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

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

The structure of Crystal Structure of the Alpha Gamma Heterodimer of Human IDH3 in Complex with Mg(2+), Citrate and Adp, PDB code: 5gre 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)	45.43 / 2.65
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	104.910, 104.910, 146.250, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / 24.1

The binding sites of Magnesium atom in the Crystal Structure of the Alpha Gamma Heterodimer of Human IDH3 in Complex with Mg(2+), Citrate and Adp (pdb code 5gre). 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+), Citrate and Adp, PDB code: 5gre:
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+), Citrate 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+), Citrate and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:49.5 occ:1.00 OD2 B:ASP215 2.2 52.6 1.0 OD2 A:ASP234 2.8 31.4 1.0 O A:HOH505 2.8 40.2 1.0 OD1 A:ASP230 2.9 46.9 1.0 O A:ASP230 3.2 37.4 1.0 CG B:ASP215 3.4 46.0 1.0 CG A:ASP230 3.4 40.6 1.0 CG A:ASP234 3.4 31.6 1.0 OD1 A:ASP234 3.5 37.5 1.0 OD2 A:ASP230 3.6 40.3 1.0 C A:ASP230 4.0 34.3 1.0 CB B:ASP215 4.1 38.5 1.0 OD1 B:ASP215 4.3 44.2 1.0 CA A:ASP230 4.4 32.0 1.0 CB A:ASP230 4.4 37.1 1.0 CB A:ASP234 4.5 33.0 1.0 OG A:SER233 4.6 28.1 1.0 NH2 A:ARG98 4.7 48.4 1.0 NH2 A:ARG119 4.9 33.3 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+), Citrate 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+), Citrate and Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:23.5 occ:1.00 O3B B:ADP401 2.1 49.1 1.0 O B:ARG272 2.4 25.9 1.0 OD1 B:ASN78 2.5 38.0 1.0 O5 B:CIT403 2.6 31.0 1.0 O B:HOH538 2.7 22.5 1.0 CG B:ASN78 3.4 36.5 1.0 PB B:ADP401 3.5 54.5 1.0 C B:ARG272 3.7 29.0 1.0 ND2 B:ASN78 3.7 33.6 1.0 C6 B:CIT403 3.8 31.6 1.0 O2B B:ADP401 3.9 52.2 1.0 C2 B:CIT403 4.2 31.6 1.0 CA B:ASN273 4.2 34.0 1.0 C1 B:CIT403 4.4 35.5 1.0 N B:THR274 4.4 37.6 1.0 N B:ASN273 4.4 35.0 1.0 O3A B:ADP401 4.4 52.0 1.0 O1B B:ADP401 4.4 49.9 1.0 CG2 B:THR274 4.5 37.3 1.0 C3 B:CIT403 4.5 28.9 1.0 O2 B:CIT403 4.6 41.7 1.0 CB B:ARG272 4.6 20.8 1.0 CB B:ASN78 4.6 34.4 1.0 O6 B:CIT403 4.7 28.4 1.0 C B:ASN273 4.7 32.1 1.0 CA B:ARG272 4.8 25.2 1.0 C4 B:CIT403 4.8 26.9 1.0 O1 B:CIT403 4.8 36.2 1.0 ND2 B:ASN93 4.9 30.8 1.0 O B:ILE79 5.0 34.2 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