Sodium in PDB 4yar: 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H

All present enzymatic activity of 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H:
1.13.11.72;

The structure of 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H, PDB code: 4yar was solved by J.R.Chekan, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.75 / 1.75
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	85.286, 95.953, 101.142, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 23.8

The structure of 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H also contains other interesting chemical elements:

Cadmium

(Cd)

10 atoms

The binding sites of Sodium atom in the 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H (pdb code 4yar). 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 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H, PDB code: 4yar:

Sodium binding site 1 out of 1 in the 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2-Hydroxyethylphosphonate Dioxygenase (Hepd) E176H within 5.0Å range: probe atom residue distance (Å) B Occ A:Na511 b:12.5 occ:1.00 O A:HOH605 1.4 49.4 1.0 O A:HOH783 2.0 45.3 1.0 OE1 A:GLN296 2.2 85.0 1.0 ND1 A:HIS330 2.4 37.0 1.0 O A:HOH806 2.6 27.8 1.0 O A:HOH702 2.6 26.3 1.0 CE1 A:HIS330 2.7 20.0 1.0 CG A:HIS330 3.3 31.6 1.0 CD A:GLN296 3.3 78.5 1.0 NE2 A:HIS330 3.5 38.6 1.0 NE2 A:GLN296 3.7 79.9 1.0 CD2 A:HIS330 3.9 35.8 1.0 CB A:HIS330 4.0 24.0 1.0 NZ A:LYS302 4.1 37.0 1.0 CD A:LYS302 4.3 50.4 1.0 O A:HOH758 4.3 41.5 1.0 CG A:GLN296 4.6 80.1 1.0 N A:HIS297 4.6 69.4 1.0 CE A:LYS302 4.7 50.7 1.0 CA A:GLN296 4.8 63.7 1.0 N A:HIS330 4.9 20.1 1.0 CB A:ALA328 4.9 19.9 1.0

S.C.Peck, J.R.Chekan, E.C.Ulrich, S.K.Nair, W.A.Van Der Donk. A Common Late-Stage Intermediate in Catalysis By 2-Hydroxyethylphosphonate Dioxygenase and Methylphosphonate Synthase. J.Am.Chem.Soc. 2015.
ISSN: ESSN 1520-5126
PubMed: 25699631
DOI: 10.1021/JACS.5B00282