Atomistry » Calcium » PDB 5i6y-5ik7 » 5i95
Atomistry »
  Calcium »
    PDB 5i6y-5ik7 »
      5i95 »

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: Sun Jul 14 20:27:49 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy