Chlorine in PDB 8zfn: Crystal Structure of Human Ppargamma Ligand Binding Domain in Complex with GW9662 and Bvt.13

The structure of Crystal Structure of Human Ppargamma Ligand Binding Domain in Complex with GW9662 and Bvt.13, PDB code: 8zfn was solved by J.Shang, D.J.Kojetin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.04 / 2.54
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	92.186, 61.991, 118.841, 90, 102.38, 90
R / Rfree (%)	24.7 / 32.1

The binding sites of Chlorine atom in the Crystal Structure of Human Ppargamma Ligand Binding Domain in Complex with GW9662 and Bvt.13 (pdb code 8zfn). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Human Ppargamma Ligand Binding Domain in Complex with GW9662 and Bvt.13, PDB code: 8zfn:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Human Ppargamma Ligand Binding Domain in Complex with GW9662 and Bvt.13


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human Ppargamma Ligand Binding Domain in Complex with GW9662 and Bvt.13 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:85.2 occ:1.00 CL20 A:PLB502 0.0 85.2 1.0 C16 A:PLB502 1.8 71.0 1.0 C15 A:PLB502 2.7 78.5 1.0 C17 A:PLB502 2.8 68.9 1.0 CE A:MET334 3.1 52.1 1.0 SD A:MET364 3.6 92.2 1.0 CB A:MET364 3.8 74.9 1.0 C14 A:PLB502 4.0 72.8 1.0 CG A:MET364 4.0 79.2 1.0 CB A:LYS367 4.0 74.6 1.0 C18 A:PLB502 4.1 66.3 1.0 CE2 A:PHE368 4.1 58.5 1.0 CD2 A:LEU330 4.1 62.5 1.0 O A:MET364 4.1 75.6 1.0 CG A:LYS367 4.2 77.9 1.0 CG A:LEU330 4.4 60.6 1.0 CZ A:PHE368 4.5 58.6 1.0 SD A:MET334 4.5 52.8 1.0 C13 A:PLB502 4.5 65.3 1.0 CA A:MET364 4.5 82.2 1.0 CD2 A:PHE368 4.6 55.1 1.0 CG1 A:VAL339 4.7 56.5 1.0 CD1 A:LEU353 4.8 67.6 1.0 C A:MET364 4.8 73.8 1.0 CD1 A:LEU330 4.9 53.1 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Human Ppargamma Ligand Binding Domain in Complex with GW9662 and Bvt.13


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human Ppargamma Ligand Binding Domain in Complex with GW9662 and Bvt.13 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:89.9 occ:1.00 CL19 A:PLB502 0.0 89.9 1.0 C14 A:PLB502 1.8 72.8 1.0 O12 A:PLB502 2.7 69.3 1.0 C15 A:PLB502 2.7 78.5 1.0 C13 A:PLB502 2.8 65.3 1.0 C11 A:PLB502 3.1 67.7 1.0 CD2 A:LEU353 3.6 74.2 1.0 CG2 A:ILE281 3.9 78.2 1.0 CG A:MET364 4.0 79.2 1.0 SG A:CYS285 4.0 76.5 1.0 C16 A:PLB502 4.0 71.0 1.0 CB A:CYS285 4.0 72.2 1.0 C18 A:PLB502 4.1 66.3 1.0 CD1 A:LEU353 4.4 67.6 1.0 N10 A:PLB502 4.4 65.0 1.0 C17 A:PLB502 4.6 68.9 1.0 CG A:LEU353 4.6 67.0 1.0 C3 A:PLB502 4.8 70.0 1.0 CB A:MET364 4.8 74.9 1.0 SD A:MET364 4.9 92.2 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Human Ppargamma Ligand Binding Domain in Complex with GW9662 and Bvt.13


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human Ppargamma Ligand Binding Domain in Complex with GW9662 and Bvt.13 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl502 b:77.7 occ:1.00 CL20 B:PLB502 0.0 77.7 1.0 C16 B:PLB502 1.8 74.1 1.0 C15 B:PLB502 2.7 74.1 1.0 C17 B:PLB502 2.7 75.6 1.0 CE B:MET364 3.2 81.5 1.0 SD B:MET334 3.7 65.4 1.0 CB B:LYS367 3.8 70.4 1.0 C14 B:PLB502 4.0 69.5 1.0 CD1 B:LEU330 4.0 65.6 1.0 CG B:LYS367 4.0 81.7 1.0 C18 B:PLB502 4.0 69.7 1.0 CB B:MET364 4.4 83.0 1.0 SD B:MET364 4.5 103.8 1.0 C13 B:PLB502 4.5 64.9 1.0 CG B:MET364 4.6 84.2 1.0 O B:MET364 4.6 77.7 1.0 CD2 B:LEU330 4.7 61.6 1.0 CE2 B:PHE368 4.8 66.5 1.0 CA B:MET364 4.9 87.2 1.0 CG B:LEU330 4.9 64.6 1.0 CZ B:PHE368 5.0 66.5 1.0 CD B:LYS367 5.0 77.0 1.0 CG B:MET334 5.0 61.3 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Human Ppargamma Ligand Binding Domain in Complex with GW9662 and Bvt.13


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Human Ppargamma Ligand Binding Domain in Complex with GW9662 and Bvt.13 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl502 b:79.8 occ:1.00 CL19 B:PLB502 0.0 79.8 1.0 C14 B:PLB502 1.8 69.5 1.0 C13 B:PLB502 2.7 64.9 1.0 C15 B:PLB502 2.8 74.1 1.0 C11 B:PLB502 2.8 68.4 1.0 O12 B:PLB502 2.9 75.6 1.0 N10 B:PLB502 3.6 68.1 1.0 CD2 B:LEU353 3.8 55.0 1.0 CG2 B:ILE281 3.8 65.5 1.0 C3 B:PLB502 4.0 74.4 1.0 C18 B:PLB502 4.0 69.7 1.0 SD B:MET364 4.0 103.8 1.0 C16 B:PLB502 4.0 74.1 1.0 SG B:CYS285 4.2 70.3 1.0 CG B:MET364 4.2 84.2 1.0 O B:HOH612 4.2 61.0 1.0 C2 B:PLB502 4.3 69.2 1.0 CB B:CYS285 4.3 64.6 1.0 C17 B:PLB502 4.5 75.6 1.0 CD1 B:LEU353 4.8 61.5 1.0 O B:ILE281 4.9 65.4 1.0 CG B:LEU353 4.9 61.2 1.0 CE B:MET364 5.0 81.5 1.0

J.Shang, D.J.Kojetin. Unanticipated Mechanisms of Covalent Inhibitor and Synthetic Ligand Cobinding to Ppar Gamma. Elife 2024.
ISSN: ESSN 2050-084X
DOI: 10.7554/ELIFE.99782.1