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

Enzymatic activity of Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Heptylamino)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-Heptylamino)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-Heptylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+, PDB code: 4dwg 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) 39.89 / 2.01
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 58.173, 58.173, 391.822, 90.00, 90.00, 120.00
R / Rfree (%) 20.2 / 26.6

Other elements in 4dwg:

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

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Heptylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ (pdb code 4dwg). 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-Heptylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+, PDB code: 4dwg:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4dwg

Go back to Magnesium Binding Sites List in 4dwg
Magnesium binding site 1 out of 3 in the Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Heptylamino)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-Heptylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:25.9
occ:1.00
 O3 A:0M8404 1.8 23.0 1.0
O A:HOH724 2.1 29.6 1.0
O A:HOH502 2.1 22.2 1.0
O4 A:0M8404 2.1 28.0 1.0
O A:HOH602 2.2 22.9 1.0
OD2 A:ASP250 2.3 32.6 1.0
CG A:ASP250 3.1 30.0 1.0
P1 A:0M8404 3.3 26.3 1.0
OD1 A:ASP250 3.3 32.1 1.0
P2 A:0M8404 3.4 28.9 1.0
C9 A:0M8404 4.0 29.5 1.0
NE2 A:GLN247 4.1 25.0 1.0
O2 A:0M8404 4.1 28.1 1.0
OD1 A:ASP254 4.1 38.4 1.0
O A:HOH689 4.1 30.4 1.0
O A:HOH722 4.1 23.5 1.0
NZ A:LYS264 4.1 39.7 1.0
O5 A:0M8404 4.2 33.7 1.0
O A:ASP250 4.2 27.8 1.0
O1 A:0M8404 4.3 29.1 1.0
CB A:ASP250 4.4 28.1 1.0
OD1 A:ASP268 4.4 35.9 1.0
OD2 A:ASP268 4.5 30.0 1.0
O6 A:0M8404 4.5 31.6 1.0
C A:ASP250 4.6 27.4 1.0
O A:HOH583 4.6 25.1 1.0
OD1 A:ASP251 4.6 25.4 1.0
CE A:LYS264 4.7 40.4 1.0
CB A:ASP254 4.8 34.6 1.0
CG A:ASP254 4.9 36.9 1.0
CG A:ASP268 4.9 34.4 1.0
MG A:MG402 5.0 32.1 1.0

Magnesium binding site 2 out of 3 in 4dwg

Go back to Magnesium Binding Sites List in 4dwg
Magnesium binding site 2 out of 3 in the Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Heptylamino)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-Heptylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:32.1
occ:1.00
 O5 A:0M8404 2.1 33.7 1.0
O2 A:0M8404 2.2 28.1 1.0
O A:HOH722 2.2 23.5 1.0
OD2 A:ASP98 2.2 26.4 1.0
O A:HOH723 2.3 21.4 1.0
OD2 A:ASP102 2.5 28.0 1.0
MG A:MG403 3.0 29.6 1.0
C9 A:0M8404 3.1 29.5 1.0
CG A:ASP98 3.2 23.1 1.0
P1 A:0M8404 3.3 26.3 1.0
P2 A:0M8404 3.3 28.9 1.0
CG A:ASP102 3.5 29.8 1.0
OD1 A:ASP98 3.6 28.4 1.0
O A:HOH583 3.8 25.1 1.0
NH2 A:ARG107 4.0 19.2 1.0
O3 A:0M8404 4.0 23.0 1.0
CB A:ASP102 4.0 33.0 1.0
O4 A:0M8404 4.0 28.0 1.0
O A:HOH501 4.2 33.5 1.0
O A:HOH502 4.3 22.2 1.0
OG A:SER104 4.5 33.7 1.0
C8 A:0M8404 4.5 29.5 1.0
O A:HOH673 4.5 28.7 1.0
O6 A:0M8404 4.5 31.6 1.0
O1 A:0M8404 4.5 29.1 1.0
OD1 A:ASP99 4.6 19.9 1.0
OD1 A:ASP102 4.6 28.0 1.0
CB A:ASP98 4.6 20.6 1.0
O A:ASP98 4.7 20.2 1.0
O A:HOH619 4.7 23.4 1.0
N1 A:0M8404 4.9 29.2 1.0
O A:HOH503 5.0 26.3 1.0
MG A:MG401 5.0 25.9 1.0
C A:ASP98 5.0 21.9 1.0

Magnesium binding site 3 out of 3 in 4dwg

Go back to Magnesium Binding Sites List in 4dwg
Magnesium binding site 3 out of 3 in the Crystal Structure of Trypanosome Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Heptylamino)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-Heptylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:29.6
occ:1.00
 O5 A:0M8404 2.0 33.7 1.0
OD2 A:ASP102 2.1 28.0 1.0
O A:HOH619 2.1 23.4 1.0
O A:HOH501 2.1 33.5 1.0
OD1 A:ASP98 2.3 28.4 1.0
O A:HOH503 2.3 26.3 1.0
MG A:MG402 3.0 32.1 1.0
CG A:ASP102 3.1 29.8 1.0
CG A:ASP98 3.1 23.1 1.0
OD2 A:ASP98 3.2 26.4 1.0
P2 A:0M8404 3.2 28.9 1.0
OD1 A:ASP102 3.3 28.0 1.0
O6 A:0M8404 3.4 31.6 1.0
OD2 A:ASP170 3.9 29.1 1.0
NZ A:LYS273 4.0 35.5 1.0
C9 A:0M8404 4.0 29.5 1.0
O A:HOH722 4.2 23.5 1.0
O4 A:0M8404 4.2 28.0 1.0
NE2 A:GLN167 4.3 24.7 1.0
O A:HOH689 4.3 30.4 1.0
CG A:ASP170 4.4 25.0 1.0
OE1 A:GLN167 4.4 27.6 1.0
N1 A:0M8404 4.5 29.2 1.0
CB A:ASP102 4.5 33.0 1.0
OD1 A:ASP170 4.5 29.4 1.0
CB A:ASP98 4.6 20.6 1.0
O2 A:0M8404 4.7 28.1 1.0
O A:HOH723 4.8 21.4 1.0
CD A:GLN167 4.9 23.2 1.0
C7 A:0M8404 4.9 25.9 1.0
NZ A:LYS207 4.9 22.1 1.0
C8 A:0M8404 4.9 29.5 1.0
O A:ASP98 5.0 20.2 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 13:28:22 2024

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