Chlorine in PDB 5u3q: Human Ppardelta Ligand-Binding Domain in Complexed with Specific Agonist 1

The structure of Human Ppardelta Ligand-Binding Domain in Complexed with Specific Agonist 1, PDB code: 5u3q was solved by C.-C.Wu, T.J.Baiga, M.Downes, J.J.La Clair, A.R.Atkins, S.B.Richard, T.A.Stockley-Noel, M.E.Bowman, R.M.Evans, J.P.Noel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.85 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.460, 94.350, 96.730, 90.00, 98.36, 90.00
R / Rfree (%)	15.9 / 18.9

The structure of Human Ppardelta Ligand-Binding Domain in Complexed with Specific Agonist 1 also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Chlorine atom in the Human Ppardelta Ligand-Binding Domain in Complexed with Specific Agonist 1 (pdb code 5u3q). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Human Ppardelta Ligand-Binding Domain in Complexed with Specific Agonist 1, PDB code: 5u3q:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Human Ppardelta Ligand-Binding Domain in Complexed with Specific Agonist 1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human Ppardelta Ligand-Binding Domain in Complexed with Specific Agonist 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl509 b:25.0 occ:1.00 HD22 B:ASN339 2.4 19.1 1.0 HA B:ASN299 2.8 19.5 1.0 O B:HOH756 2.9 24.1 1.0 HH22 B:ARG198 3.1 29.4 1.0 O B:HOH644 3.1 25.6 1.0 HB2 B:ASN339 3.2 19.1 1.0 ND2 B:ASN339 3.3 15.9 1.0 HA B:VAL336 3.3 22.5 1.0 HG22 B:VAL336 3.5 23.7 1.0 HB3 B:ASN339 3.5 19.1 1.0 HG13 B:VAL336 3.6 33.4 1.0 CA B:ASN299 3.7 16.2 1.0 CB B:ASN339 3.7 15.9 1.0 NH2 B:ARG198 3.7 24.5 1.0 HB2 B:ASN299 3.8 20.8 1.0 HH21 B:ARG198 3.8 29.4 1.0 HD21 B:ASN339 3.8 19.1 1.0 O B:VAL298 3.8 16.5 1.0 H B:LYS300 4.0 20.7 1.0 CG B:ASN339 4.0 14.9 1.0 CB B:ASN299 4.1 17.4 1.0 HB3 B:ASN299 4.2 20.8 1.0 N B:LYS300 4.2 17.3 1.0 CA B:VAL336 4.3 18.8 1.0 C B:ASN299 4.3 17.3 1.0 CG2 B:VAL336 4.4 19.7 1.0 CG1 B:VAL336 4.5 27.9 1.0 HG12 B:VAL298 4.5 18.6 1.0 C B:VAL298 4.6 16.2 1.0 CB B:VAL336 4.6 19.6 1.0 O B:HOH861 4.6 34.9 1.0 O B:HOH813 4.6 36.7 1.0 O B:VAL336 4.7 18.6 1.0 N B:ASN299 4.7 15.7 1.0 HH12 B:ARG198 4.7 22.2 1.0 HG23 B:VAL336 4.8 23.7 1.0 HB3 B:LYS300 4.8 24.2 1.0 CZ B:ARG198 4.8 24.8 1.0 O B:ALA335 4.9 14.6 1.0 HG21 B:VAL336 4.9 23.7 1.0 HG12 B:VAL336 5.0 33.4 1.0 C B:VAL336 5.0 18.9 1.0

Chlorine binding site 2 out of 2 in the Human Ppardelta Ligand-Binding Domain in Complexed with Specific Agonist 1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human Ppardelta Ligand-Binding Domain in Complexed with Specific Agonist 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl510 b:38.3 occ:1.00 HG1 B:THR193 2.2 24.1 1.0 OG1 B:THR193 3.0 20.1 1.0 HB3 B:LYS195 3.0 22.7 1.0 HG21 B:THR193 3.2 28.0 1.0 HD3 B:LYS195 3.2 36.4 1.0 HB2 B:LYS196 3.6 22.9 0.6 HB2 B:LYS196 3.7 22.3 0.4 H B:LYS196 3.8 18.5 0.6 H B:LYS196 3.8 18.4 0.4 CG2 B:THR193 3.8 23.3 1.0 CB B:THR193 3.9 22.6 1.0 HG2 B:LYS195 3.9 28.8 1.0 CB B:LYS195 3.9 18.9 1.0 HB B:THR193 4.0 27.2 1.0 HG23 B:THR193 4.0 28.0 1.0 CD B:LYS195 4.1 30.3 1.0 CG B:LYS195 4.2 24.0 1.0 N B:LYS196 4.2 15.4 0.6 N B:LYS196 4.2 15.3 0.4 HB2 B:LYS195 4.4 22.7 1.0 CB B:LYS196 4.5 19.1 0.6 CB B:LYS196 4.5 18.6 0.4 HE2 B:LYS195 4.7 58.2 1.0 HD2 B:LYS195 4.7 36.4 1.0 HG22 B:THR193 4.7 28.0 1.0 HA B:LYS196 4.8 23.3 0.6 CA B:LYS196 4.8 19.4 0.6 HB3 B:LYS196 4.8 22.3 0.4 C B:LYS195 4.8 17.7 1.0 HB3 B:LYS196 4.8 22.9 0.6 CA B:LYS196 4.8 16.8 0.4 CA B:LYS195 4.9 15.5 1.0 HA B:LYS196 4.9 20.2 0.4 CE B:LYS195 4.9 48.5 1.0 H B:LYS195 5.0 17.5 1.0

C.C.Wu, T.J.Baiga, M.Downes, J.J.La Clair, A.R.Atkins, S.B.Richard, W.Fan, T.A.Stockley-Noel, M.E.Bowman, J.P.Noel, R.M.Evans. Structural Basis For Specific Ligation of the Peroxisome Proliferator-Activated Receptor Delta. Proc. Natl. Acad. Sci. V. 114 E2563 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28320959
DOI: 10.1073/PNAS.1621513114