Calcium 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 / R_free (%)*	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
Sodium	(Na)	2 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 2 in 5i96

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Calcium Binding Sites List in 5i96

Calcium 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 Calcium with other atoms in the Ca 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:Ca501 b:14.5 occ:0.78	O	A:HOH830	2.3	25.4	1.0
	OD1	A:ASP314	2.3	14.7	1.0
	O	A:HOH605	2.4	23.7	1.0
	OD2	B:ASP291	2.4	19.9	1.0
	O	A:HOH603	2.5	24.2	0.6
	OG	A:SER317	2.5	21.0	0.7
	O	A:HOH932	2.5	30.8	1.0
	O	A:ASP314	2.6	14.8	1.0
	CG	A:ASP314	3.4	13.1	1.0
	CG	B:ASP291	3.5	17.6	1.0
	C	A:ASP314	3.5	15.1	1.0
	CB	A:SER317	3.5	22.6	0.7
	CB	A:SER317	4.0	25.3	0.3
	OD2	A:ASP318	4.0	24.3	0.3
	CA	A:ASP314	4.1	10.8	1.0
	CB	B:ASP291	4.1	18.2	1.0
	OD2	A:ASP314	4.1	12.8	1.0
	CB	A:ASP314	4.3	10.6	1.0
	O	A:HOH1027	4.4	36.4	1.0
	O	A:HOH609	4.4	36.7	1.0
	N	A:VAL315	4.4	11.4	0.7
	OD1	B:ASP291	4.5	16.7	1.0
	CA	A:VAL315	4.5	10.6	0.7
	N	A:SER317	4.5	14.0	0.7
	O	A:HOH735	4.6	36.1	1.0
	N	A:VAL315	4.6	10.8	0.3
	OG	A:SER317	4.6	26.6	0.3
	NZ	B:LYS251	4.6	12.8	1.0
	CA	A:SER317	4.6	18.7	0.7
	CG	A:ASP318	4.8	27.9	0.3
	C	A:VAL315	4.9	12.3	0.7

Calcium binding site 2 out of 2 in 5i96

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Calcium Binding Sites List in 5i96

Calcium 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 Calcium with other atoms in the Ca 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
A:Ca509 b:16.8 occ:0.80	OD1	B:ASP318	2.2	23.4	0.6
	OD1	B:ASP314	2.2	15.9	0.6
	O	B:HOH782	2.3	30.4	1.0
	OD2	A:ASP291	2.4	20.9	1.0
	O	B:HOH705	2.4	31.9	1.0
	OD1	B:ASP314	2.4	14.3	0.4
	O	B:HOH720	2.5	30.8	1.0
	O	B:ASP314	2.9	12.7	0.4
	O	B:ASP314	3.0	16.1	0.6
	OD1	B:ASP318	3.1	30.1	0.4
	OD2	B:ASP318	3.2	30.1	0.4
	CG	B:ASP314	3.3	14.3	0.4
	CG	B:ASP318	3.3	32.8	0.6
	CG	B:ASP314	3.4	14.2	0.6
	CG	A:ASP291	3.4	25.9	1.0
	CG	B:ASP318	3.5	29.5	0.4
	C	B:ASP314	3.6	11.7	0.4
	C	B:ASP314	3.8	14.4	0.6
	OD2	B:ASP314	3.8	14.3	0.4
	OD2	B:ASP318	3.9	34.1	0.6
	CB	A:ASP291	3.9	21.3	1.0
	OD2	B:ASP314	4.1	13.7	0.6
	CA	B:ASP314	4.2	11.0	0.4
	CA	B:ASP314	4.2	11.7	0.6
	CB	B:ASP314	4.3	12.1	0.4
	CB	B:ASP314	4.4	9.4	0.6
	N	B:VAL315	4.4	12.8	0.4
	OD1	A:ASP291	4.5	18.6	1.0
	CA	B:VAL315	4.5	9.4	0.4
	O	B:HOH711	4.5	40.9	1.0
	CB	B:ASP318	4.6	29.0	0.6
	NZ	A:LYS251	4.7	14.4	1.0
	N	B:VAL315	4.9	9.3	0.6
	C	B:VAL315	5.0	11.4	0.4
	CB	B:SER317	5.0	21.7	0.4
	O	B:HOH726	5.0	18.1	1.0
	N	B:ASP318	5.0	17.7	0.6

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 20:28:06 2024

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