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Fluorine in PDB 4ja8: Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor

Enzymatic activity of Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor

All present enzymatic activity of Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor:
1.1.1.42;

Protein crystallography data

The structure of Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor, PDB code: 4ja8 was solved by W.Wei, L.Chen, M.Wu, F.Jiang, J.Travins, K.Qian, B.Delabarre, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.90 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.656, 119.661, 125.542, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 21.8

Other elements in 4ja8:

The structure of Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor (pdb code 4ja8). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor, PDB code: 4ja8:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4ja8

Go back to Fluorine Binding Sites List in 4ja8
Fluorine binding site 1 out of 6 in the Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:12.1
occ:0.50
 FAD A:1K9502 0.0 12.1 0.5
CAJ A:1K9502 1.2 11.8 0.5
CBE A:1K9502 1.2 9.7 0.5
CAG A:1K9502 1.7 9.9 0.5
FAE A:1K9502 2.1 10.2 0.5
FAF A:1K9502 2.1 11.6 0.5
CAZ A:1K9502 2.2 6.9 0.5
CAZ A:1K9502 2.3 11.2 0.5
FAE A:1K9502 2.8 14.8 0.5
CAI A:1K9502 3.0 11.7 0.5
CAO A:1K9502 3.0 8.3 0.5
CBE A:1K9502 3.1 12.3 0.5
OD1 B:ASP312 3.1 11.2 1.0
CAJ A:1K9502 3.1 6.7 0.5
CAO A:1K9502 3.3 11.4 0.5
OH A:TYR311 3.4 11.6 1.0
CG2 A:VAL315 3.5 14.2 1.0
CE2 A:TYR311 3.5 8.3 1.0
CAX A:1K9502 3.6 12.4 0.5
CG1 A:VAL315 3.6 13.4 1.0
CZ A:TYR311 3.7 8.5 1.0
CB A:VAL315 3.8 11.9 1.0
FAD A:1K9502 4.0 15.4 0.5
FAF A:1K9502 4.0 16.1 0.5
CG1 B:ILE290 4.0 11.9 1.0
CG B:ASP312 4.1 14.5 1.0
CAX A:1K9502 4.3 7.2 0.5
CAG A:1K9502 4.4 5.3 0.5
CD1 B:ILE290 4.5 13.3 1.0
CD2 A:TYR311 4.5 7.3 1.0
CB B:ASP312 4.6 9.6 1.0
NE2 B:GLN316 4.7 13.7 0.5
CA B:ASP312 4.7 8.2 1.0
CE1 A:TYR311 4.8 8.0 1.0
CAI A:1K9502 4.8 6.2 0.5
NAS A:1K9502 4.9 9.9 0.5

Fluorine binding site 2 out of 6 in 4ja8

Go back to Fluorine Binding Sites List in 4ja8
Fluorine binding site 2 out of 6 in the Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:15.4
occ:0.50
 FAD A:1K9502 0.0 15.4 0.5
CAJ A:1K9502 1.2 6.7 0.5
CBE A:1K9502 1.3 12.3 0.5
CAG A:1K9502 1.8 5.3 0.5
FAE A:1K9502 2.1 14.8 0.5
FAF A:1K9502 2.1 16.1 0.5
CAZ A:1K9502 2.2 11.2 0.5
CAZ A:1K9502 2.4 6.9 0.5
FAE A:1K9502 2.8 10.2 0.5
CAO A:1K9502 3.0 11.4 0.5
OD1 A:ASP312 3.1 9.9 1.0
CAI A:1K9502 3.1 6.2 0.5
CBE A:1K9502 3.1 9.7 0.5
CAJ A:1K9502 3.1 11.8 0.5
OH B:TYR311 3.4 9.4 1.0
CAO A:1K9502 3.4 8.3 0.5
CE2 B:TYR311 3.5 9.5 1.0
CG2 B:VAL315 3.5 12.0 1.0
CG1 B:VAL315 3.5 12.2 1.0
CAX A:1K9502 3.7 7.2 0.5
CB B:VAL315 3.7 9.4 1.0
CZ B:TYR311 3.7 9.7 1.0
FAD A:1K9502 4.0 12.1 0.5
FAF A:1K9502 4.0 11.6 0.5
CG A:ASP312 4.0 10.4 1.0
CG1 A:ILE290 4.1 10.4 1.0
CAX A:1K9502 4.3 12.4 0.5
CAG A:1K9502 4.3 9.9 0.5
CD2 B:TYR311 4.5 10.9 1.0
CD1 A:ILE290 4.5 10.8 1.0
CB A:ASP312 4.6 7.5 1.0
CA A:ASP312 4.6 7.0 1.0
NE2 A:GLN316 4.7 13.9 0.5
CE1 B:TYR311 4.8 9.6 1.0
CAI A:1K9502 4.8 11.7 0.5
OD2 A:ASP312 4.9 14.1 1.0
NAS A:1K9502 5.0 6.6 0.5

