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Calcium in PDB 4aj3: 3D Structure of E. Coli Isocitrate Dehydrogenase in Complex with Isocitrate, Calcium(II) and Nadp - the Pseudo-Michaelis Complex

Enzymatic activity of 3D Structure of E. Coli Isocitrate Dehydrogenase in Complex with Isocitrate, Calcium(II) and Nadp - the Pseudo-Michaelis Complex

All present enzymatic activity of 3D Structure of E. Coli Isocitrate Dehydrogenase in Complex with Isocitrate, Calcium(II) and Nadp - the Pseudo-Michaelis Complex:
1.1.1.42;

Protein crystallography data

The structure of 3D Structure of E. Coli Isocitrate Dehydrogenase in Complex with Isocitrate, Calcium(II) and Nadp - the Pseudo-Michaelis Complex, PDB code: 4aj3 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) 44.81 / 1.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 105.297, 105.297, 145.723, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.4

Calcium Binding Sites:

The binding sites of Calcium atom in the 3D Structure of E. Coli Isocitrate Dehydrogenase in Complex with Isocitrate, Calcium(II) and Nadp - the Pseudo-Michaelis Complex (pdb code 4aj3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the 3D Structure of E. Coli Isocitrate Dehydrogenase in Complex with Isocitrate, Calcium(II) and Nadp - the Pseudo-Michaelis Complex, PDB code: 4aj3:

Calcium binding site 1 out of 1 in 4aj3

Go back to Calcium Binding Sites List in 4aj3
Calcium binding site 1 out of 1 in the 3D Structure of E. Coli Isocitrate Dehydrogenase in Complex with Isocitrate, Calcium(II) and Nadp - the Pseudo-Michaelis Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 3D Structure of E. Coli Isocitrate Dehydrogenase in Complex with Isocitrate, Calcium(II) and Nadp - the Pseudo-Michaelis Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1419

b:32.2
occ:0.45
 OD1 A:ASP307 2.4 39.8 1.0
O A:HOH2298 2.5 23.4 0.7
O A:HOH2156 2.6 26.8 0.3
O2 A:ICT1418 2.7 29.1 0.8
O7 A:ICT1418 2.7 26.7 0.8
OD1 A:ASP311 3.3 36.2 1.0
C1 A:ICT1418 3.4 29.9 0.8
CG A:ASP307 3.5 32.0 1.0
C2 A:ICT1418 3.5 27.8 0.8
O A:ASP307 3.9 25.1 1.0
OD2 A:ASP307 4.0 33.3 1.0
CG A:ASP311 4.1 31.8 1.0
OD2 A:ASP311 4.2 32.8 1.0
O A:THR338 4.2 24.4 1.0
O A:HOH2299 4.3 25.9 1.0
NH1 A:ARG129 4.3 26.6 1.0
C5N A:NAP1417 4.4 24.3 1.0
O1 A:ICT1418 4.5 34.4 0.8
C A:ASP307 4.5 25.3 1.0
CG2 A:THR338 4.6 24.8 1.0
CA A:ASP307 4.6 24.1 1.0
CB A:ASP307 4.6 21.8 1.0
C6 A:ICT1418 4.8 34.0 0.8
C4N A:NAP1417 4.8 25.3 1.0
C3 A:ICT1418 4.9 27.3 0.8
NH2 A:ARG129 4.9 26.5 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: Tue Jul 8 18:31:12 2025

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