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

Sodium binding site 1 out of 2 in 6vfz

Go back to Sodium Binding Sites List in 6vfz
Sodium 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 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 Nadph and Ag-881 (Vorasidenib) Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:52.9
occ:1.00
 OG A:SER317 2.3 40.1 1.0
O A:HOH924 2.8 17.4 1.0
CB A:ILE170 3.1 9.3 1.0
O A:HOH832 3.1 20.8 1.0
CG2 A:ILE170 3.2 14.3 1.0
CB A:SER317 3.3 33.7 1.0
CA A:SER317 3.4 24.9 1.0
CG1 A:ILE170 3.6 11.4 1.0
CD A:ARG149 3.6 24.4 1.0
N A:SER317 3.7 21.4 1.0
CB A:ARG149 3.8 14.9 1.0
O A:GLY313 3.9 14.1 1.0
CG A:ARG149 3.9 18.7 1.0
O A:ILE170 4.3 12.0 1.0
CA A:ILE170 4.4 8.8 1.0
O A:HOH721 4.5 20.0 1.0
C A:GLN316 4.5 21.3 1.0
NE A:ARG149 4.5 33.6 1.0
O A:HOH925 4.6 24.8 1.0
C A:ILE170 4.6 8.7 1.0
O A:HOH844 4.8 10.4 1.0
O A:HOH662 4.8 12.6 1.0
C A:SER317 4.8 20.9 1.0
C A:GLY313 4.9 7.2 1.0
CB A:GLN316 4.9 16.9 1.0
CD1 A:ILE170 4.9 18.6 1.0
CA A:ARG149 5.0 12.0 1.0
O A:GLN316 5.0 21.7 1.0

Sodium binding site 2 out of 2 in 6vfz

Go back to Sodium Binding Sites List in 6vfz
Sodium 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 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 Nadph and Ag-881 (Vorasidenib) Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:47.4
occ:1.00
 OG B:SER317 2.3 42.4 1.0
O B:HOH830 2.6 14.2 1.0
CB B:SER317 3.1 36.1 1.0
CA B:SER317 3.2 26.9 1.0
CB B:ILE170 3.4 15.2 1.0
CG2 B:ILE170 3.5 14.8 1.0
O B:HOH704 3.6 20.7 1.0
N B:SER317 3.7 22.7 1.0
CD B:ARG149 3.7 27.6 1.0
CB B:ARG149 3.9 20.4 1.0
CG1 B:ILE170 3.9 17.6 1.0
O B:GLY313 3.9 10.7 1.0
CG B:ARG149 3.9 19.8 1.0
O B:HOH692 4.1 22.8 1.0
NE B:ARG149 4.3 30.4 1.0
C B:GLN316 4.4 24.2 1.0
O B:ILE170 4.6 14.3 1.0
O B:HOH742 4.6 13.7 1.0
C B:SER317 4.6 28.6 1.0
CA B:ILE170 4.7 13.2 1.0
O B:HOH684 4.7 15.9 1.0
O B:HOH820 4.7 23.2 1.0
O B:GLN316 4.8 19.4 1.0
CB B:GLN316 4.9 18.1 1.0
CZ B:ARG149 4.9 26.1 1.0
NH1 B:ARG149 4.9 19.1 1.0
C B:ILE170 4.9 13.0 1.0
C B:GLY313 5.0 11.8 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 Oct 8 14:22:54 2024

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