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Calcium in PDB 4aja: 3D Structure of E. Coli Isocitrate Dehydrogenase in Complex with Isocitrate, Calcium(II) and Thionadp

Enzymatic activity of 3D Structure of E. Coli Isocitrate Dehydrogenase in Complex with Isocitrate, Calcium(II) and Thionadp

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

Protein crystallography data

The structure of 3D Structure of E. Coli Isocitrate Dehydrogenase in Complex with Isocitrate, Calcium(II) and Thionadp, PDB code: 4aja 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) 46.515 / 1.80
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 104.010, 104.010, 149.563, 90.00, 90.00, 90.00
R / Rfree (%) 18.33 / 20.4

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 Thionadp (pdb code 4aja). 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 Thionadp, PDB code: 4aja:

Calcium binding site 1 out of 1 in 4aja

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


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 Thionadp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:24.8
occ:1.00
 OD1 A:ASP307 2.4 23.4 1.0
O2 A:ICT502 2.5 26.9 1.0
OD2 A:ASP311 2.5 32.9 1.0
O7 A:ICT502 2.5 26.8 1.0
O A:HOH2411 2.6 31.4 1.0
O A:HOH2208 2.6 24.9 1.0
C1 A:ICT502 3.3 33.6 1.0
CG A:ASP311 3.3 26.5 1.0
C2 A:ICT502 3.5 28.6 1.0
CG A:ASP307 3.5 24.3 1.0
OD1 A:ASP311 3.6 32.6 1.0
O A:ASP307 4.1 19.9 1.0
OD2 A:ASP307 4.1 21.7 1.0
NH1 A:ARG129 4.4 29.4 1.0
O A:HOH2500 4.4 36.0 1.0
O1 A:ICT502 4.5 29.3 1.0
C6 A:ICT502 4.5 26.6 1.0
O A:HOH2424 4.5 33.4 1.0
C3 A:ICT502 4.6 27.7 1.0
CB A:ASP311 4.6 19.2 1.0
CA A:ASP307 4.7 17.7 1.0
CB A:ASP307 4.7 19.1 1.0
C A:ASP307 4.7 20.5 1.0
O6 A:ICT502 4.7 26.9 1.0
O5 A:ICT502 4.7 27.2 1.0
NH1 A:ARG153 4.9 23.5 1.0
O A:HOH2209 4.9 27.1 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 18:31:19 2025

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