Fluorine binding site 3 out of 6 in 4ja8

Go back to Fluorine Binding Sites List in 4ja8
Fluorine binding site 3 out of 6 in the Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:10.2
occ:0.50
 FAE A:1K9502 0.0 10.2 0.5
CBE A:1K9502 1.3 9.7 0.5
CAJ A:1K9502 1.5 11.8 0.5
FAD A:1K9502 2.1 12.1 0.5
FAF A:1K9502 2.1 11.6 0.5
CAZ A:1K9502 2.2 11.2 0.5
CAZ A:1K9502 2.3 6.9 0.5
CAG A:1K9502 2.5 9.9 0.5
FAE A:1K9502 2.5 14.8 0.5
CBE A:1K9502 2.6 12.3 0.5
CAJ A:1K9502 2.6 6.7 0.5
FAD A:1K9502 2.8 15.4 0.5
OD1 B:ASP312 3.0 11.2 1.0
CAO A:1K9502 3.4 11.4 0.5
CE2 B:TYR311 3.4 9.5 1.0
CAO A:1K9502 3.6 8.3 0.5
CAI A:1K9502 3.6 11.7 0.5
CD2 B:TYR311 3.6 10.9 1.0
CA B:ASP312 3.6 8.2 1.0
CE2 A:TYR311 3.7 8.3 1.0
FAF A:1K9502 3.9 16.1 0.5
CAX A:1K9502 4.0 12.4 0.5
CG B:ASP312 4.0 14.5 1.0
CAG A:1K9502 4.0 5.3 0.5
CB B:VAL315 4.2 9.4 1.0
CB B:ASP312 4.2 9.6 1.0
N B:ASP312 4.2 8.6 1.0
O B:TYR311 4.3 8.3 1.0
CG2 B:VAL315 4.3 12.0 1.0
OH A:TYR311 4.3 11.6 1.0
CZ B:TYR311 4.4 9.7 1.0
CZ A:TYR311 4.5 8.5 1.0
O B:ASP312 4.5 8.6 1.0
C B:TYR311 4.5 8.3 1.0
CD2 A:TYR311 4.6 7.3 1.0
C B:ASP312 4.6 8.8 1.0
CG B:TYR311 4.7 8.3 1.0
CAX A:1K9502 4.7 7.2 0.5
CG1 B:VAL315 4.7 12.2 1.0
OD1 A:ASP312 4.8 9.9 1.0
CAI A:1K9502 4.9 6.2 0.5
OH B:TYR311 5.0 9.4 1.0

