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Calcium in PDB 3inm: Crystal Structure of Human Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase R132H Mutant in Complex with Nadph, Alpha-Ketoglutarate and Calcium(2+)

Enzymatic activity of Crystal Structure of Human Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase R132H Mutant in Complex with Nadph, Alpha-Ketoglutarate and Calcium(2+)

All present enzymatic activity of Crystal Structure of Human Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase R132H Mutant in Complex with Nadph, Alpha-Ketoglutarate and Calcium(2+):
1.1.1.42;

Protein crystallography data

The structure of Crystal Structure of Human Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase R132H Mutant in Complex with Nadph, Alpha-Ketoglutarate and Calcium(2+), PDB code: 3inm was solved by E.Fontano, R.S.Brown, R.K.Suto, B.Bhyravbhatla, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.91 / 2.10
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 96.120, 274.690, 116.500, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 26.2

Other elements in 3inm:

The structure of Crystal Structure of Human Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase R132H Mutant in Complex with Nadph, Alpha-Ketoglutarate and Calcium(2+) also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase R132H Mutant in Complex with Nadph, Alpha-Ketoglutarate and Calcium(2+) (pdb code 3inm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Human Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase R132H Mutant in Complex with Nadph, Alpha-Ketoglutarate and Calcium(2+), PDB code: 3inm:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 3inm

Go back to Calcium Binding Sites List in 3inm
Calcium binding site 1 out of 3 in the Crystal Structure of Human Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase R132H Mutant in Complex with Nadph, Alpha-Ketoglutarate and Calcium(2+)


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 Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase R132H Mutant in Complex with Nadph, Alpha-Ketoglutarate and Calcium(2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca521

b:35.6
occ:1.00
 OD1 A:ASP275 2.2 38.4 1.0
O A:HOH427 2.5 34.5 1.0
O A:HOH426 2.5 37.7 1.0
OD2 B:ASP252 2.5 37.6 1.0
O2 A:AKG511 2.5 43.5 1.0
OD2 A:ASP279 2.7 39.2 1.0
O5 A:AKG511 2.7 44.3 1.0
O A:ASP275 3.0 30.2 1.0
C1 A:AKG511 3.4 45.1 1.0
CG A:ASP275 3.4 34.6 1.0
C2 A:AKG511 3.4 43.7 1.0
CG B:ASP252 3.4 32.6 1.0
CG A:ASP279 3.5 34.4 1.0
OD1 A:ASP279 3.5 38.5 1.0
CB B:ASP252 3.6 30.4 1.0
C A:ASP275 3.8 29.1 1.0
NH2 A:ARG109 3.9 32.9 1.0
OD2 A:ASP275 4.1 39.1 1.0
CA A:ASP275 4.2 29.5 1.0
O A:ALA308 4.3 29.4 1.0
NZ B:LYS212 4.4 40.7 1.0
CB A:ASP275 4.4 29.8 1.0
OG A:SER278 4.5 31.3 1.0
O1 A:AKG511 4.6 47.1 1.0
OD1 B:ASP252 4.6 37.2 1.0
O A:HOH428 4.7 38.0 1.0
N A:VAL276 4.8 28.1 1.0
C3 A:AKG511 4.9 41.2 1.0
CB A:ASP279 4.9 29.8 1.0
C5N A:NDP501 5.0 20.5 1.0

Calcium binding site 2 out of 3 in 3inm

Go back to Calcium Binding Sites List in 3inm
Calcium binding site 2 out of 3 in the Crystal Structure of Human Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase R132H Mutant in Complex with Nadph, Alpha-Ketoglutarate and Calcium(2+)


