Sodium in PDB 8qyt: Human Pyridoxine-5'-Phosphate Oxidase in Complex with Plp

The structure of Human Pyridoxine-5'-Phosphate Oxidase in Complex with Plp, PDB code: 8qyt was solved by L.Antonelli, A.Ilari, A.Fiorillo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.60 / 1.69
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	82.48, 82.48, 59.19, 90, 90, 120
R / Rfree (%)	17.3 / 21.6

The binding sites of Sodium atom in the Human Pyridoxine-5'-Phosphate Oxidase in Complex with Plp (pdb code 8qyt). 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 Human Pyridoxine-5'-Phosphate Oxidase in Complex with Plp, PDB code: 8qyt:

Sodium binding site 1 out of 1 in the Human Pyridoxine-5'-Phosphate Oxidase in Complex with Plp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Pyridoxine-5'-Phosphate Oxidase in Complex with Plp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:55.9 occ:1.00 CB A:GLN71 3.5 41.2 1.0 CG A:GLN71 3.6 43.8 1.0 CA A:GLU68 3.8 30.1 1.0 O A:GLU67 4.0 31.3 1.0 N A:GLU68 4.2 28.7 1.0 CG A:GLU68 4.2 39.9 1.0 CG A:GLU67 4.2 36.9 1.0 C A:GLU67 4.3 30.9 1.0 CB A:GLU68 4.5 31.8 1.0 CD A:GLU67 4.5 46.3 1.0 OE1 A:GLU67 4.6 45.2 1.0 O A:HOH441 4.7 40.4 1.0 O A:GLU68 4.8 30.1 1.0 C A:GLU68 4.8 28.4 1.0 CD A:GLN71 4.9 52.8 1.0 CA A:GLN71 4.9 39.5 1.0

A.Barile, C.Graziani, L.Antonelli, A.Parroni, A.Fiorillo, M.L.Di Salvo, A.Ilari, A.Giorgi, S.Rosignoli, A.Paiardini, R.Contestabile, A.Tramonti. Identification of the Pyridoxal 5'-Phosphate Allosteric Site in Human Pyridox(Am)Ine 5'-Phosphate Oxidase. Protein Sci. V. 33 E4900 2024.
ISSN: ESSN 1469-896X
PubMed: 38284493
DOI: 10.1002/PRO.4900