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Magnesium in PDB 4ajr: 3D Structure of E. Coli Isocitrate Dehydrogenase K100M Mutant in Complex with Alpha-Ketoglutarate, Magnesium(II) and Nadph - the Product Complex

Enzymatic activity of 3D Structure of E. Coli Isocitrate Dehydrogenase K100M Mutant in Complex with Alpha-Ketoglutarate, Magnesium(II) and Nadph - the Product Complex

All present enzymatic activity of 3D Structure of E. Coli Isocitrate Dehydrogenase K100M Mutant in Complex with Alpha-Ketoglutarate, Magnesium(II) and Nadph - the Product Complex:
1.1.1.42;

Protein crystallography data

The structure of 3D Structure of E. Coli Isocitrate Dehydrogenase K100M Mutant in Complex with Alpha-Ketoglutarate, Magnesium(II) and Nadph - the Product Complex, PDB code: 4ajr was solved by S.Goncalves, S.P.Miller, M.A.Carrondo, A.M.Dean, P.M.Matias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.894 / 2.69
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 105.788, 105.788, 145.488, 90.00, 90.00, 90.00
R / Rfree (%) 16.04 / 20.91

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 3D Structure of E. Coli Isocitrate Dehydrogenase K100M Mutant in Complex with Alpha-Ketoglutarate, Magnesium(II) and Nadph - the Product Complex (pdb code 4ajr). 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 3D Structure of E. Coli Isocitrate Dehydrogenase K100M Mutant in Complex with Alpha-Ketoglutarate, Magnesium(II) and Nadph - the Product Complex, PDB code: 4ajr:

Magnesium binding site 1 out of 1 in 4ajr

Go back to Magnesium Binding Sites List in 4ajr
Magnesium binding site 1 out of 1 in the 3D Structure of E. Coli Isocitrate Dehydrogenase K100M Mutant in Complex with Alpha-Ketoglutarate, Magnesium(II) and Nadph - the Product Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 3D Structure of E. Coli Isocitrate Dehydrogenase K100M Mutant in Complex with Alpha-Ketoglutarate, Magnesium(II) and Nadph - the Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1419

b:29.5
occ:1.00
 OD1 A:ASP307 2.4 34.1 1.0
O A:HOH2106 2.5 23.4 1.0
O A:HOH2051 2.7 27.8 0.7
O5 A:AKG1418 2.8 43.0 1.0
O2 A:AKG1418 2.8 37.7 1.0
C1 A:AKG1418 3.3 42.1 1.0
CG A:ASP307 3.4 31.0 1.0
C2 A:AKG1418 3.4 41.6 1.0
OD1 A:ASP311 3.6 32.0 1.0
OD2 A:ASP307 3.7 39.5 1.0
C5N A:NAP1417 3.9 28.9 1.0
O A:THR338 4.1 24.9 1.0
C4N A:NAP1417 4.2 31.5 1.0
O1 A:AKG1418 4.3 37.4 1.0
O A:HOH2107 4.3 20.6 1.0
O A:ASP307 4.3 23.6 1.0
NH1 A:ARG129 4.4 29.8 1.0
CG A:ASP311 4.4 33.1 1.0
NH2 A:ARG129 4.6 30.7 1.0
OD2 A:ASP311 4.6 25.1 1.0
CB A:ASP307 4.6 23.2 1.0
CA A:ASP307 4.8 19.8 1.0
CG2 A:THR338 4.8 21.0 1.0
C A:ASP307 4.9 22.3 1.0
C3 A:AKG1418 4.9 32.7 1.0
CZ A:ARG129 4.9 30.5 1.0
O A:HOH2126 5.0 22.2 0.9
OH A:TYR160 5.0 39.6 1.0

Reference:

S.Goncalves, S.P.Miller, M.A.Carrondo, A.M.Dean, P.M.Matias. Induced Fit and the Catalytic Mechanism of Isocitrate Dehydrogenase. Biochemistry V. 51 7098 2012.
ISSN: ISSN 0006-2960
PubMed: 22891681
DOI: 10.1021/BI300483W
Page generated: Mon Dec 14 09:07:55 2020

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