Chlorine in PDB 6adi: Crystal Structures of IDH2 R140Q in Complex with Ag-881

Enzymatic activity of Crystal Structures of IDH2 R140Q in Complex with Ag-881

All present enzymatic activity of Crystal Structures of IDH2 R140Q in Complex with Ag-881:
1.1.1.42;

Protein crystallography data

The structure of Crystal Structures of IDH2 R140Q in Complex with Ag-881, PDB code: 6adi was solved by R.Ma, C.H.Yun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.61 / 1.97
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.781, 118.419, 126.082, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 22.6

Other elements in 6adi:

The structure of Crystal Structures of IDH2 R140Q in Complex with Ag-881 also contains other interesting chemical elements:

Fluorine (F) 12 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structures of IDH2 R140Q in Complex with Ag-881 (pdb code 6adi). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structures of IDH2 R140Q in Complex with Ag-881, PDB code: 6adi:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6adi

Go back to Chlorine Binding Sites List in 6adi
Chlorine binding site 1 out of 2 in the Crystal Structures of IDH2 R140Q in Complex with Ag-881


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structures of IDH2 R140Q in Complex with Ag-881 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:15.2
occ:0.57
CL1 A:9UO502 0.0 15.2 0.6
C13 A:9UO502 0.9 14.1 0.4
C14 A:9UO502 1.0 13.3 0.4
C15 A:9UO502 1.7 14.0 0.6
C12 A:9UO502 2.3 14.4 0.4
C15 A:9UO502 2.3 15.1 0.4
N17 A:9UO502 2.5 14.6 0.6
C14 A:9UO502 2.8 13.9 0.6
OD1 A:ASP312 2.9 7.7 1.0
N17 A:9UO502 3.2 15.4 0.4
C11 A:9UO502 3.2 15.0 0.4
CG A:ASP312 3.6 7.9 1.0
C11 A:9UO502 3.7 15.2 0.6
CA A:ASP312 3.7 6.8 1.0
CL1 A:9UO502 3.8 11.1 0.4
CB A:ASP312 3.8 6.7 1.0
C13 A:9UO502 4.0 12.8 0.6
OH B:TYR311 4.1 8.8 1.0
CE2 B:TYR311 4.1 10.8 1.0
CG1 A:ILE290 4.3 9.8 1.0
NE2 A:GLN316 4.3 22.3 1.0
C12 A:9UO502 4.3 13.7 0.6
CD1 A:ILE290 4.4 7.7 1.0
CG1 B:VAL315 4.4 17.3 1.0
O A:ASP312 4.5 7.0 1.0
CZ B:TYR311 4.5 11.5 1.0
CG2 B:VAL315 4.6 13.5 1.0
CB A:VAL315 4.6 12.1 1.0
CE2 A:TYR311 4.6 9.3 1.0
C A:ASP312 4.6 7.1 1.0
CG1 A:VAL315 4.7 14.1 1.0
OD2 A:ASP312 4.7 10.5 1.0
CD2 A:TYR311 4.7 9.0 1.0
C10 A:9UO502 4.7 14.8 0.4
N A:ASP312 4.7 6.5 1.0
CG2 A:VAL315 4.7 12.6 1.0
C10 A:9UO502 4.9 14.0 0.6
CB B:VAL315 4.9 13.3 1.0

Chlorine binding site 2 out of 2 in 6adi

Go back to Chlorine Binding Sites List in 6adi
Chlorine binding site 2 out of 2 in the Crystal Structures of IDH2 R140Q in Complex with Ag-881


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structures of IDH2 R140Q in Complex with Ag-881 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:11.1
occ:0.43
CL1 A:9UO502 0.0 11.1 0.4
C13 A:9UO502 0.7 12.8 0.6
C14 A:9UO502 1.0 13.9 0.6
C15 A:9UO502 1.7 15.1 0.4
C12 A:9UO502 2.1 13.7 0.6
C15 A:9UO502 2.4 14.0 0.6
N17 A:9UO502 2.4 15.4 0.4
C14 A:9UO502 2.8 13.3 0.4
OD1 B:ASP312 2.8 11.1 1.0
C11 A:9UO502 3.1 15.2 0.6
N17 A:9UO502 3.1 14.6 0.6
CG B:ASP312 3.5 11.7 1.0
C11 A:9UO502 3.6 15.0 0.4
CA B:ASP312 3.7 5.5 1.0
CB B:ASP312 3.7 6.2 1.0
CL1 A:9UO502 3.8 15.2 0.6
C13 A:9UO502 4.0 14.1 0.4
NE2 B:GLN316 4.1 20.0 1.0
CD1 B:ILE290 4.2 6.9 1.0
OH A:TYR311 4.2 8.4 1.0
CG1 B:ILE290 4.2 9.6 1.0
C12 A:9UO502 4.2 14.4 0.4
CE2 A:TYR311 4.3 9.3 1.0
O B:ASP312 4.3 9.1 1.0
CG1 A:VAL315 4.4 14.1 1.0
C B:ASP312 4.5 7.9 1.0
CG2 A:VAL315 4.5 12.6 1.0
C10 A:9UO502 4.5 14.0 0.6
CB B:VAL315 4.6 13.3 1.0
OD2 B:ASP312 4.6 9.4 1.0
CZ A:TYR311 4.7 13.5 1.0
CG1 B:VAL315 4.7 17.3 1.0
N B:ASP312 4.7 5.8 1.0
C10 A:9UO502 4.8 14.8 0.4
CE2 B:TYR311 4.8 10.8 1.0
CD2 B:TYR311 4.8 9.4 1.0
CG2 B:VAL315 4.9 13.5 1.0
CB A:VAL315 4.9 12.1 1.0
N18 A:9UO502 5.0 16.6 0.4

Reference:

R.Ma, C.H.Yun. Crystal Structures of Pan-Idh Inhibitor Ag-881 in Complex with Mutant Human IDH1 and IDH2 Biochem. Biophys. Res. V. 503 2912 2018COMMUN..
ISSN: ESSN 1090-2104
PubMed: 30131249
DOI: 10.1016/J.BBRC.2018.08.068
Page generated: Sat Dec 12 12:43:30 2020

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