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 Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase R132H Mutant in Complex with Nadph, Alpha-Ketoglutarate and Calcium(2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca521

b:33.0
occ:1.00
 OD1 B:ASP275 2.2 37.1 1.0
O B:HOH427 2.4 42.0 1.0
O B:HOH428 2.5 26.4 1.0
OD2 A:ASP252 2.5 33.8 1.0
OD2 B:ASP279 2.5 34.0 1.0
O2 B:AKG511 2.7 42.0 1.0
O B:ASP275 2.8 26.9 1.0
O5 B:AKG511 2.8 37.8 1.0
CG A:ASP252 3.4 30.1 1.0
CG B:ASP279 3.4 28.4 1.0
CG B:ASP275 3.4 33.2 1.0
C1 B:AKG511 3.5 42.0 1.0
C2 B:AKG511 3.6 40.3 1.0
OD1 B:ASP279 3.6 33.2 1.0
C B:ASP275 3.6 26.5 1.0
CB A:ASP252 3.6 27.5 1.0
NH2 B:ARG109 3.8 28.4 1.0
OD2 B:ASP275 4.1 38.3 1.0
CA B:ASP275 4.2 27.5 1.0
CB B:ASP275 4.4 28.4 1.0
OD1 A:ASP252 4.4 39.2 1.0
OG B:SER278 4.6 26.4 1.0
N B:VAL276 4.6 25.3 1.0
O B:ALA308 4.6 27.2 1.0
O1 B:AKG511 4.7 45.4 1.0
CB B:ASP279 4.7 23.3 1.0
O B:HOH429 4.8 35.1 1.0
CA A:ASP252 4.8 25.6 1.0
CA B:VAL276 4.9 24.6 1.0

Calcium binding site 3 out of 3 in 3inm

Go back to Calcium Binding Sites List in 3inm
Calcium binding site 3 out of 3 in the Crystal Structure of Human Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase R132H Mutant in Complex with Nadph, Alpha-Ketoglutarate and Calcium(2+)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human Cytosolic Nadp(+)-Dependent Isocitrate Dehydrogenase R132H Mutant in Complex with Nadph, Alpha-Ketoglutarate and Calcium(2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca521

b:41.9
occ:1.00
 OD1 C:ASP275 2.1 40.2 1.0
O C:HOH426 2.6 47.1 1.0
O2 C:AKG511 2.7 46.7 1.0
O5 C:AKG511 2.8 48.4 1.0
O C:ASP275 2.8 30.5 1.0
O C:HOH427 2.8 36.2 1.0
OD2 C:ASP279 2.8 38.5 1.0
CG C:ASP275 3.3 37.6 1.0
C1 C:AKG511 3.5 48.0 1.0
C2 C:AKG511 3.5 48.2 1.0
CG C:ASP279 3.6 33.8 1.0
C C:ASP275 3.6 31.0 1.0
NH2 C:ARG109 3.7 38.0 1.0
OD1 C:ASP279 3.8 36.2 1.0
CA C:ASP275 4.0 31.5 1.0
OD2 C:ASP275 4.1 42.8 1.0
CB C:ASP275 4.3 32.8 1.0
O C:ALA308 4.3 31.6 1.0
OG C:SER278 4.7 31.6 1.0
O1 C:AKG511 4.7 50.0 1.0
N C:VAL276 4.8 29.6 1.0
CZ C:ARG109 4.8 34.6 1.0
CB C:ASP279 5.0 30.3 1.0
C3 C:AKG511 5.0 44.7 1.0

Reference:

L.Dang, D.W.White, S.Gross, B.D.Bennett, M.A.Bittinger, E.M.Driggers, V.R.Fantin, H.G.Jang, S.Jin, M.C.Keenan, K.M.Marks, R.M.Prins, P.S.Ward, K.E.Yen, L.M.Liau, J.D.Rabinowitz, L.C.Cantley, C.B.Thompson, M.G.Vander Heiden, S.M.Su. Cancer-Associated IDH1 Mutations Produce 2-Hydroxyglutarate. Nature V. 462 739 2009.
ISSN: ISSN 0028-0836
PubMed: 19935646
DOI: 10.1038/NATURE08617
Page generated: Tue Jul 8 13:24:49 2025

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