Fluorine binding site 4 out of 6 in 4ja8

Go back to Fluorine Binding Sites List in 4ja8
Fluorine binding site 4 out of 6 in the Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:14.8
occ:0.50
 FAE A:1K9502 0.0 14.8 0.5
CBE A:1K9502 1.3 12.3 0.5
CAJ A:1K9502 1.5 6.7 0.5
FAD A:1K9502 2.1 15.4 0.5
FAF A:1K9502 2.1 16.1 0.5
CAZ A:1K9502 2.2 11.2 0.5
CAZ A:1K9502 2.3 6.9 0.5
FAE A:1K9502 2.5 10.2 0.5
CAG A:1K9502 2.6 5.3 0.5
CAJ A:1K9502 2.6 11.8 0.5
CBE A:1K9502 2.6 9.7 0.5
FAD A:1K9502 2.8 12.1 0.5
OD1 A:ASP312 3.0 9.9 1.0
CE2 A:TYR311 3.5 8.3 1.0
CAO A:1K9502 3.5 8.3 0.5
CAO A:1K9502 3.5 11.4 0.5
CA A:ASP312 3.6 7.0 1.0
CD2 A:TYR311 3.6 7.3 1.0
CAI A:1K9502 3.7 6.2 0.5
CE2 B:TYR311 3.7 9.5 1.0
FAF A:1K9502 3.9 11.6 0.5
CG A:ASP312 3.9 10.4 1.0
CAG A:1K9502 3.9 9.9 0.5
CAX A:1K9502 4.0 7.2 0.5
N A:ASP312 4.1 7.9 1.0
CB A:ASP312 4.2 7.5 1.0
CG2 A:VAL315 4.2 14.2 1.0
CB A:VAL315 4.2 11.9 1.0
O A:TYR311 4.3 8.7 1.0
OH B:TYR311 4.4 9.4 1.0
CZ A:TYR311 4.4 8.5 1.0
C A:TYR311 4.4 8.1 1.0
CZ B:TYR311 4.5 9.7 1.0
CD2 B:TYR311 4.6 10.9 1.0
O A:ASP312 4.6 7.0 1.0
CAX A:1K9502 4.6 12.4 0.5
CG A:TYR311 4.6 7.8 1.0
C A:ASP312 4.6 6.3 1.0
CAI A:1K9502 4.8 11.7 0.5
CG1 A:VAL315 4.8 13.4 1.0
OD1 B:ASP312 4.8 11.2 1.0
OH A:TYR311 4.9 11.6 1.0

Fluorine binding site 5 out of 6 in 4ja8

Go back to Fluorine Binding Sites List in 4ja8
Fluorine binding site 5 out of 6 in the Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:11.6
occ:0.50
 FAF A:1K9502 0.0 11.6 0.5
CAG A:1K9502 0.8 9.9 0.5
CBE A:1K9502 1.3 9.7 0.5
CAJ A:1K9502 1.4 11.8 0.5
CAI A:1K9502 1.5 11.7 0.5
FAD A:1K9502 2.1 12.1 0.5
FAE A:1K9502 2.1 10.2 0.5
CAZ A:1K9502 2.2 6.9 0.5
CAZ A:1K9502 2.3 11.2 0.5
CAX A:1K9502 2.4 12.4 0.5
CAO A:1K9502 2.6 11.4 0.5
CAO A:1K9502 2.7 8.3 0.5
NE2 B:GLN316 3.1 13.7 0.5
CAJ A:1K9502 3.5 6.7 0.5
CBE A:1K9502 3.5 12.3 0.5
OD1 B:ASP312 3.6 11.2 1.0
NAS A:1K9502 3.6 9.9 0.5
O B:ASP312 3.6 8.6 1.0
CA B:ASP312 3.7 8.2 1.0
FAE A:1K9502 3.9 14.8 0.5
CB B:ASP312 3.9 9.6 1.0
FAD A:1K9502 4.0 15.4 0.5
CG B:GLN316 4.0 10.9 0.5
CD B:GLN316 4.0 11.6 0.5
CAX A:1K9502 4.1 7.2 0.5
CG B:ASP312 4.1 14.5 1.0
C B:ASP312 4.2 8.8 1.0
CB B:VAL315 4.3 9.4 1.0
OAA A:1K9502 4.4 7.7 0.5
FAF A:1K9502 4.5 16.1 0.5
CG1 B:VAL315 4.5 12.2 1.0
CAG A:1K9502 4.6 5.3 0.5
CG1 A:VAL315 4.7 13.4 1.0
N B:GLN316 4.7 11.9 0.5
N B:GLN316 4.7 11.6 0.5
CAW A:1K9502 4.8 11.6 0.5
CD1 B:ILE290 4.8 13.3 1.0
CAI A:1K9502 4.8 6.2 0.5
N B:ASP312 4.9 8.6 1.0
CB B:GLN316 4.9 13.0 0.5
CG1 B:ILE290 4.9 11.9 1.0
OE1 B:GLN316 5.0 13.7 0.5

