Magnesium in PDB 6l57: Crystal Structure of the Alpha Gamma Heterodimer of Human IDH3 in Complex with Cit , Mg and Atp Binding at Allosteric Site.

All present enzymatic activity of Crystal Structure of the Alpha Gamma Heterodimer of Human IDH3 in Complex with Cit , Mg and Atp Binding at Allosteric Site.:
1.1.1.41;

The structure of Crystal Structure of the Alpha Gamma Heterodimer of Human IDH3 in Complex with Cit , Mg and Atp Binding at Allosteric Site., PDB code: 6l57 was solved by P.Sun, J.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.06 / 2.30
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	104.211, 104.211, 145.547, 90.00, 90.00, 120.00
R / Rfree (%)	19.7 / 23.4

The binding sites of Magnesium atom in the Crystal Structure of the Alpha Gamma Heterodimer of Human IDH3 in Complex with Cit , Mg and Atp Binding at Allosteric Site. (pdb code 6l57). 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 Cit , Mg and Atp Binding at Allosteric Site., PDB code: 6l57:
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 Cit , Mg and Atp Binding at Allosteric Site.


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 Cit , Mg and Atp Binding at Allosteric Site. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:58.3 occ:1.00 OD2 B:ASP215 2.2 52.4 1.0 OD1 A:ASP230 2.5 58.1 1.0 OD2 A:ASP234 2.6 53.3 1.0 O A:ASP230 2.9 46.5 1.0 O A:HOH511 3.0 63.6 1.0 CG A:ASP234 3.1 47.9 1.0 CG A:ASP230 3.3 52.3 1.0 OD1 A:ASP234 3.3 49.7 1.0 CG B:ASP215 3.3 53.9 1.0 C A:ASP230 3.7 45.1 1.0 OD2 A:ASP230 3.9 52.9 1.0 CB B:ASP215 3.9 47.1 1.0 CA A:ASP230 4.1 43.9 1.0 CB A:ASP234 4.1 45.2 1.0 CB A:ASP230 4.3 45.2 1.0 OG A:SER233 4.3 48.7 1.0 OD1 B:ASP215 4.3 51.9 1.0 NH2 A:ARG98 4.4 52.0 1.0 N A:ILE231 4.8 42.5 1.0 N A:ASP234 4.9 45.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Alpha Gamma Heterodimer of Human IDH3 in Complex with Cit , Mg and Atp Binding at Allosteric Site.


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 Cit , Mg and Atp Binding at Allosteric Site. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:60.4 occ:1.00 O B:ARG272 2.6 45.9 1.0 O B:HOH554 2.7 53.2 1.0 OD1 B:ASN78 2.8 50.2 1.0 O B:HOH522 2.8 51.5 1.0 O5 B:CIT401 3.1 49.6 1.0 O A:HOH537 3.2 47.1 1.0 CG B:ASN78 3.7 48.7 1.0 C B:ARG272 3.8 41.9 1.0 CA B:ASN273 4.1 47.9 1.0 N B:THR274 4.2 47.8 1.0 CG2 B:THR274 4.2 49.1 1.0 C6 B:CIT401 4.3 51.8 1.0 ND2 B:ASN78 4.3 46.1 1.0 N B:ASN273 4.4 45.5 1.0 O1 B:CIT401 4.5 56.2 1.0 C2 B:CIT401 4.5 50.2 1.0 C B:ASN273 4.5 47.5 1.0 O A:HOH533 4.6 43.1 1.0 C1 B:CIT401 4.7 49.7 1.0 CB B:ASN78 4.8 47.2 1.0 CB B:ARG272 4.9 40.8 1.0 C3 B:CIT401 4.9 44.0 1.0 C4 B:CIT401 4.9 38.7 1.0 CA B:ARG272 4.9 42.7 1.0

P.Sun, T.Bai, T.Ma, J.Ding. Molecular Mechanism of the Dual Regulatory Roles of Atp on the Alpha Gamma Heterodimer of Human Nad-Dependent Isocitrate Dehydrogenase. Sci Rep V. 10 6225 2020.
ISSN: ESSN 2045-2322
PubMed: 32277159
DOI: 10.1038/S41598-020-63425-6