Sodium in PDB 8vfk: Crystal Structure of Delta 109-117 D-Dopachrome Tautomerase (D-Dt)

All present enzymatic activity of Crystal Structure of Delta 109-117 D-Dopachrome Tautomerase (D-Dt):
4.1.1.84;

The structure of Crystal Structure of Delta 109-117 D-Dopachrome Tautomerase (D-Dt), PDB code: 8vfk was solved by A.Parkins, A.Pilien, A.Wolff, M.C.Thompson, G.Pantouris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.38 / 1.59
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	75.496, 75.496, 96.72, 90, 90, 120
R / Rfree (%)	17.6 / 18.5

The binding sites of Sodium atom in the Crystal Structure of Delta 109-117 D-Dopachrome Tautomerase (D-Dt) (pdb code 8vfk). 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 Delta 109-117 D-Dopachrome Tautomerase (D-Dt), PDB code: 8vfk:

Sodium binding site 1 out of 1 in the Crystal Structure of Delta 109-117 D-Dopachrome Tautomerase (D-Dt)


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 Delta 109-117 D-Dopachrome Tautomerase (D-Dt) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:39.9 occ:1.00 O A:HOH327 2.5 42.1 1.0 O A:GLY65 3.1 24.8 1.0 N A:GLY68 3.2 16.6 1.0 C A:GLY65 3.4 20.9 1.0 CA A:GLY68 3.4 18.3 1.0 N A:VAL66 3.7 30.0 1.0 C A:VAL66 3.7 30.0 1.0 N A:VAL67 3.8 30.0 1.0 CA A:VAL66 3.8 30.0 1.0 OD2 A:ASP72 3.9 32.4 1.0 C A:GLY68 4.2 17.3 1.0 O A:HOH334 4.2 20.3 1.0 C A:VAL67 4.2 30.0 1.0 O A:VAL66 4.2 30.0 1.0 CA A:GLY65 4.3 18.4 1.0 N A:THR69 4.4 16.8 1.0 CA A:VAL67 4.6 30.0 1.0 CG A:ASP72 4.8 29.6 1.0 O A:GLY68 4.9 18.2 1.0 CG2 A:THR69 4.9 20.0 1.0

A.Parkins, A.Pilien, A.Wolff, M.C.Thompson, G.Pantouris. The C-Terminal Region of D-Dt Regulates Molecular Recognition For Protein-Ligand Complexes J.Med.Chem. 2024.
ISSN: ISSN 0022-2623
DOI: 10.1021/ACS.JMEDCHEM.4C00177