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Magnesium in PDB 3icm: Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with Isopentenyl Pyrophosphate, MG2+ and 1-(2-Hydroxy-2,2-Bis- Phosphono-Ethyl)-3-Phenyl-Pyridinium

Enzymatic activity of Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with Isopentenyl Pyrophosphate, MG2+ and 1-(2-Hydroxy-2,2-Bis- Phosphono-Ethyl)-3-Phenyl-Pyridinium

All present enzymatic activity of Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with Isopentenyl Pyrophosphate, MG2+ and 1-(2-Hydroxy-2,2-Bis- Phosphono-Ethyl)-3-Phenyl-Pyridinium:
2.5.1.10;

Protein crystallography data

The structure of Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with Isopentenyl Pyrophosphate, MG2+ and 1-(2-Hydroxy-2,2-Bis- Phosphono-Ethyl)-3-Phenyl-Pyridinium, PDB code: 3icm 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) 40.05 / 2.20
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 58.335, 58.335, 394.229, 90.00, 90.00, 120.00
R / Rfree (%) 18.6 / 25.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with Isopentenyl Pyrophosphate, MG2+ and 1-(2-Hydroxy-2,2-Bis- Phosphono-Ethyl)-3-Phenyl-Pyridinium (pdb code 3icm). 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, MG2+ and 1-(2-Hydroxy-2,2-Bis- Phosphono-Ethyl)-3-Phenyl-Pyridinium, PDB code: 3icm:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3icm

Go back to Magnesium Binding Sites List in 3icm
Magnesium binding site 1 out of 3 in the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with Isopentenyl Pyrophosphate, MG2+ and 1-(2-Hydroxy-2,2-Bis- Phosphono-Ethyl)-3-Phenyl-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, MG2+ and 1-(2-Hydroxy-2,2-Bis- Phosphono-Ethyl)-3-Phenyl-Pyridinium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:35.2
occ:1.00
 O11 A:P2H363 1.9 37.7 1.0
O A:HOH565 2.0 26.6 1.0
OD2 A:ASP98 2.1 28.1 1.0
O A:HOH492 2.2 21.5 1.0
O15 A:P2H363 2.2 38.5 1.0
OD2 A:ASP102 2.2 30.1 1.0
CG A:ASP98 3.1 26.7 1.0
P9 A:P2H363 3.2 40.0 1.0
MG A:MG403 3.3 27.6 1.0
CG A:ASP102 3.3 31.6 1.0
OD1 A:ASP98 3.5 25.7 1.0
P14 A:P2H363 3.5 35.4 1.0
O A:HOH613 3.7 35.2 1.0
C8 A:P2H363 3.8 36.7 1.0
C7 A:P2H363 3.8 36.7 1.0
CB A:ASP102 3.9 31.2 1.0
O12 A:P2H363 3.9 33.6 1.0
O17 A:P2H363 4.2 37.4 1.0
NH1 A:ARG107 4.2 21.5 1.0
OG A:SER104 4.4 31.9 1.0
O10 A:P2H363 4.4 34.1 1.0
OD1 A:ASP102 4.4 31.2 1.0
O A:HOH367 4.4 34.0 1.0
CB A:ASP98 4.5 20.6 1.0
O A:HOH364 4.5 27.6 1.0
OD1 A:ASP99 4.5 19.1 1.0
O16 A:P2H363 4.6 37.9 1.0
O A:HOH391 4.7 36.9 1.0
O A:ASP98 4.7 19.3 1.0
C A:ASP98 4.9 21.1 1.0
MG A:MG402 5.0 31.8 1.0

