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

Enzymatic activity of Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(Cyclohexylamino)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-(Cyclohexylamino)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-(Cyclohexylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+, PDB code: 4dzw 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) 65.84 / 3.05
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 57.975, 57.975, 395.026, 90.00, 90.00, 120.00
R / Rfree (%) 22.7 / 29.7

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 2 in 4dzw

Go back to Magnesium Binding Sites List in 4dzw
Magnesium binding site 1 out of 2 in the Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(Cyclohexylamino)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-(Cyclohexylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:40.0
occ:1.00
 O5 A:0MQ401 2.4 44.0 1.0
OD2 A:ASP102 2.7 41.2 1.0
OD2 A:ASP98 3.0 37.9 1.0
C2 A:0MQ401 3.2 44.1 1.0
O3 A:0MQ401 3.2 44.6 1.0
P2 A:0MQ401 3.5 43.1 1.0
C1 A:0MQ401 3.7 44.1 1.0
CG A:ASP102 3.7 41.5 1.0
NZ A:LYS273 3.7 44.3 1.0
O4 A:0MQ401 3.9 43.4 1.0
P1 A:0MQ401 3.9 44.9 1.0
CG A:ASP98 4.0 36.3 1.0
N1 A:0MQ401 4.1 44.6 1.0
CE A:LYS273 4.1 45.1 1.0
OD1 A:ASP98 4.3 37.4 1.0
OD1 A:ASP102 4.3 40.6 1.0
O2 A:0MQ401 4.4 45.1 1.0
O6 A:0MQ401 4.7 42.5 1.0
CB A:ASP102 4.8 41.8 1.0

Magnesium binding site 2 out of 2 in 4dzw

Go back to Magnesium Binding Sites List in 4dzw
Magnesium binding site 2 out of 2 in the Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(Cyclohexylamino)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-(Cyclohexylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:27.0
occ:1.00
 OD2 A:ASP250 2.5 50.1 1.0
O6 A:0MQ401 2.6 42.5 1.0
O2 A:0MQ401 2.7 45.1 1.0
O5 A:0MQ401 3.2 44.0 1.0
OD2 A:ASP268 3.3 51.4 1.0
P2 A:0MQ401 3.5 43.1 1.0
CG A:ASP250 3.6 49.7 1.0
OD1 A:ASP268 3.7 52.2 1.0
OD1 A:ASP254 3.8 49.5 1.0
CG A:ASP268 3.9 52.0 1.0
OD1 A:ASP251 4.1 47.6 1.0
P1 A:0MQ401 4.2 44.9 1.0
NZ A:LYS264 4.3 59.1 1.0
CB A:ASP254 4.3 50.4 1.0
NE2 A:GLN247 4.3 49.2 1.0
OD1 A:ASP250 4.3 50.6 1.0
CG A:ASP254 4.3 50.0 1.0
O A:ASP250 4.5 48.9 1.0
C1 A:0MQ401 4.6 44.1 1.0
CB A:ASP250 4.7 49.1 1.0
C A:ASP250 4.7 48.8 1.0
O4 A:0MQ401 4.7 43.4 1.0
O3 A:0MQ401 4.9 44.6 1.0
CA A:ASP251 4.9 48.6 1.0
N A:ASP251 5.0 48.7 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 13:31:41 2024

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