Magnesium in PDB 5grl: Crystal Structure of the Alpha Gamma Heterodimer of Human IDH3 in Complex with Mg(2+), Isocitrate and Adp

All present enzymatic activity of Crystal Structure of the Alpha Gamma Heterodimer of Human IDH3 in Complex with Mg(2+), Isocitrate and Adp:
1.1.1.41;

The structure of Crystal Structure of the Alpha Gamma Heterodimer of Human IDH3 in Complex with Mg(2+), Isocitrate and Adp, PDB code: 5grl was solved by T.Ma, J.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.79
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	111.238, 111.238, 145.478, 90.00, 90.00, 120.00
R / Rfree (%)	22.6 / 27.4

The binding sites of Magnesium atom in the Crystal Structure of the Alpha Gamma Heterodimer of Human IDH3 in Complex with Mg(2+), Isocitrate and Adp (pdb code 5grl). 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 the Alpha Gamma Heterodimer of Human IDH3 in Complex with Mg(2+), Isocitrate and Adp, PDB code: 5grl:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Alpha Gamma Heterodimer of Human IDH3 in Complex with Mg(2+), Isocitrate and Adp


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 the Alpha Gamma Heterodimer of Human IDH3 in Complex with Mg(2+), Isocitrate and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:23.6 occ:1.00 OD1 A:ASP230 2.3 35.0 1.0 OD2 B:ASP215 2.3 42.1 1.0 OD1 A:ASP234 2.9 35.4 1.0 CG B:ASP215 3.3 38.6 1.0 O A:ASP230 3.3 37.1 1.0 CG A:ASP230 3.3 34.8 1.0 CG A:ASP234 3.6 36.5 1.0 OD2 A:ASP234 3.7 37.3 1.0 OD2 A:ASP230 3.9 35.2 1.0 CB B:ASP215 4.0 33.3 1.0 OD1 B:ASP215 4.2 40.0 1.0 C A:ASP230 4.2 32.2 1.0 CA A:ASP230 4.5 31.8 1.0 CB A:ASP230 4.5 33.5 1.0 NH1 A:ARG119 4.5 32.6 1.0 OG A:SER233 4.8 35.4 1.0 NH2 A:ARG98 4.8 46.0 1.0 NZ B:LYS182 4.8 27.5 1.0 CB A:ASP234 4.8 33.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Alpha Gamma Heterodimer of Human IDH3 in Complex with Mg(2+), Isocitrate and Adp


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 the Alpha Gamma Heterodimer of Human IDH3 in Complex with Mg(2+), Isocitrate and Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:10.0 occ:1.00 O2B B:ADP401 2.3 18.9 1.0 OD1 B:ASN78 2.4 28.5 1.0 O4 B:ICT402 2.5 31.8 1.0 O B:ARG272 2.5 16.8 1.0 CG B:ASN78 3.3 24.9 1.0 ND2 B:ASN78 3.6 24.4 1.0 C5 B:ICT402 3.6 33.4 1.0 PB B:ADP401 3.7 19.0 1.0 C B:ARG272 3.7 16.8 1.0 O3 B:ICT402 4.1 36.5 1.0 O5 B:ICT402 4.2 32.9 1.0 O3B B:ADP401 4.2 17.9 1.0 CA B:ASN273 4.3 18.6 1.0 N B:ASN273 4.5 18.0 1.0 O1B B:ADP401 4.5 18.3 1.0 O3A B:ADP401 4.6 17.8 1.0 CB B:ARG272 4.6 15.6 1.0 C2 B:ICT402 4.7 35.1 1.0 CB B:ASN78 4.7 23.1 1.0 O B:ILE79 4.7 20.8 1.0 N B:THR274 4.7 19.3 1.0 O7 B:ICT402 4.8 37.1 1.0 CA B:ARG272 4.8 16.3 1.0 C B:ASN273 4.9 18.5 1.0 C4 B:ICT402 4.9 34.5 1.0 CG2 B:THR274 4.9 20.5 1.0 C6 B:ICT402 4.9 34.5 1.0

T.Ma, Y.Peng, W.Huang, J.Ding. Molecular Mechanism of the Allosteric Regulation of the Alpha Gamma Heterodimer of Human Nad-Dependent Isocitrate Dehydrogenase. Sci Rep V. 7 40921 2017.
ISSN: ESSN 2045-2322
PubMed: 28098230
DOI: 10.1038/SREP40921