Magnesium binding site 2 out of 3 in 3icm

Go back to Magnesium Binding Sites List in 3icm
Magnesium binding site 2 out of 3 in the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with Isopentenyl Pyrophosphate, MG2+ and 1-(2-Hydroxy-2,2-Bis- Phosphono-Ethyl)-3-Phenyl-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, MG2+ and 1-(2-Hydroxy-2,2-Bis- Phosphono-Ethyl)-3-Phenyl-Pyridinium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:31.8
occ:1.00
 O12 A:P2H363 2.0 33.6 1.0
O17 A:P2H363 2.1 37.4 1.0
OD2 A:ASP250 2.1 33.0 1.0
O A:HOH368 2.2 35.7 1.0
O A:HOH366 2.2 28.0 1.0
O A:HOH367 2.4 34.0 1.0
CG A:ASP250 3.1 31.6 1.0
P14 A:P2H363 3.3 35.4 1.0
P9 A:P2H363 3.3 40.0 1.0
O13 A:P2H363 3.4 32.5 1.0
C8 A:P2H363 3.4 36.7 1.0
OD1 A:ASP250 3.6 33.7 1.0
O A:HOH482 4.0 31.5 1.0
O11 A:P2H363 4.1 37.7 1.0
O15 A:P2H363 4.1 38.5 1.0
O A:HOH492 4.2 21.5 1.0
NE2 A:GLN247 4.2 26.9 1.0
CB A:ASP250 4.3 29.0 1.0
NZ A:LYS264 4.4 40.5 1.0
O10 A:P2H363 4.4 34.1 1.0
O16 A:P2H363 4.4 37.9 1.0
O A:ASP250 4.4 30.4 1.0
OD2 A:ASP268 4.4 37.6 1.0
OD1 A:ASP254 4.4 34.2 1.0
OD1 A:ASP268 4.5 34.5 1.0
CE A:LYS264 4.5 40.3 1.0
O A:HOH560 4.6 51.2 1.0
O A:HOH613 4.6 35.2 1.0
C A:ASP250 4.6 30.5 1.0
OD1 A:ASP251 4.7 27.9 1.0
CB A:ASP254 4.9 35.1 1.0
C7 A:P2H363 4.9 36.7 1.0
CG A:ASP268 4.9 38.4 1.0
MG A:MG401 5.0 35.2 1.0

Magnesium binding site 3 out of 3 in 3icm

Go back to Magnesium Binding Sites List in 3icm
Magnesium binding site 3 out of 3 in the Trypanosoma Cruzi Farnesyl Diphosphate Synthase Homodimer in Complex with Isopentenyl Pyrophosphate, MG2+ and 1-(2-Hydroxy-2,2-Bis- Phosphono-Ethyl)-3-Phenyl-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, MG2+ and 1-(2-Hydroxy-2,2-Bis- Phosphono-Ethyl)-3-Phenyl-Pyridinium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:27.6
occ:1.00
 OD1 A:ASP98 2.1 25.7 1.0
O A:HOH365 2.2 21.6 1.0
OD2 A:ASP102 2.2 30.1 1.0
O15 A:P2H363 2.3 38.5 1.0
O A:HOH364 2.4 27.6 1.0
CG A:ASP102 3.1 31.6 1.0
CG A:ASP98 3.1 26.7 1.0
OD1 A:ASP102 3.2 31.2 1.0
MG A:MG401 3.3 35.2 1.0
OD2 A:ASP98 3.3 28.1 1.0
P14 A:P2H363 3.4 35.4 1.0
O16 A:P2H363 3.5 37.9 1.0
OD2 A:ASP170 3.7 28.7 1.0
OE1 A:GLN167 3.8 29.2 1.0
NE2 A:GLN167 3.9 18.4 1.0
NZ A:LYS273 4.1 36.2 1.0
C7 A:P2H363 4.1 36.7 1.0
CG A:ASP170 4.2 27.2 1.0
OD1 A:ASP170 4.3 26.5 1.0
CD A:GLN167 4.3 23.6 1.0
O A:HOH482 4.3 31.5 1.0
C17 A:P2H363 4.4 32.9 1.0
O A:HOH492 4.5 21.5 1.0
O17 A:P2H363 4.5 37.4 1.0
CB A:ASP98 4.5 20.6 1.0
CB A:ASP102 4.6 31.2 1.0
C8 A:P2H363 4.6 36.7 1.0
N12 A:P2H363 4.7 35.4 1.0
O11 A:P2H363 4.7 37.7 1.0
NZ A:LYS207 4.8 20.7 1.0
C23 A:P2H363 4.8 34.9 1.0
O A:HOH565 4.9 26.6 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: Mon Dec 14 08:16:41 2020

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