Calcium in PDB 4ja8: Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor

All present enzymatic activity of Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor:
1.1.1.42;

The structure of Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor, PDB code: 4ja8 was solved by W.Wei, L.Chen, M.Wu, F.Jiang, J.Travins, K.Qian, B.Delabarre, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.90 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.656, 119.661, 125.542, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 21.8

The structure of Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Calcium atom in the Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor (pdb code 4ja8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor, PDB code: 4ja8:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:21.3 occ:1.00 OD2 A:ASP314 2.1 13.0 1.0 OD1 B:ASP291 2.3 24.5 1.0 OD2 A:ASP318 2.5 24.2 1.0 O B:HOH602 2.6 31.6 1.0 O B:HOH601 2.6 32.5 1.0 OD1 A:ASP318 2.6 24.5 1.0 O A:HOH871 2.7 33.0 1.0 CG A:ASP318 2.9 17.3 1.0 CG A:ASP314 3.3 11.6 1.0 O A:ASP314 3.3 11.9 1.0 CG B:ASP291 3.4 21.3 1.0 OD1 A:ASP314 3.9 12.2 1.0 CB B:ASP291 4.0 15.1 1.0 C A:ASP314 4.0 10.2 1.0 OD2 B:ASP291 4.4 15.4 1.0 CB A:ASP314 4.4 8.5 1.0 CA A:ASP314 4.4 8.6 1.0 CB A:ASP318 4.4 17.4 1.0 NZ B:LYS251 4.5 13.4 1.0 O A:HOH1013 4.7 37.0 1.0 N A:VAL315 5.0 9.0 1.0

Calcium binding site 2 out of 2 in the Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:20.1 occ:1.00 OD2 B:ASP314 2.2 13.4 1.0 OD2 A:ASP291 2.3 21.8 1.0 OD2 B:ASP318 2.4 24.4 1.0 O A:HOH601 2.4 39.6 1.0 O B:HOH847 2.5 54.1 1.0 O B:HOH603 2.5 27.9 1.0 O B:HOH819 2.6 35.1 1.0 OD1 B:ASP318 2.7 28.9 1.0 CG B:ASP318 2.9 16.7 1.0 CG B:ASP314 3.3 12.8 1.0 O B:ASP314 3.5 11.6 1.0 CG A:ASP291 3.5 19.9 1.0 OD1 B:ASP314 4.0 13.6 1.0 CB A:ASP291 4.0 15.5 1.0 C B:ASP314 4.2 10.9 1.0 O B:HOH802 4.3 39.2 1.0 OD1 A:ASP291 4.4 16.4 1.0 CA B:ASP314 4.5 9.6 1.0 CB B:ASP314 4.5 8.7 1.0 CB B:ASP318 4.5 16.0 1.0 NZ A:LYS251 4.5 15.1 1.0 O A:HOH1051 4.7 37.8 1.0 O B:HOH796 4.8 30.4 1.0

F.Wang, J.Travins, B.Delabarre, V.Penard-Lacronique, S.Schalm, E.Hansen, K.Straley, A.Kernytsky, W.Liu, C.Gliser, H.Yang, S.Gross, E.Artin, V.Saada, E.Mylonas, C.Quivoron, J.Popovici-Muller, J.O.Saunders, F.G.Salituro, S.Yan, S.Murray, W.Wei, Y.Gao, L.Dang, M.Dorsch, S.Agresta, D.P.Schenkein, S.A.Biller, S.M.Su, S.De Botton, K.E.Yen. Targeted Inhibition of Mutant IDH2 in Leukemia Cells Induces Cellular Differentiation. Science V. 340 622 2013.
ISSN: ISSN 0036-8075
PubMed: 23558173
DOI: 10.1126/SCIENCE.1234769