Magnesium in PDB 5h3e: Crystal Structure of Mouse Isocitrate Dehydrogenases 2 K256Q Mutant Complexed with Isocitrate

All present enzymatic activity of Crystal Structure of Mouse Isocitrate Dehydrogenases 2 K256Q Mutant Complexed with Isocitrate:
1.1.1.42;

The structure of Crystal Structure of Mouse Isocitrate Dehydrogenases 2 K256Q Mutant Complexed with Isocitrate, PDB code: 5h3e 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)	19.32 / 2.21
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	58.150, 58.150, 206.915, 90.00, 90.00, 120.00
R / Rfree (%)	20.9 / 24.3

The binding sites of Magnesium atom in the Crystal Structure of Mouse Isocitrate Dehydrogenases 2 K256Q Mutant Complexed with Isocitrate (pdb code 5h3e). 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 K256Q Mutant Complexed with Isocitrate, PDB code: 5h3e:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Mouse Isocitrate Dehydrogenases 2 K256Q Mutant 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 K256Q Mutant Complexed with Isocitrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:31.9 occ:1.00 OD1 A:ASP314 2.2 25.8 1.0 O2 A:ICT502 2.3 31.9 1.0 OD2 B:ASP291 2.3 27.1 1.0 O7 A:ICT502 2.4 32.7 1.0 C1 A:ICT502 3.2 32.6 1.0 C2 A:ICT502 3.3 32.8 1.0 CG B:ASP291 3.3 26.8 1.0 CG A:ASP314 3.3 25.2 1.0 OD1 A:ASP318 3.6 31.1 1.0 CB B:ASP291 3.7 26.8 1.0 O A:ASP314 3.8 22.8 1.0 OD2 A:ASP318 3.9 30.7 1.0 OD2 A:ASP314 3.9 26.6 1.0 CG A:ASP318 4.1 30.4 1.0 NH1 A:ARG149 4.2 30.3 1.0 O1 A:ICT502 4.4 32.9 1.0 NZ B:LYS251 4.4 25.8 1.0 OD1 B:ASP291 4.5 26.9 1.0 C A:ASP314 4.5 23.2 1.0 CB A:ASP314 4.5 24.6 1.0 CA A:ASP314 4.5 24.1 1.0 C3 A:ICT502 4.5 33.4 1.0 C6 A:ICT502 4.5 33.5 1.0 O5 A:ICT502 4.7 35.6 1.0 O A:ALA347 4.9 42.8 1.0 NH1 A:ARG172 4.9 26.4 1.0 O6 A:ICT502 5.0 32.1 1.0 OG A:SER317 5.0 26.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Mouse Isocitrate Dehydrogenases 2 K256Q Mutant 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 K256Q Mutant Complexed with Isocitrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:34.5 occ:1.00 OD1 B:ASP314 2.2 30.3 1.0 OD2 A:ASP291 2.2 29.0 1.0 O1 B:ICT502 2.3 31.4 1.0 O7 B:ICT502 2.8 30.7 1.0 CG A:ASP291 3.2 28.7 1.0 C1 B:ICT502 3.3 30.9 1.0 CG B:ASP314 3.3 29.9 1.0 O B:ASP314 3.5 28.9 1.0 CB A:ASP291 3.5 28.4 1.0 C2 B:ICT502 3.6 31.1 1.0 OD2 B:ASP318 3.7 32.3 1.0 OD1 B:ASP318 3.7 32.5 1.0 OD2 B:ASP314 3.9 30.5 1.0 CG B:ASP318 3.9 31.6 1.0 O B:ALA347 4.0 36.5 1.0 NH1 B:ARG149 4.1 27.0 1.0 C B:ASP314 4.2 28.6 1.0 CA B:ASP314 4.3 28.8 1.0 OD1 A:ASP291 4.4 29.5 1.0 CB B:ASP314 4.4 29.3 1.0 O2 B:ICT502 4.4 30.5 1.0 OG B:SER317 4.6 26.2 1.0 NZ A:LYS251 4.7 26.2 1.0 C6 B:ICT502 4.7 31.4 1.0 O6 B:ICT502 4.7 31.9 1.0 C3 B:ICT502 4.8 31.5 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