Calcium in PDB 1xkd: Ternary Complex of Isocitrate Dehydrogenase From the Hyperthermophile Aeropyrum Pernix

All present enzymatic activity of Ternary Complex of Isocitrate Dehydrogenase From the Hyperthermophile Aeropyrum Pernix:
1.1.1.42;

The structure of Ternary Complex of Isocitrate Dehydrogenase From the Hyperthermophile Aeropyrum Pernix, PDB code: 1xkd was solved by M.Karlstrom, R.Stokke, I.H.Steen, N.-K.Birkeland, R.Ladenstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.70 / 2.30
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	107.575, 107.575, 171.045, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 24.8

The binding sites of Calcium atom in the Ternary Complex of Isocitrate Dehydrogenase From the Hyperthermophile Aeropyrum Pernix (pdb code 1xkd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Ternary Complex of Isocitrate Dehydrogenase From the Hyperthermophile Aeropyrum Pernix, PDB code: 1xkd:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Ternary Complex of Isocitrate Dehydrogenase From the Hyperthermophile Aeropyrum Pernix


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ternary Complex of Isocitrate Dehydrogenase From the Hyperthermophile Aeropyrum Pernix within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1005 b:30.2 occ:1.00 OD2 B:ASP311 2.1 26.0 1.0 O B:HOH1006 2.1 24.7 1.0 O7 B:ICT1004 2.3 20.1 1.0 O2 B:ICT1004 2.3 25.9 1.0 OD2 A:ASP287 2.3 18.8 1.0 O B:HOH1005 2.4 26.8 1.0 C1 B:ICT1004 3.1 24.7 1.0 C2 B:ICT1004 3.2 24.2 1.0 CG B:ASP311 3.2 24.1 1.0 CG A:ASP287 3.4 21.2 1.0 OD1 B:ASP311 3.7 25.2 1.0 OD2 B:ASP315 3.7 20.3 1.0 NH2 B:ARG136 3.9 16.5 1.0 CB A:ASP287 4.0 20.7 1.0 O B:ASP311 4.2 21.5 1.0 O1 B:ICT1004 4.2 27.7 1.0 C6 B:ICT1004 4.3 23.7 1.0 NZ A:LYS233 4.3 21.2 1.0 C3 B:ICT1004 4.4 24.5 1.0 CG B:ASP315 4.4 23.4 1.0 OD1 A:ASP287 4.4 21.1 1.0 O5 B:ICT1004 4.4 23.6 1.0 O B:HOH1012 4.4 23.7 1.0 CB B:ASP311 4.5 22.1 1.0 O B:VAL342 4.6 30.5 1.0 O B:HOH1007 4.6 33.6 1.0 NH2 B:ARG159 4.6 21.7 1.0 O6 B:ICT1004 4.6 24.3 1.0 CA B:ASP311 4.7 21.9 1.0 C5N B:NAP1003 4.7 32.2 1.0 OD1 B:ASP315 4.8 23.5 1.0 C B:ASP311 4.8 21.5 1.0 CZ B:ARG136 4.8 15.0 1.0 NH1 B:ARG136 4.8 14.9 1.0 CG1 B:VAL342 4.8 28.7 1.0

Calcium binding site 2 out of 2 in the Ternary Complex of Isocitrate Dehydrogenase From the Hyperthermophile Aeropyrum Pernix


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ternary Complex of Isocitrate Dehydrogenase From the Hyperthermophile Aeropyrum Pernix within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1006 b:23.7 occ:1.00 OD2 A:ASP311 2.2 26.9 1.0 OD2 B:ASP287 2.3 19.5 1.0 O7 A:ICT1002 2.4 30.2 1.0 OD1 A:ASP315 2.4 22.9 1.0 O A:HOH1137 2.5 25.3 1.0 O A:HOH1136 2.6 30.9 1.0 O2 A:ICT1002 2.6 27.9 1.0 O A:HOH1135 2.7 24.2 1.0 CG A:ASP311 3.3 24.6 1.0 C1 A:ICT1002 3.4 28.4 1.0 CG B:ASP287 3.4 21.5 1.0 CG A:ASP315 3.4 24.0 1.0 C2 A:ICT1002 3.4 30.1 1.0 OD1 A:ASP311 3.7 26.1 1.0 OD2 A:ASP315 3.8 24.0 1.0 CB B:ASP287 4.0 20.0 1.0 O6 A:ICT1002 4.1 31.4 1.0 NH2 A:ARG136 4.2 37.9 1.0 O A:ASP311 4.3 21.2 1.0 C6 A:ICT1002 4.4 29.2 1.0 OD1 B:ASP287 4.4 21.4 1.0 NZ B:LYS233 4.5 21.9 1.0 O1 A:ICT1002 4.5 29.5 1.0 C3 A:ICT1002 4.6 29.4 1.0 CB A:ASP311 4.6 22.3 1.0 CB A:ASP315 4.7 21.7 1.0 CA A:ASP311 4.8 21.9 1.0 C A:ASP311 4.8 21.6 1.0 NH1 A:ARG136 4.8 38.5 1.0 O5 A:ICT1002 4.9 25.5 1.0 NH2 A:ARG159 4.9 22.6 1.0 CZ A:ARG136 5.0 37.7 1.0

M.Karlstrom, R.Stokke, I.H.Steen, N.-K.Birkeland, R.Ladenstein. Isocitrate Dehydrogenase From the Hyperthermophile Aeropyrum Pernix: X-Ray Structure Analysis of A Ternary Enzyme-Substrate Complex and Thermal Stability. J.Mol.Biol. V. 345 559 2005.
ISSN: ISSN 0022-2836
PubMed: 15581899
DOI: 10.1016/J.JMB.2004.10.025