Calcium in PDB 8gru: Crystal Structure of A Constitutively Active Mutant of the Alpha Beta Heterodimer of Human IDH3 in Complex with Ict, Nad and Ca

The structure of Crystal Structure of A Constitutively Active Mutant of the Alpha Beta Heterodimer of Human IDH3 in Complex with Ict, Nad and Ca, PDB code: 8gru was solved by P.Sun, X.Chen, J.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.96 / 2.85
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	134.043, 163.833, 163.129, 90, 90, 90
R / Rfree (%)	20.8 / 26.3

The binding sites of Calcium atom in the Crystal Structure of A Constitutively Active Mutant of the Alpha Beta Heterodimer of Human IDH3 in Complex with Ict, Nad and Ca (pdb code 8gru). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of A Constitutively Active Mutant of the Alpha Beta Heterodimer of Human IDH3 in Complex with Ict, Nad and Ca, PDB code: 8gru:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of A Constitutively Active Mutant of the Alpha Beta Heterodimer of Human IDH3 in Complex with Ict, Nad and Ca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Constitutively Active Mutant of the Alpha Beta Heterodimer of Human IDH3 in Complex with Ict, Nad and Ca within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:73.1 occ:1.00 OD1 A:ASP230 2.6 43.5 1.0 OD2 B:ASP217 2.8 37.7 1.0 O7 A:ICT403 3.1 45.2 1.0 OD1 A:ASP234 3.4 31.8 1.0 C1 A:ICT403 3.5 53.7 1.0 O2 A:ICT403 3.5 68.1 1.0 OD2 A:ASP234 3.6 37.5 1.0 C2 A:ICT403 3.7 51.0 1.0 O A:VAL262 3.7 38.6 1.0 CG A:ASP234 3.8 38.4 1.0 CG A:ASP230 3.8 41.5 1.0 CG B:ASP217 3.8 36.4 1.0 NH1 A:ARG98 3.9 48.6 1.0 O A:ASP230 4.0 37.7 1.0 O1 A:ICT403 4.1 45.7 1.0 CB B:ASP217 4.2 40.9 1.0 CG1 A:VAL262 4.3 39.3 1.0 OD2 A:ASP230 4.3 45.0 1.0 C5N A:NAD401 4.5 47.4 1.0 C4N A:NAD401 4.7 41.5 1.0 CZ A:ARG98 4.8 43.4 1.0 C A:ASP230 4.8 38.6 1.0 C A:VAL262 4.8 42.8 1.0 OG A:SER233 4.8 39.5 1.0 NH2 A:ARG98 4.9 49.9 1.0 OD1 B:ASP217 4.9 35.3 1.0 CA A:ASP230 4.9 41.0 1.0 CB A:ASP230 4.9 37.9 1.0 CB A:ASP234 5.0 35.4 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of A Constitutively Active Mutant of the Alpha Beta Heterodimer of Human IDH3 in Complex with Ict, Nad and Ca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Constitutively Active Mutant of the Alpha Beta Heterodimer of Human IDH3 in Complex with Ict, Nad and Ca within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca402 b:67.8 occ:1.00 OD1 C:ASP230 2.6 50.0 1.0 O7 C:ICT403 2.8 52.6 1.0 OD2 D:ASP217 2.8 43.5 1.0 OD1 C:ASP234 3.3 42.5 1.0 NH1 C:ARG98 3.7 48.2 1.0 OD2 C:ASP234 3.7 43.6 1.0 CG C:ASP234 3.7 45.0 1.0 C2 C:ICT403 3.7 57.4 1.0 C1 C:ICT403 3.8 60.5 1.0 CG C:ASP230 3.8 47.3 1.0 CG D:ASP217 3.8 39.9 1.0 O C:VAL262 3.9 50.1 1.0 O1 C:ICT403 3.9 64.2 1.0 O C:ASP230 4.1 40.7 1.0 CB D:ASP217 4.1 40.8 1.0 CG1 C:VAL262 4.2 34.0 1.0 O2 C:ICT403 4.2 54.1 1.0 OD2 C:ASP230 4.3 47.3 1.0 NH2 C:ARG98 4.4 56.5 1.0 CZ C:ARG98 4.5 44.7 1.0 C5N C:NAD401 4.6 53.2 1.0 O5 C:ICT403 4.6 60.4 1.0 C4N C:NAD401 4.7 53.9 1.0 OG C:SER233 4.8 46.9 1.0 C C:VAL262 4.8 46.5 1.0 C C:ASP230 4.8 43.1 1.0 CA C:ASP230 4.8 47.8 1.0 CB C:ASP234 4.8 39.0 1.0 CB C:ASP230 4.9 44.2 1.0 OD1 D:ASP217 4.9 40.0 1.0

X.Chen, P.Sun, Y.Liu, S.Shen, T.Ma, J.Ding. Structures of A Constitutively Active Mutant of Human IDH3 Reveal New Insights Into the Mechanisms of Allosteric Activation and the Catalytic Reaction. J.Biol.Chem. V. 298 02695 2022.
ISSN: ESSN 1083-351X
PubMed: 36375638
DOI: 10.1016/J.JBC.2022.102695