Magnesium in PDB 5aes: Crystal Structure of Murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with A Pnp-Derived Inhibitor

All present enzymatic activity of Crystal Structure of Murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with A Pnp-Derived Inhibitor:
3.1.3.74;

The structure of Crystal Structure of Murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with A Pnp-Derived Inhibitor, PDB code: 5aes was solved by G.Knobloch, N.Jabari, M.Koehn, A.Gohla, H.Schindelin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.714 / 2.75
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	166.810, 166.810, 166.810, 90.00, 90.00, 90.00
R / Rfree (%)	18.95 / 24.66

The binding sites of Magnesium atom in the Crystal Structure of Murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with A Pnp-Derived Inhibitor (pdb code 5aes). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with A Pnp-Derived Inhibitor, PDB code: 5aes:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with A Pnp-Derived Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with A Pnp-Derived Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg305 b:28.5 occ:1.00 OAC A:5B0306 2.0 19.7 1.0 O A:HOH2002 2.1 36.2 1.0 O A:HOH2003 2.1 34.5 1.0 OD2 A:ASP25 2.1 33.4 1.0 OD1 A:ASP234 2.1 38.8 1.0 O A:ASP27 2.1 26.2 1.0 CG A:ASP234 3.1 35.5 1.0 CG A:ASP25 3.2 28.2 1.0 C A:ASP27 3.3 26.8 1.0 OD2 A:ASP234 3.4 33.4 1.0 PAP A:5B0306 3.4 31.9 1.0 OD1 A:ASP25 3.7 25.9 1.0 HB2 A:ASP27 3.7 46.0 1.0 HA3 A:GLY28 3.8 32.6 1.0 OD2 A:ASP239 3.9 27.5 1.0 HG21 A:VAL29 3.9 45.5 1.0 H A:ASP234 3.9 39.8 1.0 O A:HOH2019 3.9 30.5 1.0 OAF A:5B0306 4.0 32.5 1.0 OAE A:5B0306 4.0 33.8 1.0 HB2 A:ARG235 4.1 35.0 1.0 CA A:ASP27 4.1 27.0 1.0 HAE A:5B0306 4.2 40.6 1.0 CB A:ASP27 4.2 38.4 1.0 O A:HOH2018 4.2 33.4 1.0 HB3 A:ASP27 4.3 46.0 1.0 H A:ASP27 4.3 31.6 1.0 N A:GLY28 4.3 28.1 1.0 N A:ASP27 4.3 26.3 1.0 HB3 A:ASP25 4.4 20.1 1.0 CB A:ASP234 4.4 34.1 1.0 CA A:GLY28 4.5 27.2 1.0 CB A:ASP25 4.5 16.8 1.0 HAF A:5B0306 4.5 39.0 1.0 HB3 A:ASP234 4.5 40.9 1.0 N A:ASP234 4.7 33.1 1.0 H4 A:5B0306 4.7 29.8 1.0 CG2 A:VAL29 4.7 38.0 1.0 CAJ A:5B0306 4.7 24.8 1.0 HZ2 A:LYS209 4.7 34.3 1.0 CG A:ASP239 4.8 26.7 1.0 HG22 A:VAL29 4.8 45.5 1.0 H A:ARG235 4.9 36.9 1.0 OD1 A:ASP239 4.9 23.3 1.0 H5 A:5B0306 4.9 34.0 1.0 HD2 A:ARG235 4.9 33.2 1.0 HZ3 A:LYS209 4.9 34.3 1.0 H A:CYS26 4.9 40.8 1.0 HB2 A:ASP25 4.9 20.1 1.0 C A:CYS26 4.9 32.4 1.0 HB3 A:ARG235 4.9 35.0 1.0 CB A:ARG235 5.0 29.1 1.0 HG21 A:VAL257 5.0 25.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with A Pnp-Derived Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with A Pnp-Derived Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg305 b:31.1 occ:1.00 OD2 B:ASP25 2.0 30.6 1.0 OD1 B:ASP234 2.1 45.6 1.0 O B:HOH2001 2.1 39.0 1.0 O B:HOH2002 2.1 33.5 1.0 OAC B:5B0306 2.1 35.1 1.0 O B:ASP27 2.1 52.8 1.0 CG B:ASP234 3.1 43.8 1.0 CG B:ASP25 3.1 33.7 1.0 C B:ASP27 3.3 48.0 1.0 PAP B:5B0306 3.5 34.9 1.0 OD2 B:ASP234 3.5 41.1 1.0 HB3 B:ASP27 3.6 72.5 1.0 OD1 B:ASP25 3.6 35.6 1.0 HA3 B:GLY28 3.8 35.6 1.0 H B:ASP234 3.8 49.8 1.0 OD1 B:ASP27 3.8 68.9 1.0 OD2 B:ASP239 3.9 48.9 1.0 HG21 B:VAL29 4.0 45.2 1.0 OAF B:5B0306 4.0 34.6 1.0 HB2 B:ARG235 4.1 51.6 1.0 CA B:ASP27 4.1 51.6 1.0 CB B:ASP27 4.2 60.4 1.0 O B:HOH2012 4.2 47.5 1.0 OAE B:5B0306 4.2 42.8 1.0 H B:ASP27 4.2 56.5 1.0 N B:ASP27 4.2 47.1 1.0 N B:GLY28 4.3 32.2 1.0 CB B:ASP234 4.4 45.1 1.0 HB3 B:ASP25 4.4 46.2 1.0 HAE B:5B0306 4.4 51.3 1.0 CB B:ASP25 4.4 38.5 1.0 CA B:GLY28 4.4 29.6 1.0 HB3 B:ASP234 4.4 54.1 1.0 CG B:ASP27 4.5 67.2 1.0 HAF B:5B0306 4.5 41.6 1.0 N B:ASP234 4.6 41.5 1.0 H5 B:5B0306 4.6 32.2 1.0 CG B:ASP239 4.8 43.6 1.0 H B:CYS26 4.8 51.9 1.0 H B:ARG235 4.8 54.7 1.0 CAJ B:5B0306 4.8 23.6 1.0 CG2 B:VAL29 4.9 37.7 1.0 HD2 B:ARG235 4.9 43.6 1.0 OD1 B:ASP239 4.9 38.5 1.0 HB2 B:ASP25 4.9 46.2 1.0 CB B:ARG235 4.9 43.0 1.0 C B:CYS26 4.9 43.0 1.0 CA B:ASP234 4.9 47.4 1.0 HB3 B:ARG235 4.9 51.6 1.0 HG21 B:VAL257 4.9 43.9 1.0 HZ2 B:LYS209 5.0 48.9 1.0 HG22 B:VAL29 5.0 45.2 1.0 H3 B:5B0306 5.0 28.3 1.0 N B:ARG235 5.0 45.6 1.0

G.Knobloch, N.Jabari, S.Stadlbauer, H.Schindelin, M.Kohn, A.Gohla. Synthesis of Hydrolysis-Resistant Pyridoxal 5'-Phosphate Analogs and Their Biochemical and X-Ray Crystallographic Characterization with the Pyridoxal Phosphatase Chronophin. Bioorg.Med.Chem. 2015.
ISSN: ESSN 1464-3391
PubMed: 25783190
DOI: 10.1016/J.BMC.2015.02.049