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Magnesium in PDB 4e1e: Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Hexylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+

Enzymatic activity of Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Hexylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+

All present enzymatic activity of Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Hexylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+:
2.5.1.10;

Protein crystallography data

The structure of Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Hexylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+, PDB code: 4e1e was solved by S.Aripirala, L.M.Amzel, S.B.Gabelli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.97 / 2.65
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 58.575, 58.575, 393.933, 90.00, 90.00, 120.00
R / Rfree (%) 23.2 / 30.8

Other elements in 4e1e:

The structure of Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Hexylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ also contains other interesting chemical elements:

Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Hexylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ (pdb code 4e1e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Hexylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+, PDB code: 4e1e:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4e1e

Go back to Magnesium Binding Sites List in 4e1e
Magnesium binding site 1 out of 3 in the Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Hexylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Hexylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:35.0
occ:1.00
 O A:HOH512 2.1 37.7 1.0
O5 A:0MW404 2.2 42.3 1.0
OD2 A:ASP250 2.2 42.1 1.0
O A:HOH511 2.3 35.0 1.0
O2 A:0MW404 2.3 42.3 1.0
CG A:ASP250 3.2 43.4 1.0
P2 A:0MW404 3.5 41.5 1.0
OD1 A:ASP250 3.6 42.9 1.0
P1 A:0MW404 3.7 43.3 1.0
OD2 A:ASP268 3.8 56.4 1.0
O4 A:0MW404 3.8 41.8 1.0
OD1 A:ASP254 4.0 54.8 1.0
NE2 A:GLN247 4.1 43.8 1.0
OD1 A:ASP268 4.1 57.7 1.0
OD1 A:ASP251 4.2 47.0 1.0
O A:ASP250 4.3 44.4 1.0
C9 A:0MW404 4.3 42.4 1.0
CG A:ASP268 4.4 56.4 1.0
O1 A:0MW404 4.4 44.1 1.0
CG A:ASP254 4.5 54.0 1.0
CB A:ASP250 4.5 44.0 1.0
C A:ASP250 4.5 44.6 1.0
CB A:ASP254 4.6 52.8 1.0
O6 A:0MW404 4.6 41.6 1.0
NZ A:LYS264 4.8 51.5 1.0
O3 A:0MW404 4.9 43.1 1.0
MG A:MG402 4.9 33.3 1.0
N A:ASP251 4.9 45.0 1.0
CE A:LYS264 5.0 52.1 1.0

Magnesium binding site 2 out of 3 in 4e1e

Go back to Magnesium Binding Sites List in 4e1e
Magnesium binding site 2 out of 3 in the Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Hexylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Hexylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:33.3
occ:1.00
 O1 A:0MW404 1.9 44.1 1.0
OD2 A:ASP102 2.2 40.9 1.0
O A:HOH507 2.2 34.8 1.0
O4 A:0MW404 2.4 41.8 1.0
OD2 A:ASP98 2.4 37.3 1.0
P1 A:0MW404 3.1 43.3 1.0
MG A:MG403 3.2 30.5 1.0
C9 A:0MW404 3.3 42.4 1.0
CG A:ASP102 3.3 40.9 1.0
CG A:ASP98 3.5 37.7 1.0
P2 A:0MW404 3.5 41.5 1.0
O A:HOH512 3.6 37.7 1.0
O2 A:0MW404 3.7 42.3 1.0
CB A:ASP102 3.8 41.0 1.0
OD1 A:ASP98 3.8 39.0 1.0
OG A:SER104 4.3 42.2 1.0
O5 A:0MW404 4.3 42.3 1.0
O3 A:0MW404 4.3 43.1 1.0
OD1 A:ASP102 4.4 41.2 1.0
NH2 A:ARG107 4.4 31.9 1.0
O A:HOH509 4.5 35.5 1.0
O6 A:0MW404 4.7 41.6 1.0
OD1 A:ASP99 4.7 35.5 1.0
C8 A:0MW404 4.8 41.8 1.0
CB A:ASP98 4.8 37.0 1.0
O A:ASP98 4.8 38.0 1.0
MG A:MG401 4.9 35.0 1.0
OG1 A:THR267 4.9 55.0 1.0

Magnesium binding site 3 out of 3 in 4e1e

Go back to Magnesium Binding Sites List in 4e1e
Magnesium binding site 3 out of 3 in the Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Hexylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Hexylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:30.5
occ:1.00
 O A:HOH508 2.2 19.8 1.0
O A:HOH510 2.2 16.3 1.0
O4 A:0MW404 2.2 41.8 1.0
OD2 A:ASP102 2.2 40.9 1.0
OD1 A:ASP98 2.3 39.0 1.0
O A:HOH509 2.3 35.5 1.0
CG A:ASP102 3.0 40.9 1.0
OD1 A:ASP102 3.1 41.2 1.0
CG A:ASP98 3.1 37.7 1.0
P2 A:0MW404 3.2 41.5 1.0
O6 A:0MW404 3.2 41.6 1.0
MG A:MG402 3.2 33.3 1.0
OD2 A:ASP98 3.2 37.3 1.0
OD2 A:ASP170 3.7 44.9 1.0
C9 A:0MW404 3.9 42.4 1.0
OE1 A:GLN167 3.9 40.5 1.0
CB A:ASP102 4.4 41.0 1.0
O5 A:0MW404 4.5 42.3 1.0
NE2 A:GLN167 4.5 39.1 1.0
CB A:ASP98 4.5 37.0 1.0
CG A:ASP170 4.5 44.1 1.0
NZ A:LYS273 4.6 53.1 1.0
O1 A:0MW404 4.6 44.1 1.0
CD A:GLN167 4.7 40.2 1.0
C6 A:0MW404 4.8 41.4 1.0
O A:HOH507 4.8 34.8 1.0
NZ A:LYS207 4.9 39.4 1.0
OD1 A:ASP170 4.9 44.1 1.0
O A:ASP98 4.9 38.0 1.0
N1 A:0MW404 4.9 41.9 1.0

Reference:

S.Aripirala, S.H.Szajnman, J.Jakoncic, J.B.Rodriguez, R.Docampo, S.B.Gabelli, L.M.Amzel. Design, Synthesis, Calorimetry, and Crystallographic Analysis of 2-Alkylaminoethyl-1,1-Bisphosphonates As Inhibitors of Trypanosoma Cruzi Farnesyl Diphosphate Synthase. J.Med.Chem. V. 55 6445 2012.
ISSN: ISSN 0022-2623
PubMed: 22715997
DOI: 10.1021/JM300425Y
Page generated: Fri Aug 16 13:33:17 2024

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