Sodium in PDB 6dft: Trypanosoma Brucei Deoxyhypusine Synthase

All present enzymatic activity of Trypanosoma Brucei Deoxyhypusine Synthase:
2.5.1.46;

The structure of Trypanosoma Brucei Deoxyhypusine Synthase, PDB code: 6dft was solved by D.R.Tomchick, M.A.Phillips, G.A.Afanador, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.75 / 3.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.358, 242.162, 266.303, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 26.2

The binding sites of Sodium atom in the Trypanosoma Brucei Deoxyhypusine Synthase (pdb code 6dft). 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 Trypanosoma Brucei Deoxyhypusine Synthase, PDB code: 6dft:

Sodium binding site 1 out of 1 in the Trypanosoma Brucei Deoxyhypusine Synthase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Trypanosoma Brucei Deoxyhypusine Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:27.4 occ:1.00 ND2 A:ASN100 3.5 38.2 1.0 OH A:TYR213 3.8 51.1 1.0 NE2 A:HIS167 3.9 46.4 1.0 CB A:PHE208 4.0 47.8 1.0 C4N A:NAD502 4.0 43.9 1.0 OE2 B:GLU290 4.1 52.9 1.0 CE1 A:HIS167 4.1 59.5 1.0 C7N A:NAD502 4.2 41.4 1.0 CE2 A:TYR213 4.2 49.3 1.0 N7N A:NAD502 4.3 43.0 1.0 O7N A:NAD502 4.3 45.1 1.0 CZ A:TYR213 4.5 55.3 1.0 C3N A:NAD502 4.5 41.5 1.0 ND2 B:ASN301 4.6 47.9 1.0 CG A:ASN100 4.7 42.5 1.0 O A:HIS207 4.7 50.2 1.0 CG A:PHE208 4.7 46.2 1.0 CD1 A:PHE208 4.9 59.6 1.0 CG B:ASN301 5.0 40.9 1.0 CA A:PHE208 5.0 43.0 1.0 C5N A:NAD502 5.0 49.4 1.0

G.A.Afanador, D.R.Tomchick, M.A.Phillips. Trypanosomatid Deoxyhypusine Synthase Activity Is Dependent on Shared Active-Site Complementation Between Pseudoenzyme Paralogs. Structure V. 26 1499 2018.
ISSN: ISSN 1878-4186
PubMed: 30197036
DOI: 10.1016/J.STR.2018.07.012