Magnesium in PDB 5h3f: Crystal Structure of Mouse Isocitrate Dehydrogenases 2 Complexed with Isocitrate

All present enzymatic activity of Crystal Structure of Mouse Isocitrate Dehydrogenases 2 Complexed with Isocitrate:
1.1.1.42;

The structure of Crystal Structure of Mouse Isocitrate Dehydrogenases 2 Complexed with Isocitrate, PDB code: 5h3f was solved by Y.Xu, L.Liu, T.Miyakawa, A.Nakamura, M.Tanokura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.89 / 3.29
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	135.853, 135.853, 220.162, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 22.2

The binding sites of Magnesium atom in the Crystal Structure of Mouse Isocitrate Dehydrogenases 2 Complexed with Isocitrate (pdb code 5h3f). 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 Mouse Isocitrate Dehydrogenases 2 Complexed with Isocitrate, PDB code: 5h3f:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Mouse Isocitrate Dehydrogenases 2 Complexed with Isocitrate


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 Mouse Isocitrate Dehydrogenases 2 Complexed with Isocitrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:93.2 occ:1.00 O2 A:ICT501 2.3 0.0 1.0 OD1 A:ASP314 2.4 0.9 1.0 OD2 B:ASP291 2.6 1.0 1.0 O7 A:ICT501 2.8 0.6 1.0 OD1 A:ASP318 3.2 1.0 1.0 C1 A:ICT501 3.3 0.4 1.0 CG B:ASP291 3.5 0.2 1.0 CG A:ASP314 3.5 0.4 1.0 O A:ASP314 3.5 0.2 1.0 C2 A:ICT501 3.6 0.6 1.0 CB B:ASP291 3.7 0.9 1.0 CG A:ASP318 3.8 0.3 1.0 OD2 A:ASP318 3.8 0.7 1.0 NH1 A:ARG149 4.0 0.7 1.0 OD2 A:ASP314 4.1 0.5 1.0 C A:ASP314 4.3 0.2 1.0 O1 A:ICT501 4.4 0.1 1.0 CA A:ASP314 4.5 0.1 1.0 CB A:ASP314 4.6 0.4 1.0 O6 A:ICT501 4.7 0.5 1.0 OD1 B:ASP291 4.7 0.8 1.0 OG A:SER317 4.8 0.8 1.0 NZ B:LYS251 4.9 0.9 1.0 C3 A:ICT501 4.9 0.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Mouse Isocitrate Dehydrogenases 2 Complexed with Isocitrate


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 Mouse Isocitrate Dehydrogenases 2 Complexed with Isocitrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:97.3 occ:1.00 OD2 A:ASP291 2.6 0.5 1.0 O7 B:ICT501 2.6 0.1 1.0 O1 B:ICT501 2.6 0.2 1.0 OD1 B:ASP314 2.7 0.0 1.0 OD2 B:ASP318 3.0 0.8 1.0 OD1 B:ASP318 3.4 0.7 1.0 C1 B:ICT501 3.5 0.8 1.0 C2 B:ICT501 3.5 0.8 1.0 CG B:ASP318 3.5 0.6 1.0 CG A:ASP291 3.6 0.2 1.0 CG B:ASP314 3.9 0.8 1.0 O B:ASP314 4.0 0.6 1.0 CB A:ASP291 4.0 0.2 1.0 NH1 B:ARG149 4.1 0.8 1.0 OD2 B:ASP314 4.6 0.3 1.0 O2 B:ICT501 4.7 0.8 1.0 OD1 A:ASP291 4.7 0.2 1.0 O5 B:ICT501 4.7 0.5 1.0 C B:ASP314 4.8 0.5 1.0 NH2 B:ARG149 4.8 0.6 1.0 CZ B:ARG149 4.9 0.4 1.0 C3 B:ICT501 4.9 0.2 1.0 CA B:ASP314 4.9 0.8 1.0 CB B:ASP318 5.0 0.6 1.0

Y.Xu, L.Liu, A.Nakamura, S.Someya, T.Miyakawa, M.Tanokura. Studies on the Regulatory Mechanism of Isocitrate Dehydrogenase 2 Using Acetylation Mimics Sci Rep V. 7 9785 2017.
ISSN: ESSN 2045-2322
PubMed: 28852116
DOI: 10.1038/S41598-017-10337-7