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

Enzymatic activity of Crystal Structure of the Alpha Gamma Heterodimer of Human IDH3 in Complex with Mg(2+) and Nadh

All present enzymatic activity of Crystal Structure of the Alpha Gamma Heterodimer of Human IDH3 in Complex with Mg(2+) and Nadh:
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+) and Nadh, PDB code: 5yvt was solved by T.Ma, J.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.40
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 118.027, 118.027, 142.109, 90.00, 90.00, 120.00
R / Rfree (%) 21.1 / 23.6

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+) and Nadh (pdb code 5yvt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of the Alpha Gamma Heterodimer of Human IDH3 in Complex with Mg(2+) and Nadh, PDB code: 5yvt:

Magnesium binding site 1 out of 1 in 5yvt

Go back to Magnesium Binding Sites List in 5yvt
Magnesium binding site 1 out of 1 in the Crystal Structure of the Alpha Gamma Heterodimer of Human IDH3 in Complex with Mg(2+) and Nadh


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 Nadh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:52.6
occ:1.00
 O A:HOH517 2.0 49.0 1.0
OD2 B:ASP215 2.1 46.4 1.0
O B:HOH569 2.1 51.4 1.0
OD1 A:ASP230 2.2 56.0 1.0
O A:HOH503 2.2 58.7 1.0
OD2 A:ASP234 2.4 53.6 1.0
CG A:ASP230 3.1 55.1 1.0
CG B:ASP215 3.1 45.5 1.0
OD2 A:ASP230 3.3 58.2 1.0
CG A:ASP234 3.4 51.8 1.0
CB B:ASP215 3.6 45.1 1.0
OD1 A:ASP234 3.7 50.3 1.0
OD1 B:ASP215 4.2 46.7 1.0
CB A:ASP230 4.5 53.1 1.0
O A:ASP230 4.7 49.8 1.0
C A:ASP230 4.7 50.3 1.0
CB A:ASP234 4.7 49.1 1.0
CA B:ASP215 4.9 44.3 1.0
CA A:ASP230 5.0 50.7 1.0

Reference:

Y.Liu, L.Hu, T.Ma, J.Yang, J.Ding. Insights Into the Inhibitory Mechanisms of Nadh on the Alpha Gamma Heterodimer of Human Nad-Dependent Isocitrate Dehydrogenase. Sci Rep V. 8 3146 2018.
ISSN: ESSN 2045-2322
PubMed: 29453450
DOI: 10.1038/S41598-018-21584-7
Page generated: Mon Dec 14 22:15:08 2020

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