 in the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with Minodronate and Isopentenyl Disphosphate


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 Minodronate and Isopentenyl Disphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:28.1
occ:1.00
 O6 A:M0N363 1.9 33.8 1.0
O A:HOH369 2.0 28.1 1.0
O3 A:M0N363 2.1 32.0 1.0
O A:HOH368 2.1 19.4 1.0
O A:HOH372 2.2 20.7 1.0
OD2 A:ASP250 2.3 28.6 1.0
C9 A:M0N363 3.0 29.6 1.0
P2 A:M0N363 3.2 30.1 1.0
P1 A:M0N363 3.2 29.2 1.0
CG A:ASP250 3.3 32.8 1.0
OD1 A:ASP250 3.7 32.8 1.0
O A:M0N363 3.8 32.3 1.0
O A:HOH377 3.8 35.6 1.0
O A:HOH366 3.9 30.4 1.0
OD1 A:ASP254 4.0 40.7 1.0
OD2 A:ASP268 4.0 31.3 1.0
O1 A:M0N363 4.1 32.3 1.0
O4 A:M0N363 4.1 28.3 1.0
OD1 A:ASP268 4.1 35.6 1.0
NE2 A:GLN247 4.2 32.2 1.0
O5 A:M0N363 4.2 24.7 1.0
O2 A:M0N363 4.3 31.4 1.0
O A:ASP250 4.5 33.1 1.0
CG A:ASP268 4.5 33.1 1.0
C8 A:M0N363 4.5 27.4 1.0
CG A:ASP254 4.5 40.6 1.0
CB A:ASP250 4.5 32.9 1.0
NZ A:LYS264 4.6 35.0 1.0
OD1 A:ASP251 4.7 32.5 1.0
O A:HOH453 4.7 28.8 1.0
CB A:ASP254 4.7 41.7 1.0
C A:ASP250 4.8 33.2 1.0
CE A:LYS264 4.8 35.6 1.0
MG A:MG401 4.8 25.9 1.0

Magnesium binding site 3 out of 3 in 3ick

Go back to Magnesium Binding Sites List in 3ick
Magnesium binding site 3 out of 3 in the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with Minodronate and Isopentenyl Disphosphate


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 Minodronate and Isopentenyl Disphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:30.5
occ:1.00
 O A:HOH370 2.0 37.7 1.0
OD2 A:ASP102 2.1 32.7 1.0
O A:HOH364 2.2 37.0 1.0
O A:HOH367 2.2 30.4 1.0
OD1 A:ASP98 2.2 35.3 1.0
O1 A:M0N363 2.2 32.3 1.0
CG A:ASP102 2.9 34.2 1.0
OD1 A:ASP102 3.1 31.5 1.0
MG A:MG401 3.2 25.9 1.0
CG A:ASP98 3.3 35.3 1.0
P1 A:M0N363 3.3 29.2 1.0
OD2 A:ASP170 3.5 33.6 1.0
O2 A:M0N363 3.6 31.4 1.0
OD2 A:ASP98 3.6 35.3 1.0
NZ A:LYS273 4.0 32.2 1.0
CG A:ASP170 4.1 30.6 1.0
OE1 A:GLN167 4.2 30.6 1.0
O3 A:M0N363 4.2 32.0 1.0
O A:HOH377 4.2 35.6 1.0
NE2 A:GLN167 4.3 31.4 1.0
O A:HOH366 4.4 30.4 1.0
CB A:ASP102 4.4 35.2 1.0
OD1 A:ASP170 4.4 34.2 1.0
C8 A:M0N363 4.5 27.4 1.0
CB A:ASP98 4.6 32.6 1.0
CD A:GLN167 4.7 30.4 1.0
C2 A:M0N363 4.8 28.1 1.0
O A:HOH376 4.8 30.4 1.0
NZ A:LYS207 4.8 24.1 1.0
O4 A:M0N363 4.8 28.3 1.0
C9 A:M0N363 4.8 29.6 1.0
N2 A:M0N363 4.9 27.7 1.0
C3 A:M0N363 4.9 29.5 1.0
O A:HOH365 4.9 29.6 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 16:03:57 2024

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