Potassium 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:

Chlorine

(Cl)

2 atoms

The binding sites of Potassium 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 Potassium atom.
In total 2 binding sites of Potassium where determined in the Human Ppardelta Ligand-Binding Domain in Complexed with Specific Agonist 1, PDB code: 5u3q:
Jump to Potassium binding site number: 1; 2;

Potassium 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 Potassium with other atoms in the K 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 A:K511 b:31.1 occ:1.00 HD22 A:ASN339 2.5 27.1 1.0 HA A:ASN299 2.9 23.9 1.0 O A:HOH750 3.0 29.1 1.0 O A:HOH656 3.0 29.1 1.0 HB2 A:ASN339 3.2 24.3 1.0 HA A:VAL336 3.2 27.4 1.0 ND2 A:ASN339 3.3 22.6 1.0 O A:HOH732 3.3 32.6 1.0 HG22 A:VAL336 3.3 32.7 1.0 HG13 A:VAL336 3.4 36.0 1.0 HB3 A:ASN339 3.5 24.3 1.0 CB A:ASN339 3.7 20.3 1.0 CA A:ASN299 3.8 19.9 1.0 HD21 A:ASN339 3.9 27.1 1.0 H A:LYS300 4.0 28.8 1.0 CG A:ASN339 4.0 23.6 1.0 HB2 A:ASN299 4.1 28.1 1.0 O A:VAL298 4.1 26.5 1.0 CA A:VAL336 4.1 22.8 1.0 HG12 A:VAL298 4.1 32.6 1.0 N A:LYS300 4.2 24.0 1.0 CG2 A:VAL336 4.2 27.3 1.0 C A:ASN299 4.3 20.4 1.0 CG1 A:VAL336 4.3 30.0 1.0 CB A:ASN299 4.4 23.4 1.0 HH21 A:ARG198 4.4 63.2 1.0 CB A:VAL336 4.4 24.8 1.0 O A:VAL336 4.5 25.6 1.0 HB3 A:ASN299 4.5 28.1 1.0 O A:HOH831 4.6 43.0 1.0 HB3 A:LYS300 4.7 32.5 1.0 C A:VAL298 4.7 23.5 1.0 HG23 A:VAL336 4.7 32.7 1.0 N A:ASN299 4.8 19.9 1.0 C A:VAL336 4.8 23.9 1.0 HG21 A:VAL336 4.8 32.7 1.0 HG12 A:VAL336 4.8 36.0 1.0 HG11 A:VAL336 4.9 36.0 1.0 NH2 A:ARG198 4.9 52.7 1.0 O A:ALA335 4.9 22.3 1.0 HH22 A:ARG198 5.0 63.2 1.0

Potassium 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 Potassium with other atoms in the K 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:K512 b:77.5 occ:1.00 O B:HOH808 2.7 56.6 1.0 OE2 B:GLU435 2.7 62.6 1.0 O B:HOH858 2.8 38.8 1.0 HG2 B:GLU435 2.8 41.4 1.0 O B:PRO431 3.2 23.5 1.0 HB2 B:GLN434 3.4 27.8 1.0 HA B:PRO431 3.4 25.9 1.0 HB2 B:PRO431 3.5 32.5 1.0 CD B:GLU435 3.5 47.6 1.0 CG B:GLU435 3.6 34.5 1.0 HB3 B:PRO431 3.7 32.5 1.0 HB3 B:GLN434 3.8 27.8 1.0 CB B:PRO431 3.8 27.1 1.0 CA B:PRO431 3.9 21.6 1.0 C B:PRO431 3.9 19.6 1.0 CB B:GLN434 4.0 23.2 1.0 HG3 B:GLU435 4.1 41.4 1.0 H B:GLU435 4.1 29.8 1.0 HG3 A:MET365 4.1 46.9 1.0 O A:HOH791 4.2 51.3 1.0 N B:GLU435 4.3 24.9 1.0 HA B:GLU435 4.6 32.9 1.0 C B:GLN434 4.7 24.4 1.0 OE1 B:GLU435 4.7 38.1 1.0 CB B:GLU435 4.7 29.3 1.0 CA B:GLU435 4.8 27.4 1.0 HG3 B:GLN434 4.9 32.3 1.0 CA B:GLN434 4.9 23.0 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