Magnesium in PDB 5gri: Crystal Structure of the Alpha Gamma Heterodimer of Human IDH3 in Complex with Mg(2+) and Citrate

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

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

Resolution Low / High (Å)	46.01 / 2.31
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.040, 112.040, 144.950, 90.00, 90.00, 120.00
R / Rfree (%)	24.1 / 27.1

The binding sites of Magnesium atom in the Crystal Structure of the Alpha Gamma Heterodimer of Human IDH3 in Complex with Mg(2+) and Citrate (pdb code 5gri). 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+) and Citrate, PDB code: 5gri:
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+) and Citrate


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+) and Citrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:32.9 occ:1.00 OD2 A:ASP234 2.2 32.4 1.0 OD1 A:ASP230 2.2 28.5 1.0 O A:ASP230 2.6 25.9 1.0 OD2 B:ASP215 2.6 30.4 1.0 CG A:ASP234 3.1 31.4 1.0 CG A:ASP230 3.3 27.7 1.0 O A:HOH511 3.4 29.8 1.0 C A:ASP230 3.4 25.4 1.0 CG B:ASP215 3.5 28.0 1.0 OD1 A:ASP234 3.7 32.0 1.0 CB B:ASP215 3.8 26.1 1.0 CA A:ASP230 3.9 25.7 1.0 O A:HOH506 4.0 25.7 1.0 OD2 A:ASP230 4.0 28.8 1.0 CB A:ASP234 4.1 30.1 1.0 CB A:ASP230 4.2 26.7 1.0 OG A:SER233 4.2 29.3 1.0 NH2 A:ARG119 4.4 34.8 1.0 N A:ILE231 4.5 25.0 1.0 OD1 B:ASP215 4.7 30.1 1.0 O B:HOH521 4.8 26.7 1.0 CA A:ILE231 4.9 25.0 1.0 N A:ASP234 4.9 28.9 1.0 NZ B:LYS182 5.0 29.9 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+) and Citrate


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+) and Citrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:28.2 occ:1.00 O B:ARG272 2.4 18.1 1.0 O5 B:CIT401 2.4 21.3 1.0 OD1 B:ASN78 2.6 23.2 1.0 O A:HOH516 2.7 27.4 1.0 O B:HOH559 2.7 19.7 1.0 O B:HOH584 2.9 32.0 1.0 CG B:ASN78 3.2 22.7 1.0 ND2 B:ASN78 3.5 22.6 1.0 C B:ARG272 3.6 17.8 1.0 C6 B:CIT401 3.6 21.0 1.0 CA B:ASN273 4.1 20.3 1.0 C2 B:CIT401 4.2 21.3 1.0 OG1 B:THR274 4.2 26.4 1.0 N B:ASN273 4.3 19.1 1.0 N B:THR274 4.3 22.3 1.0 C3 B:CIT401 4.4 20.2 1.0 O1 B:CIT401 4.4 23.6 1.0 C1 B:CIT401 4.4 22.5 1.0 CB B:ARG272 4.5 16.0 1.0 CB B:ASN78 4.5 22.1 1.0 O6 B:CIT401 4.5 21.9 1.0 C B:ASN273 4.6 21.2 1.0 CA B:ARG272 4.7 16.6 1.0 C4 B:CIT401 4.7 18.9 1.0 O A:HOH504 4.8 20.8 1.0 ND2 B:ASN93 4.8 17.2 1.0 O B:ILE79 4.9 24.5 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