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Sodium 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:

Calcium (Ca) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 3 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3inm

Go back to Sodium Binding Sites List in 3inm
Sodium 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 Sodium with other atoms in the Na 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:Na522

b:30.0
occ:1.00
 O3X A:NDP501 3.0 27.5 1.0
CD2 A:HIS315 3.8 30.4 1.0
CB A:ARG314 3.8 35.4 1.0
O2X A:NDP501 3.9 32.4 1.0
P2B A:NDP501 4.0 31.3 1.0
NE2 A:HIS315 4.0 33.2 1.0
CG A:ARG314 4.4 38.3 1.0
O1X A:NDP501 4.5 30.5 1.0
C A:ARG314 4.7 34.1 1.0
O A:HOH436 4.7 52.5 1.0
SD A:MET318 4.8 47.1 1.0
O A:ARG314 4.8 34.9 1.0
O3B A:NDP501 4.8 29.9 1.0
O A:HOH1029 4.9 43.2 1.0
N A:HIS315 4.9 32.9 1.0
CA A:ARG314 4.9 34.5 1.0
CG A:HIS315 5.0 31.7 1.0
CD A:ARG314 5.0 43.0 1.0

Sodium binding site 2 out of 3 in 3inm

Go back to Sodium Binding Sites List in 3inm
Sodium 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 Sodium with other atoms in the Na 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:Na522

b:30.0
occ:1.00
 O3X B:NDP501 2.9 28.8 1.0
O2X B:NDP501 3.7 28.4 1.0
CB B:ARG314 3.8 25.4 1.0
P2B B:NDP501 3.9 25.8 1.0
CD2 B:HIS315 4.0 24.1 1.0
CD B:ARG314 4.2 34.5 1.0
NE2 B:HIS315 4.3 25.1 1.0
O1X B:NDP501 4.5 28.8 1.0
CG B:ARG314 4.6 29.3 1.0
O3B B:NDP501 4.7 25.1 1.0
C B:ARG314 4.8 24.2 1.0
O B:ARG314 4.9 22.3 1.0
CA B:ARG314 4.9 24.4 1.0

Sodium binding site 3 out of 3 in 3inm

Go back to Sodium Binding Sites List in 3inm
Sodium 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 Sodium with other atoms in the Na 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:Na522

b:30.0
occ:1.00
 O3X C:NDP501 3.2 32.9 1.0
CB C:ARG314 3.6 33.1 1.0
CG C:ARG314 3.9 36.8 1.0
CD2 C:HIS315 4.2 27.0 1.0
CD C:ARG314 4.3 43.4 1.0
O2X C:NDP501 4.3 33.7 1.0
P2B C:NDP501 4.3 34.0 1.0
NE2 C:HIS315 4.5 29.2 1.0
C C:ARG314 4.6 31.8 1.0
CE C:MET318 4.7 44.8 1.0
O C:ARG314 4.7 32.2 1.0
CA C:ARG314 4.7 32.8 1.0
SD C:MET318 4.8 48.0 1.0
O3B C:NDP501 4.9 28.2 1.0
O1X C:NDP501 4.9 37.9 1.0
NE C:ARG314 5.0 46.9 1.0
N C:HIS315 5.0 30.9 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: Mon Oct 7 10:59:51 2024

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