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Calcium in PDB 5i95: Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase R140Q Mutant Homodimer Bound to Nadph and Alpha-Ketoglutaric Acid

Enzymatic activity of Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase R140Q Mutant Homodimer Bound to Nadph and Alpha-Ketoglutaric Acid

All present enzymatic activity of Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase R140Q Mutant Homodimer Bound to Nadph and Alpha-Ketoglutaric Acid:
1.1.1.42;

Protein crystallography data

The structure of Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase R140Q Mutant Homodimer Bound to Nadph and Alpha-Ketoglutaric Acid, PDB code: 5i95 was solved by B.Zhang, L.Jin, W.Wu, F.Jiang, B.Delabarre, J.A.Travins, A.K.Padyana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.83 / 1.54
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 67.178, 154.875, 93.570, 90.00, 90.00, 90.00
R / Rfree (%) 14.2 / 17.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase R140Q Mutant Homodimer Bound to Nadph and Alpha-Ketoglutaric Acid (pdb code 5i95). 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 Human Mitochondrial Isocitrate Dehydrogenase R140Q Mutant Homodimer Bound to Nadph and Alpha-Ketoglutaric Acid, PDB code: 5i95:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5i95

Go back to Calcium Binding Sites List in 5i95
Calcium binding site 1 out of 2 in the Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase R140Q Mutant Homodimer Bound to Nadph and Alpha-Ketoglutaric Acid


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 Human Mitochondrial Isocitrate Dehydrogenase R140Q Mutant Homodimer Bound to Nadph and Alpha-Ketoglutaric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:9.7
occ:0.50
 CA A:CA502 0.0 9.7 0.5
CA A:CA502 1.5 13.1 0.5
O1 A:AKG508 2.0 20.8 1.0
O A:HOH658 2.1 15.6 1.0
OD1 A:ASP314 2.1 18.0 1.0
O5 A:AKG508 2.2 18.4 1.0
C1 A:AKG508 2.7 24.7 1.0
C2 A:AKG508 2.7 22.2 1.0
O A:HOH619 3.0 40.7 1.0
CG A:ASP314 3.3 17.5 1.0
OD2 A:ASP318 3.4 19.1 0.5
OD2 A:ASP314 3.9 23.9 1.0
O A:ASP314 3.9 11.5 1.0
O2 A:AKG508 3.9 28.5 1.0
O A:ALA347 4.1 16.1 1.0
C3 A:AKG508 4.2 23.5 1.0
OD1 A:ASP318 4.2 11.7 0.5
CG A:ASP318 4.3 17.2 0.5
NH2 A:ARG149 4.3 16.0 1.0
C5N A:NDP501 4.3 11.9 1.0
OD1 A:ASP318 4.3 23.5 0.5
O A:HOH746 4.4 13.1 1.0
C A:ASP314 4.4 9.5 1.0
CB A:ASP314 4.4 11.4 1.0
OD2 A:ASP318 4.5 8.8 0.5
CA A:ASP314 4.5 9.7 1.0
C4N A:NDP501 4.5 12.7 1.0
CG A:ASP318 4.5 10.0 0.5
C4 A:AKG508 4.8 22.4 1.0

Calcium binding site 2 out of 2 in 5i95

Go back to Calcium Binding Sites List in 5i95
Calcium binding site 2 out of 2 in the Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase R140Q Mutant Homodimer Bound to Nadph and Alpha-Ketoglutaric Acid


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 Human Mitochondrial Isocitrate Dehydrogenase R140Q Mutant Homodimer Bound to Nadph and Alpha-Ketoglutaric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:13.1
occ:0.50
 CA A:CA502 0.0 13.1 0.5
CA A:CA502 1.5 9.7 0.5
O A:HOH619 1.7 40.7 1.0
OD2 A:ASP318 2.2 19.1 0.5
OD1 A:ASP314 2.3 18.0 1.0
O A:HOH658 2.6 15.6 1.0
O1 A:AKG508 2.6 20.8 1.0
O A:ASP314 2.7 11.5 1.0
CG A:ASP318 3.2 17.2 0.5
OD1 A:ASP318 3.2 11.7 0.5
OD1 A:ASP318 3.5 23.5 0.5
C A:ASP314 3.5 9.5 1.0
CG A:ASP314 3.5 17.5 1.0
CG A:ASP318 3.6 10.0 0.5
C1 A:AKG508 3.7 24.7 1.0
NH2 A:ARG149 3.7 16.0 1.0
O5 A:AKG508 3.7 18.4 1.0
CA A:ASP314 3.9 9.7 1.0
OG A:SER317 3.9 11.4 1.0
OD2 A:ASP318 3.9 8.8 0.5
C2 A:AKG508 4.1 22.2 1.0
O A:ALA347 4.2 16.1 1.0
CB A:ASP314 4.3 11.4 1.0
CB A:ASP318 4.4 9.9 0.5
CB A:ASP318 4.5 14.0 0.5
OD2 A:ASP314 4.5 23.9 1.0
N A:VAL315 4.5 7.4 1.0
N A:ASP318 4.6 9.6 1.0
O2 A:AKG508 4.7 28.5 1.0
O A:HOH746 4.8 13.1 1.0
CZ A:ARG149 4.9 15.2 1.0
CA A:VAL315 5.0 7.6 1.0
CA A:ASP318 5.0 9.7 0.5

Reference:

K.Yen, J.Travins, F.Wang, M.D.David, E.Artin, K.Straley, A.Padyana, S.Gross, B.Delabarre, E.Tobin, Y.Chen, R.Nagaraja, S.Choe, L.Jin, Z.Konteatis, G.Cianchetta, J.O.Saunders, F.G.Salituro, C.Quivoron, P.Opolon, O.Bawa, V.Saada, A.Paci, S.Broutin, O.A.Bernard, S.De Botton, B.S.Marteyn, M.Pilichowska, Y.Xu, C.Fang, F.Jiang, W.Wei, S.Jin, L.Silverman, W.Liu, H.Yang, L.Dang, M.Dorsch, V.Penard-Lacronique, S.A.Biller, S.M.Su. Ag-221, A First-in-Class Therapy Targeting Acute Myeloid Leukemia Harboring Oncogenic IDH2 Mutations. Cancer Discov V. 7 478 2017.
ISSN: ESSN 2159-8290
PubMed: 28193778
DOI: 10.1158/2159-8290.CD-16-1034
Page generated: Wed Jul 9 06:45:05 2025

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