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Magnesium in PDB 6l59: Crystal Structure of the Alpha Gamma Heterodimer of Human IDH3 in Complex with Cit, Mg and Atp Binding at Allosteric Site and Mg, Atp Binding at Active Site.

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

Protein crystallography data

The structure of Crystal Structure of the Alpha Gamma Heterodimer of Human IDH3 in Complex with Cit, Mg and Atp Binding at Allosteric Site and Mg, Atp Binding at Active Site., PDB code: 6l59 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) 32.32 / 2.25
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 111.964, 111.964, 145.578, 90.00, 90.00, 120.00
R / Rfree (%) 20 / 22.7

Magnesium Binding Sites:

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 and Mg, Atp Binding at Active Site. (pdb code 6l59). 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 and Mg, Atp Binding at Active Site., PDB code: 6l59:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6l59

Go back to Magnesium Binding Sites List in 6l59
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 and Mg, Atp Binding at Active 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 and Mg, Atp Binding at Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:50.5
occ:1.00
 O A:ASP230 2.4 40.1 1.0
OD1 A:ASP230 2.4 43.5 1.0
OD2 A:ASP234 2.5 44.3 1.0
OD2 B:ASP215 2.6 56.4 1.0
CG A:ASP234 3.0 46.2 1.0
C A:ASP230 3.3 38.8 1.0
OD1 A:ASP234 3.4 44.9 1.0
CG A:ASP230 3.4 47.7 1.0
CG B:ASP215 3.6 52.5 1.0
O A:HOH525 3.7 47.5 1.0
CA A:ASP230 3.8 36.8 1.0
CB A:ASP234 3.9 41.9 1.0
CB B:ASP215 3.9 46.7 1.0
OG A:SER233 3.9 40.1 1.0
O A:HOH504 4.1 49.5 1.0
CB A:ASP230 4.2 42.5 1.0
OD2 A:ASP230 4.3 48.4 1.0
N A:ILE231 4.4 39.9 1.0
N A:ASP234 4.5 38.1 1.0
OD1 B:ASP215 4.7 55.9 1.0
CA A:ASP234 4.7 35.4 1.0
CA A:ILE231 4.7 40.1 1.0
NH2 A:ARG98 4.8 45.9 1.0
NH1 A:ARG119 4.9 43.4 1.0

Magnesium binding site 2 out of 2 in 6l59

Go back to Magnesium Binding Sites List in 6l59
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 and Mg, Atp Binding at Active 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 and Mg, Atp Binding at Active Site. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:47.2
occ:1.00
 O A:HOH540 2.4 46.6 1.0
O B:ARG272 2.5 41.2 1.0
O5 B:CIT403 2.6 40.5 1.0
OD1 B:ASN78 2.6 46.8 1.0
O B:HOH581 2.7 47.2 1.0
O B:HOH568 3.0 48.3 1.0
O B:HOH634 3.2 50.1 1.0
CG B:ASN78 3.4 42.5 1.0
C B:ARG272 3.7 38.0 1.0
C6 B:CIT403 3.8 41.6 1.0
ND2 B:ASN78 3.8 37.1 1.0
C2 B:CIT403 4.2 41.1 1.0
CA B:ASN273 4.2 44.4 1.0
N B:ASN273 4.4 36.6 1.0
C3 B:CIT403 4.5 39.8 1.0
C1 B:CIT403 4.5 41.6 1.0
N B:THR274 4.5 39.4 1.0
CG2 B:THR274 4.6 44.5 1.0
O1 B:CIT403 4.6 42.2 1.0
CB B:ARG272 4.6 36.4 1.0
O A:HOH523 4.6 35.7 1.0
CB B:ASN78 4.6 38.1 1.0
C4 B:CIT403 4.7 35.3 1.0
O6 B:CIT403 4.7 40.8 1.0
C B:ASN273 4.7 38.3 1.0
CA B:ARG272 4.8 35.0 1.0
ND2 B:ASN273 4.9 37.2 1.0

Reference:

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
Page generated: Tue Oct 1 10:21:14 2024

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