Fluorine binding site 6 out of 6 in 4ja8

Go back to Fluorine Binding Sites List in 4ja8
Fluorine binding site 6 out of 6 in the Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with Agi-6780 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:16.1
occ:0.50
 FAF A:1K9502 0.0 16.1 0.5
CAG A:1K9502 0.8 5.3 0.5
CBE A:1K9502 1.3 12.3 0.5
CAJ A:1K9502 1.3 6.7 0.5
CAI A:1K9502 1.7 6.2 0.5
FAE A:1K9502 2.1 14.8 0.5
FAD A:1K9502 2.1 15.4 0.5
CAZ A:1K9502 2.3 11.2 0.5
CAZ A:1K9502 2.3 6.9 0.5
CAX A:1K9502 2.5 7.2 0.5
CAO A:1K9502 2.7 11.4 0.5
CAO A:1K9502 2.8 8.3 0.5
NE2 A:GLN316 3.2 13.9 0.5
CAJ A:1K9502 3.4 11.8 0.5
OD1 A:ASP312 3.5 9.9 1.0
CA A:ASP312 3.5 7.0 1.0
CBE A:1K9502 3.5 9.7 0.5
O A:ASP312 3.7 7.0 1.0
NAS A:1K9502 3.7 6.6 0.5
CB A:ASP312 3.8 7.5 1.0
FAE A:1K9502 3.9 10.2 0.5
FAD A:1K9502 4.0 12.1 0.5
CG A:ASP312 4.0 10.4 1.0
CD A:GLN316 4.1 9.9 0.5
CAX A:1K9502 4.1 12.4 0.5
C A:ASP312 4.1 6.3 1.0
CG A:GLN316 4.1 11.7 0.5
CB A:VAL315 4.3 11.9 1.0
OAA A:1K9502 4.3 14.1 0.5
FAF A:1K9502 4.5 11.6 0.5
CAG A:1K9502 4.6 9.9 0.5
CG1 A:VAL315 4.7 13.4 1.0
CG1 B:VAL315 4.7 12.2 1.0
N A:ASP312 4.7 7.9 1.0
CD1 A:ILE290 4.7 10.8 1.0
N A:GLN316 4.8 11.5 0.5
CB A:GLN316 4.8 12.0 0.5
N A:GLN316 4.8 11.8 0.5
CAI A:1K9502 4.9 11.7 0.5
CAW A:1K9502 4.9 7.5 0.5
CG2 A:VAL315 4.9 14.2 1.0
CG1 A:ILE290 5.0 10.4 1.0
O A:TYR311 5.0 8.7 1.0
OE1 A:GLN316 5.0 12.5 0.5

Reference:

F.Wang, J.Travins, B.Delabarre, V.Penard-Lacronique, S.Schalm, E.Hansen, K.Straley, A.Kernytsky, W.Liu, C.Gliser, H.Yang, S.Gross, E.Artin, V.Saada, E.Mylonas, C.Quivoron, J.Popovici-Muller, J.O.Saunders, F.G.Salituro, S.Yan, S.Murray, W.Wei, Y.Gao, L.Dang, M.Dorsch, S.Agresta, D.P.Schenkein, S.A.Biller, S.M.Su, S.De Botton, K.E.Yen. Targeted Inhibition of Mutant IDH2 in Leukemia Cells Induces Cellular Differentiation. Science V. 340 622 2013.
ISSN: ISSN 0036-8075
PubMed: 23558173
DOI: 10.1126/SCIENCE.1234769
Page generated: Thu Aug 1 02:48:43 2024

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