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Calcium in PDB 6vfz: Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor.

Enzymatic activity of Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor.

All present enzymatic activity of Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with Nadph and Ag-881 (Vorasidenib) 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 Nadph and Ag-881 (Vorasidenib) Inhibitor., PDB code: 6vfz was solved by A.Padyana, L.Jin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.06 / 1.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.068, 119.797, 130.973, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20.9

Other elements in 6vfz:

The structure of Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with Nadph and Ag-881 (Vorasidenib) Inhibitor. also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Chlorine (Cl) 2 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 Nadph and Ag-881 (Vorasidenib) Inhibitor. (pdb code 6vfz). 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 Nadph and Ag-881 (Vorasidenib) Inhibitor., PDB code: 6vfz:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6vfz

Go back to Calcium Binding Sites List in 6vfz
Calcium binding site 1 out of 2 in the Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with Nadph and Ag-881 (Vorasidenib) 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 Nadph and Ag-881 (Vorasidenib) Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:20.4
occ:1.00
 OD1 A:ASP318 2.3 23.0 1.0
OD1 A:ASP314 2.3 14.4 1.0
O A:HOH710 2.4 34.6 1.0
OD2 B:ASP291 2.4 26.4 1.0
O A:HOH739 2.4 26.4 1.0
O A:HOH884 2.5 27.6 1.0
O A:ASP314 2.8 14.3 1.0
CG A:ASP314 3.3 17.9 1.0
CG A:ASP318 3.3 28.1 1.0
CG B:ASP291 3.5 27.3 1.0
C A:ASP314 3.7 10.3 1.0
OD2 A:ASP318 3.7 30.4 1.0
CB B:ASP291 3.9 27.1 1.0
OD2 A:ASP314 4.0 15.3 1.0
CA A:ASP314 4.2 6.7 1.0
O A:HOH877 4.2 40.0 1.0
O A:HOH930 4.3 53.5 1.0
CB A:ASP314 4.3 9.9 1.0
O A:HOH874 4.4 40.6 1.0
OD1 B:ASP291 4.5 21.3 1.0
O A:HOH821 4.6 40.0 1.0
CB A:ASP318 4.6 21.0 1.0
NZ B:LYS251 4.7 16.4 1.0
N A:VAL315 4.7 12.3 1.0
N A:ASP318 4.8 16.6 1.0
CB A:SER317 4.9 33.7 1.0

Calcium binding site 2 out of 2 in 6vfz

Go back to Calcium Binding Sites List in 6vfz
Calcium binding site 2 out of 2 in the Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase (IDH2) R140Q Mutant Homodimer in Complex with Nadph and Ag-881 (Vorasidenib) 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 Nadph and Ag-881 (Vorasidenib) Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:22.5
occ:1.00
 O B:HOH778 2.3 28.2 1.0
OD1 B:ASP318 2.3 26.6 1.0
OD1 B:ASP314 2.3 18.0 1.0
OD2 A:ASP291 2.4 26.7 1.0
O B:HOH772 2.5 32.4 1.0
O B:HOH696 2.5 25.0 1.0
O B:ASP314 2.9 16.3 1.0
CG B:ASP314 3.3 17.9 1.0
CG B:ASP318 3.4 38.1 1.0
CG A:ASP291 3.5 29.7 1.0
C B:ASP314 3.7 16.7 1.0
CB A:ASP291 3.9 24.3 1.0
OD2 B:ASP318 3.9 35.3 1.0
OD2 B:ASP314 3.9 20.8 1.0
CA B:ASP314 4.2 10.6 1.0
CB B:ASP314 4.3 11.1 1.0
OD1 A:ASP291 4.6 26.0 1.0
NZ A:LYS251 4.6 16.0 1.0
CB B:ASP318 4.7 33.8 1.0
N B:VAL315 4.7 13.5 1.0
O B:HOH766 4.8 49.3 1.0
N B:ASP318 4.9 28.6 1.0
CB B:SER317 4.9 36.1 1.0

Reference:

Z.Konteatis, E.Artin, B.Nicolay, K.Straley, A.K.Padyana, L.Jin, Y.Chen, R.Narayaraswamy, S.Tong, F.Wang, D.Zhou, D.Cui, Z.Cai, Z.Luo, C.Fang, H.Tang, X.Lv, R.Nagaraja, H.Yang, S.M.Su, Z.Sui, L.Dang, K.Yen, J.Popovici-Muller, P.Codega, C.Campos, I.K.Mellinghoff, S.Biller. Vorasidenib (Ag-881): A First-in-Class, Brain-Penetrant Dual Inhibitor of Mutant IDH1 and 2 For Treatment of Glioma Acs Med.Chem.Lett. 2020.
ISSN: ISSN 1948-5875
DOI: 10.1021/ACSMEDCHEMLETT.9B00509
Page generated: Tue Jul 16 16:51:39 2024

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