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Sodium 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:

Magnesium (Mg) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was 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:

Sodium binding site 1 out of 1 in 4dwb

Go back to Sodium Binding Sites List in 4dwb
Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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:Na505

b:28.0
occ:1.00
 O A:ILE129 2.8 20.8 1.0
O A:HOH625 3.1 20.6 0.5
CG2 A:ILE129 3.5 16.9 1.0
N A:SER133 3.6 21.7 1.0
CB A:LYS132 3.7 21.6 1.0
C A:ILE129 3.7 20.5 1.0
CA A:ILE129 4.0 19.7 1.0
CD A:LYS132 4.1 29.9 1.0
C A:LYS132 4.2 21.6 1.0
OG A:SER133 4.2 28.9 1.0
CB A:ILE129 4.3 21.4 1.0
CA A:LYS132 4.3 20.3 1.0
CG A:LYS132 4.4 22.5 1.0
CA A:SER133 4.4 22.1 1.0
CB A:SER133 4.7 22.9 1.0
CE1 A:HIS93 4.7 18.4 1.0
N A:LYS132 4.8 20.8 1.0
CE A:LYS132 4.9 30.4 1.0
ND1 A:HIS93 4.9 14.9 1.0
N A:ILE130 4.9 20.3 1.0
CG1 A:ILE129 5.0 20.9 1.0
O A:LYS132 5.0 20.9 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: Mon Oct 7 15:00:55 2024

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