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

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

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

Protein crystallography data

The structure of Crystal Structure of Trypanosoma Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Pentylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+, PDB code: 4dwb 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) 19.89 / 2.10
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 57.871, 57.871, 392.442, 90.00, 90.00, 120.00
R / Rfree (%) 21.8 / 27.9

Other elements in 4dwb:

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

Magnesium binding site 1 out of 3 in 4dwb

Go back to Magnesium Binding Sites List in 4dwb
Magnesium binding site 1 out of 3 in the Crystal Structure of Trypanosoma Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Pentylamino)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 Trypanosoma Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Pentylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg506

b:40.9
occ:1.00
 O A:HOH601 2.2 30.2 1.0
OD2 A:ASP102 2.2 37.1 1.0
OD1 A:ASP98 2.3 32.6 1.0
O A:HOH623 2.3 46.0 1.0
O14 A:0M7509 2.5 35.9 1.0
O A:HOH602 2.6 39.3 1.0
MG A:MG507 3.1 43.3 1.0
CG A:ASP102 3.1 38.1 1.0
CG A:ASP98 3.2 31.2 1.0
OD1 A:ASP102 3.4 38.4 1.0
OD2 A:ASP98 3.4 31.7 1.0
OD2 A:ASP170 3.6 33.0 1.0
P1 A:0M7509 3.7 33.6 1.0
O16 A:0M7509 3.8 35.3 1.0
NE2 A:GLN167 3.9 27.8 1.0
CG A:ASP170 4.1 25.8 1.0
NZ A:LYS273 4.1 38.8 1.0
OE1 A:GLN167 4.3 33.0 1.0
OD1 A:ASP170 4.3 35.0 1.0
CD A:GLN167 4.4 31.5 1.0
C4 A:0M7509 4.5 35.8 1.0
O A:HOH604 4.6 29.3 1.0
CB A:ASP102 4.6 38.0 1.0
CB A:ASP98 4.6 27.1 1.0
C7 A:0M7509 4.7 39.0 1.0
C2 A:0M7509 4.8 34.1 1.0
O15 A:0M7509 4.8 31.4 1.0
O13 A:0M7509 4.8 30.6 1.0
NZ A:LYS207 4.8 28.8 1.0
O A:HOH603 4.9 24.7 1.0

Magnesium binding site 2 out of 3 in 4dwb

Go back to Magnesium Binding Sites List in 4dwb
Magnesium binding site 2 out of 3 in the Crystal Structure of Trypanosoma Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Pentylamino)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 Trypanosoma Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Pentylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg507

b:43.3
occ:1.00
 O14 A:0M7509 2.0 35.9 1.0
O A:HOH604 2.0 29.3 1.0
O13 A:0M7509 2.1 30.6 1.0
OD2 A:ASP102 2.3 37.1 1.0
O A:HOH603 2.5 24.7 1.0
OD2 A:ASP98 2.5 31.7 1.0
MG A:MG506 3.1 40.9 1.0
P1 A:0M7509 3.3 33.6 1.0
P3 A:0M7509 3.3 29.9 1.0
CG A:ASP102 3.4 38.1 1.0
CG A:ASP98 3.4 31.2 1.0
OD1 A:ASP98 3.5 32.6 1.0
C2 A:0M7509 3.6 34.1 1.0
C4 A:0M7509 3.7 35.8 1.0
O15 A:0M7509 3.9 31.4 1.0
CB A:ASP102 3.9 38.0 1.0
O11 A:0M7509 4.1 33.3 1.0
NH2 A:ARG107 4.1 20.2 1.0
O A:HOH602 4.2 39.3 1.0
O A:HOH605 4.3 18.7 1.0
O16 A:0M7509 4.4 35.3 1.0
OD1 A:ASP102 4.5 38.4 1.0
O12 A:0M7509 4.5 34.7 1.0
OG A:SER104 4.7 40.5 1.0
O A:HOH623 4.7 46.0 1.0
MG A:MG508 4.9 30.6 1.0
CB A:ASP98 4.9 27.1 1.0
O A:HOH601 4.9 30.2 1.0
OD1 A:ASP99 4.9 22.5 1.0
O A:ASP98 5.0 28.5 1.0

Magnesium binding site 3 out of 3 in 4dwb

Go back to Magnesium Binding Sites List in 4dwb
Magnesium binding site 3 out of 3 in the Crystal Structure of Trypanosoma Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Pentylamino)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 Trypanosoma Cruzi Farnesyl Diphosphate Synthase in Complex with [2-(N-Pentylamino)Ethane-1,1-Diyl]Bisphosphonic Acid and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg508

b:30.6
occ:1.00
 O15 A:0M7509 1.8 31.4 1.0
O11 A:0M7509 2.1 33.3 1.0
O A:HOH606 2.1 26.3 1.0
O A:HOH605 2.2 18.7 1.0
O A:HOH607 2.2 30.1 1.0
OD2 A:ASP250 2.3 37.9 1.0
P1 A:0M7509 3.2 33.6 1.0
CG A:ASP250 3.2 34.4 1.0
P3 A:0M7509 3.3 29.9 1.0
C2 A:0M7509 3.4 34.1 1.0
OD1 A:ASP250 3.6 36.8 1.0
OD1 A:ASP254 4.0 29.9 1.0
NZ A:LYS264 4.0 40.4 1.0
O14 A:0M7509 4.1 35.9 1.0
O13 A:0M7509 4.1 30.6 1.0
NE2 A:GLN247 4.1 24.5 1.0
O16 A:0M7509 4.2 35.3 1.0
O A:HOH604 4.2 29.3 1.0
OD2 A:ASP268 4.3 36.7 1.0
O12 A:0M7509 4.4 34.7 1.0
CB A:ASP250 4.4 31.7 1.0
OD1 A:ASP251 4.5 28.4 1.0
OD1 A:ASP268 4.5 41.3 1.0
CE A:LYS264 4.5 43.9 1.0
C A:ASP250 4.8 30.9 1.0
CG A:ASP254 4.8 35.5 1.0
CG A:ASP268 4.8 43.0 1.0
O A:ASP250 4.8 28.5 1.0
MG A:MG507 4.9 43.3 1.0
CB A:ASP254 4.9 36.7 1.0
C4 A:0M7509 4.9 35.8 1.0
N A:ASP251 5.0 32.1 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 13:27:40 2024

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