Magnesium in PDB 9em1: Human Pyridoxal Phosphatase in Complex with 7,8-Dihydroxyflavone and Phosphate

All present enzymatic activity of Human Pyridoxal Phosphatase in Complex with 7,8-Dihydroxyflavone and Phosphate:
3.1.3.16; 3.1.3.74;

The structure of Human Pyridoxal Phosphatase in Complex with 7,8-Dihydroxyflavone and Phosphate, PDB code: 9em1 was solved by M.Brenner, A.Gohla, H.Schindelin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.16 / 1.50
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	53.963, 53.963, 211.752, 90, 90, 90
R / Rfree (%)	17 / 19.4

The binding sites of Magnesium atom in the Human Pyridoxal Phosphatase in Complex with 7,8-Dihydroxyflavone and Phosphate (pdb code 9em1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Human Pyridoxal Phosphatase in Complex with 7,8-Dihydroxyflavone and Phosphate, PDB code: 9em1:

Magnesium binding site 1 out of 1 in the Human Pyridoxal Phosphatase in Complex with 7,8-Dihydroxyflavone and Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Pyridoxal Phosphatase in Complex with 7,8-Dihydroxyflavone and Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:19.7 occ:1.00 O4 A:PO4304 2.0 25.4 1.0 OD2 A:ASP25 2.0 27.5 1.0 O A:HOH449 2.1 23.1 1.0 OD1 A:ASP238 2.1 22.8 1.0 O A:HOH430 2.1 27.1 1.0 O A:ASP27 2.2 22.6 1.0 CG A:ASP25 3.0 25.5 1.0 CG A:ASP238 3.1 22.6 1.0 C A:ASP27 3.4 19.6 1.0 P A:PO4304 3.4 24.5 1.0 OD2 A:ASP238 3.5 23.2 1.0 OD1 A:ASP25 3.5 27.8 1.0 HB2 A:ASP27 3.5 26.2 1.0 HG23 A:VAL29 3.8 28.9 1.0 O A:HOH573 3.9 40.4 1.0 O1 A:PO4304 3.9 25.6 1.0 H A:ASP238 3.9 22.9 1.0 OD2 A:ASP243 4.0 23.7 1.0 O2 A:PO4304 4.0 24.8 1.0 HA3 A:GLY28 4.1 24.6 1.0 H A:ASP27 4.1 26.7 1.0 HB2 A:ARG239 4.1 29.7 1.0 CA A:ASP27 4.1 20.6 1.0 N A:ASP27 4.2 22.3 1.0 CB A:ASP27 4.2 21.8 1.0 O A:HOH574 4.3 41.8 1.0 O A:HOH454 4.3 31.8 1.0 CB A:ASP25 4.3 23.2 1.0 HB3 A:ASP25 4.4 27.9 1.0 N A:GLY28 4.4 20.6 1.0 HZ3 A:LYS213 4.4 46.1 1.0 CB A:ASP238 4.5 20.1 1.0 O3 A:PO4304 4.5 28.2 1.0 HZ1 A:LYS213 4.6 46.1 1.0 HB3 A:ASP238 4.6 24.2 1.0 CG2 A:VAL29 4.7 24.1 1.0 CA A:GLY28 4.7 20.5 1.0 H A:CYS26 4.7 25.3 1.0 O A:HOH638 4.7 42.4 1.0 N A:ASP238 4.7 19.1 1.0 HB3 A:ASP27 4.7 26.2 1.0 HD2 A:ARG239 4.7 34.2 1.0 HB2 A:ASP25 4.7 27.9 1.0 HG21 A:VAL29 4.8 28.9 1.0 C A:CYS26 4.8 23.9 1.0 NZ A:LYS213 4.9 38.5 1.0 CG A:ASP243 4.9 25.0 1.0 OD1 A:ASP243 5.0 26.2 1.0 H A:ARG239 5.0 26.0 1.0 CB A:ARG239 5.0 24.8 1.0 N A:CYS26 5.0 21.1 1.0

M.Brenner, C.Zink, L.Witzinger, A.Keller, K.Hadamek, S.Bothe, M.Neuenschwander, C.Villmann, J.P.Von Kries, H.Schindelin, E.Jeanclos, A.Gohla. 7,8-Dihydroxyflavone Is A Direct Inhibitor of Pyridoxal Phosphatase Elife V.3094 2024.
ISSN: ESSN 2050-084X
DOI: 10.1101/2023.10.04.560852