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Sodium in PDB 5i96: Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with Ag-221 (Enasidenib) Inhibitor.

Enzymatic activity of Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with Ag-221 (Enasidenib) Inhibitor.

All present enzymatic activity of Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with Ag-221 (Enasidenib) Inhibitor.:
1.1.1.42;

Protein crystallography data

The structure of Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with Ag-221 (Enasidenib) Inhibitor., PDB code: 5i96 was solved by W.Wei, B.Zhang, L.Jin, 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) 41.90 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.368, 120.348, 124.734, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 19.9

Other elements in 5i96:

The structure of Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with Ag-221 (Enasidenib) Inhibitor. also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with Ag-221 (Enasidenib) Inhibitor. (pdb code 5i96). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with Ag-221 (Enasidenib) Inhibitor., PDB code: 5i96:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5i96

Go back to Sodium Binding Sites List in 5i96
Sodium binding site 1 out of 2 in the Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with Ag-221 (Enasidenib) Inhibitor.


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 Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with Ag-221 (Enasidenib) Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na507

b:15.9
occ:1.00
 O A:HOH1000 2.2 30.8 1.0
OE2 A:GLU345 2.3 24.3 1.0
OD1 A:ASN136 2.3 25.2 1.0
O A:HOH719 2.4 19.2 1.0
OE1 A:GLU343 2.4 16.4 0.7
O A:HOH665 2.5 27.3 1.0
OE2 A:GLU343 2.5 15.2 0.7
CD A:GLU343 2.8 14.3 0.7
OE1 A:GLU343 3.0 18.8 0.3
CG A:ASN136 3.2 28.1 1.0
CD A:GLU343 3.3 16.6 0.3
OE2 A:GLU343 3.4 16.4 0.3
CD A:GLU345 3.5 19.7 1.0
O A:HOH763 3.7 27.3 1.0
ND2 A:ASN136 3.8 27.0 1.0
CB A:GLU345 3.9 14.7 1.0
O A:GLU343 4.3 6.9 0.3
CG A:GLU343 4.3 11.5 0.7
CG A:GLU345 4.3 24.4 1.0
CG A:GLU343 4.3 13.3 0.3
OE1 A:GLU345 4.4 19.7 1.0
O A:HOH1201 4.4 28.9 1.0
CB A:ASN136 4.4 15.5 1.0
OG A:SER332 4.4 24.5 0.6
O A:HOH992 4.6 45.8 1.0
CD A:LYS112 4.6 9.6 1.0
O A:HOH813 4.7 32.2 1.0
O A:GLU343 4.8 10.2 0.7
O A:SER332 4.9 9.5 0.4
CB A:GLU343 5.0 10.7 0.7

Sodium binding site 2 out of 2 in 5i96

Go back to Sodium Binding Sites List in 5i96
Sodium binding site 2 out of 2 in the Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with Ag-221 (Enasidenib) Inhibitor.


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 Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with Ag-221 (Enasidenib) Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na504

b:27.3
occ:1.00
 OE1 B:GLU345 2.4 36.8 1.0
O B:HOH791 2.4 41.0 1.0
OD1 B:ASN136 2.4 40.3 1.0
OE2 B:GLU343 2.5 39.9 1.0
O B:HOH743 2.5 36.9 1.0
O B:HOH826 2.6 49.9 1.0
OE1 B:GLU343 2.6 38.4 1.0
CD B:GLU343 2.9 40.3 1.0
CG B:ASN136 3.4 40.2 1.0
CD B:GLU345 3.6 36.4 1.0
CB B:GLU345 3.9 28.4 1.0
ND2 B:ASN136 4.0 38.0 1.0
CG B:GLU345 4.3 36.7 1.0
CG B:GLU343 4.4 28.1 1.0
OE2 B:GLU345 4.5 37.1 1.0
CB B:ASN136 4.5 28.4 1.0
O B:GLU343 4.6 27.1 1.0
CD B:LYS112 4.6 27.5 1.0

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: Mon Oct 7 21:33:23 2024

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