Magnesium in PDB 8qfw: Murine Pyridoxal Phosphatase in Complex with 7,8-Dihydroxyflavone

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

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

Resolution Low / High (Å)	44.64 / 2.00
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	167.011, 167.011, 167.011, 90, 90, 90
R / Rfree (%)	18.4 / 20.9

The binding sites of Magnesium atom in the Murine Pyridoxal Phosphatase in Complex with 7,8-Dihydroxyflavone (pdb code 8qfw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Murine Pyridoxal Phosphatase in Complex with 7,8-Dihydroxyflavone, PDB code: 8qfw:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Murine Pyridoxal Phosphatase in Complex with 7,8-Dihydroxyflavone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Murine Pyridoxal Phosphatase in Complex with 7,8-Dihydroxyflavone within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:33.0 occ:1.00 O4 A:PO4302 2.0 32.5 1.0 O A:HOH447 2.1 32.3 1.0 OD1 A:ASP234 2.1 35.1 1.0 O A:HOH445 2.1 33.9 1.0 OD2 A:ASP25 2.2 36.9 1.0 O A:ASP27 2.2 32.0 1.0 CG A:ASP234 3.1 34.5 1.0 CG A:ASP25 3.2 36.1 1.0 C A:ASP27 3.3 34.5 1.0 OD2 A:ASP234 3.4 34.8 1.0 P A:PO4302 3.4 33.9 1.0 HB2 A:ASP27 3.4 45.6 1.0 OD1 A:ASP25 3.6 33.7 1.0 O A:HOH511 3.7 45.6 1.0 HG23 A:VAL29 3.8 41.1 1.0 O3 A:PO4302 3.8 34.1 1.0 OD2 A:ASP239 3.9 33.5 1.0 HA3 A:GLY28 4.0 40.4 1.0 H A:ASP234 4.0 39.8 1.0 O1 A:PO4302 4.0 32.2 1.0 CA A:ASP27 4.1 33.6 1.0 H A:ASP27 4.1 38.6 1.0 CB A:ASP27 4.2 38.0 1.0 HB2 A:ARG235 4.2 45.7 1.0 N A:ASP27 4.2 32.1 1.0 O A:HOH467 4.2 37.9 1.0 HZ3 A:LYS209 4.3 41.4 1.0 N A:GLY28 4.4 35.1 1.0 O A:HOH561 4.4 37.4 1.0 CB A:ASP234 4.5 32.7 1.0 HB3 A:ASP27 4.5 45.6 1.0 HB3 A:ASP25 4.5 38.8 1.0 O2 A:PO4302 4.5 35.8 1.0 CB A:ASP25 4.5 32.3 1.0 CA A:GLY28 4.6 33.6 1.0 O A:HOH421 4.6 53.2 1.0 HB3 A:ASP234 4.6 39.3 1.0 CG2 A:VAL29 4.7 34.2 1.0 HG22 A:VAL29 4.7 41.1 1.0 HZ1 A:LYS209 4.7 41.4 1.0 N A:ASP234 4.8 33.1 1.0 H A:CYS26 4.8 36.1 1.0 HD2 A:ARG235 4.8 50.6 1.0 C A:CYS26 4.9 33.4 1.0 CG A:ASP239 4.9 36.5 1.0 HG23 A:VAL257 4.9 52.9 1.0 NZ A:LYS209 5.0 34.4 1.0 HB2 A:ASP25 5.0 38.8 1.0 H A:ARG235 5.0 42.5 1.0 OD1 A:ASP239 5.0 33.1 1.0

Magnesium binding site 2 out of 2 in the Murine Pyridoxal Phosphatase in Complex with 7,8-Dihydroxyflavone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Murine Pyridoxal Phosphatase in Complex with 7,8-Dihydroxyflavone within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:37.8 occ:1.00 O B:HOH421 1.9 40.0 1.0 O4 B:PO4302 2.1 40.9 1.0 OD1 B:ASP234 2.1 36.0 1.0 OD2 B:ASP25 2.1 40.8 1.0 O B:HOH436 2.2 36.4 1.0 O B:ASP27 2.2 35.7 1.0 CG B:ASP234 3.1 36.5 1.0 CG B:ASP25 3.2 37.9 1.0 OD2 B:ASP234 3.3 38.3 1.0 C B:ASP27 3.4 37.8 1.0 HB2 B:ASP27 3.4 45.6 1.0 P B:PO4302 3.5 44.3 1.0 OD1 B:ASP25 3.7 40.4 1.0 O B:HOH481 3.7 46.2 1.0 OD2 B:ASP239 3.9 38.9 1.0 HG23 B:VAL29 3.9 45.8 1.0 H B:ASP234 4.0 45.0 1.0 O2 B:PO4302 4.0 42.3 1.0 HA3 B:GLY28 4.0 46.6 1.0 HB2 B:ARG235 4.0 46.5 1.0 O3 B:PO4302 4.0 39.7 1.0 CA B:ASP27 4.1 39.1 1.0 CB B:ASP27 4.2 37.9 1.0 H B:ASP27 4.2 44.4 1.0 N B:ASP27 4.3 36.9 1.0 O B:HOH433 4.4 40.3 1.0 N B:GLY28 4.4 39.4 1.0 HB3 B:ASP25 4.4 48.8 1.0 CB B:ASP234 4.4 36.9 1.0 HZ1 B:LYS209 4.5 50.4 1.0 CB B:ASP25 4.5 40.6 1.0 HB3 B:ASP27 4.5 45.6 1.0 O1 B:PO4302 4.6 41.8 1.0 CA B:GLY28 4.6 38.7 1.0 HB3 B:ASP234 4.6 44.4 1.0 N B:ASP234 4.7 37.4 1.0 HD2 B:ARG235 4.8 50.9 1.0 CG B:ASP239 4.8 41.1 1.0 CG2 B:VAL29 4.8 38.1 1.0 H B:ARG235 4.8 44.6 1.0 H B:CYS26 4.8 46.2 1.0 CB B:ARG235 4.9 38.6 1.0 HG22 B:VAL29 4.9 45.8 1.0 HB3 B:ARG235 4.9 46.5 1.0 HZ2 B:LYS209 4.9 50.4 1.0 OD1 B:ASP239 4.9 42.0 1.0 HB2 B:ASP25 4.9 48.8 1.0 HG23 B:VAL257 4.9 48.4 1.0 C B:CYS26 5.0 38.7 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