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

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

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

Protein crystallography data

The structure of Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 1-(2,2-Bis-Phosphono-Ethyl)-3-Butyl-Pyridinium and Isopentenyl Pyrophosphate, PDB code: 3icz 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) 44.94 / 2.15
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 58.398, 58.398, 391.809, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 25.7

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 3 in 3icz

Go back to Magnesium Binding Sites List in 3icz
Magnesium binding site 1 out of 3 in the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 1-(2,2-Bis-Phosphono-Ethyl)-3-Butyl-Pyridinium and Isopentenyl Pyrophosphate


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 1-(2,2-Bis-Phosphono-Ethyl)-3-Butyl-Pyridinium and Isopentenyl Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:26.8
occ:1.00
 O12 A:PB6363 2.0 22.5 1.0
O A:HOH365 2.1 26.9 1.0
OD2 A:ASP98 2.1 25.4 1.0
O A:HOH366 2.1 29.3 1.0
O15 A:PB6363 2.2 26.7 1.0
OD2 A:ASP102 2.2 23.9 1.0
CG A:ASP98 3.0 24.3 1.0
MG A:MG403 3.2 11.7 1.0
P9 A:PB6363 3.3 29.0 1.0
CG A:ASP102 3.3 28.6 1.0
OD1 A:ASP98 3.3 22.8 1.0
P14 A:PB6363 3.4 28.1 1.0
C8 A:PB6363 3.6 27.7 1.0
CB A:ASP102 3.8 28.0 1.0
O A:HOH434 3.8 28.1 1.0
C7 A:PB6363 3.8 28.8 1.0
O11 A:PB6363 4.0 28.2 1.0
O17 A:PB6363 4.1 22.3 1.0
O A:HOH364 4.3 25.2 1.0
CB A:ASP98 4.4 22.6 1.0
O A:HOH369 4.4 27.4 1.0
OG A:SER104 4.4 32.2 1.0
OD1 A:ASP102 4.4 24.8 1.0
O10 A:PB6363 4.4 24.1 1.0
O A:ASP98 4.4 24.2 1.0
OD1 A:ASP99 4.5 29.1 1.0
O16 A:PB6363 4.6 25.4 1.0
NH1 A:ARG107 4.6 27.9 1.0
O A:HOH414 4.6 31.1 1.0
O A:HOH391 4.7 24.7 1.0
C A:ASP98 4.7 24.2 1.0
O A:HOH367 4.8 23.8 1.0
O A:HOH370 4.8 19.8 1.0
N12 A:PB6363 4.9 27.7 1.0
MG A:MG402 4.9 24.8 1.0

Magnesium binding site 2 out of 3 in 3icz

Go back to Magnesium Binding Sites List in 3icz
Magnesium binding site 2 out of 3 in the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 1-(2,2-Bis-Phosphono-Ethyl)-3-Butyl-Pyridinium and Isopentenyl Pyrophosphate


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 1-(2,2-Bis-Phosphono-Ethyl)-3-Butyl-Pyridinium and Isopentenyl Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:24.8
occ:1.00
 O11 A:PB6363 2.0 28.2 1.0
OD2 A:ASP250 2.0 24.9 1.0
O17 A:PB6363 2.1 22.3 1.0
O A:HOH369 2.1 27.4 1.0
O A:HOH368 2.2 23.8 1.0
O A:HOH371 2.2 25.2 1.0
CG A:ASP250 2.9 26.5 1.0
P9 A:PB6363 3.2 29.0 1.0
P14 A:PB6363 3.3 28.1 1.0
OD1 A:ASP250 3.3 22.3 1.0
C8 A:PB6363 3.5 27.7 1.0
O A:HOH377 4.0 28.9 1.0
O12 A:PB6363 4.0 22.5 1.0
NZ A:LYS264 4.0 31.9 1.0
CB A:ASP250 4.2 27.4 1.0
NE2 A:GLN247 4.2 25.3 1.0
OD1 A:ASP254 4.2 41.6 1.0
OD2 A:ASP268 4.2 28.8 1.0
O A:ASP250 4.3 27.2 1.0
O15 A:PB6363 4.3 26.7 1.0
O10 A:PB6363 4.3 24.1 1.0
O A:HOH366 4.4 29.3 1.0
O16 A:PB6363 4.4 25.4 1.0
OD1 A:ASP268 4.5 32.5 1.0
OD1 A:ASP251 4.5 31.0 1.0
C A:ASP250 4.5 28.4 1.0
CE A:LYS264 4.6 34.6 1.0
CB A:ASP254 4.7 34.5 1.0
O A:HOH434 4.8 28.1 1.0
CG A:ASP268 4.8 31.7 1.0
CG A:ASP254 4.8 39.9 1.0
MG A:MG401 4.9 26.8 1.0
N A:ASP251 5.0 27.8 1.0
CA A:ASP250 5.0 28.3 1.0

Magnesium binding site 3 out of 3 in 3icz

Go back to Magnesium Binding Sites List in 3icz
Magnesium binding site 3 out of 3 in the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with 1-(2,2-Bis-Phosphono-Ethyl)-3-Butyl-Pyridinium and Isopentenyl Pyrophosphate


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 1-(2,2-Bis-Phosphono-Ethyl)-3-Butyl-Pyridinium and Isopentenyl Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:11.7
occ:1.00
 O A:HOH370 2.0 19.8 1.0
O A:HOH367 2.0 23.8 1.0
OD1 A:ASP98 2.0 22.8 1.0
O A:HOH364 2.0 25.2 1.0
O15 A:PB6363 2.1 26.7 1.0
OD2 A:ASP102 2.1 23.9 1.0
CG A:ASP102 3.0 28.6 1.0
CG A:ASP98 3.0 24.3 1.0
OD1 A:ASP102 3.1 24.8 1.0
MG A:MG401 3.2 26.8 1.0
P14 A:PB6363 3.3 28.1 1.0
OD2 A:ASP98 3.4 25.4 1.0
O16 A:PB6363 3.4 25.4 1.0
OD2 A:ASP170 3.7 37.9 1.0
NE2 A:GLN167 4.0 20.0 1.0
OE1 A:GLN167 4.0 29.0 1.0
O A:HOH366 4.1 29.3 1.0
NZ A:LYS273 4.1 32.5 1.0
OD1 A:ASP170 4.2 34.5 1.0
CG A:ASP170 4.2 32.4 1.0
O A:HOH377 4.3 28.9 1.0
O17 A:PB6363 4.4 22.3 1.0
CB A:ASP98 4.4 22.6 1.0
CB A:ASP102 4.4 28.0 1.0
CD A:GLN167 4.5 23.1 1.0
C7 A:PB6363 4.5 28.8 1.0
C17 A:PB6363 4.5 27.8 1.0
C8 A:PB6363 4.6 27.7 1.0
N12 A:PB6363 4.7 27.7 1.0
O12 A:PB6363 4.7 22.5 1.0
O A:HOH414 4.7 31.1 1.0
NZ A:LYS207 4.8 20.0 1.0
O A:HOH365 4.8 26.9 1.0
O A:ASP98 4.9 24.2 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 16:05:22 2024

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