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

Enzymatic activity of 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;

Protein crystallography data

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

Magnesium Binding Sites:

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 5gre

Go back to Magnesium Binding Sites List in 5gre
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 5gre

Go back to Magnesium Binding Sites List in 5gre
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

Reference:

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
Page generated: Tue Aug 12 10:25:46 2025

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