Potassium in PDB 5u3s: Human Ppardelta Ligand-Binding Domain in Complexed with Specific Agonist 3

The structure of Human Ppardelta Ligand-Binding Domain in Complexed with Specific Agonist 3, PDB code: 5u3s 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)	47.68 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.550, 94.190, 96.320, 90.00, 98.08, 90.00
R / Rfree (%)	19 / 24.6

The binding sites of Potassium atom in the Human Ppardelta Ligand-Binding Domain in Complexed with Specific Agonist 3 (pdb code 5u3s). 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 3, PDB code: 5u3s:
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 3


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 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:K507 b:42.2 occ:1.00 HD22 A:ASN339 2.4 23.9 1.0 HA A:ASN299 2.8 33.2 1.0 O A:HOH683 2.9 32.7 1.0 O A:HOH655 3.0 26.6 1.0 HH22 A:ARG198 3.2 42.3 1.0 HB2 A:ASN339 3.2 28.1 1.0 ND2 A:ASN339 3.3 20.0 1.0 HA A:VAL336 3.4 22.0 1.0 HB3 A:ASN339 3.5 28.1 1.0 CB A:ASN339 3.7 23.4 1.0 CA A:ASN299 3.7 27.6 1.0 HG13 A:VAL336 3.7 40.3 1.0 NH2 A:ARG198 3.7 35.2 1.0 HG22 A:VAL336 3.7 30.9 1.0 HD21 A:ASN339 3.8 23.9 1.0 HH21 A:ARG198 3.8 42.3 1.0 HB2 A:ASN299 3.9 24.1 1.0 O A:VAL298 3.9 20.5 1.0 H A:LYS300 3.9 29.8 1.0 CG A:ASN339 4.0 24.4 1.0 CB A:ASN299 4.2 20.1 1.0 N A:LYS300 4.2 24.8 1.0 HB3 A:ASN299 4.2 24.1 1.0 C A:ASN299 4.3 33.2 1.0 CA A:VAL336 4.4 18.3 1.0 HG12 A:VAL298 4.5 24.2 1.0 CG2 A:VAL336 4.6 25.7 1.0 CG1 A:VAL336 4.6 33.6 1.0 C A:VAL298 4.6 28.1 1.0 N A:ASN299 4.7 26.2 1.0 HH12 A:ARG198 4.8 23.1 1.0 CB A:VAL336 4.8 23.7 1.0 O A:VAL336 4.8 24.4 1.0 CZ A:ARG198 4.8 35.1 1.0 HB3 A:LYS300 4.9 26.0 1.0 O A:ALA335 4.9 23.6 1.0

Potassium binding site 2 out of 2 in the Human Ppardelta Ligand-Binding Domain in Complexed with Specific Agonist 3


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 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:K507 b:43.4 occ:1.00 HD22 B:ASN339 2.3 50.8 1.0 O B:HOH680 2.9 40.1 1.0 HA B:ASN299 2.9 33.2 1.0 HB2 B:ASN339 3.0 33.1 1.0 O B:HOH691 3.0 32.3 1.0 ND2 B:ASN339 3.1 42.3 1.0 HA B:VAL336 3.2 32.6 1.0 HG13 B:VAL336 3.3 49.0 1.0 HB3 B:ASN339 3.3 33.1 1.0 HG22 B:VAL336 3.3 33.2 1.0 CB B:ASN339 3.5 27.6 1.0 HH12 B:ARG198 3.7 97.8 1.0 HD21 B:ASN339 3.7 50.8 1.0 CG B:ASN339 3.8 43.1 1.0 CA B:ASN299 3.9 27.6 1.0 H B:LYS300 4.0 45.3 1.0 CA B:VAL336 4.1 27.2 1.0 O B:VAL298 4.1 29.6 1.0 CG1 B:VAL336 4.1 40.8 1.0 HG12 B:VAL298 4.2 38.0 1.0 CG2 B:VAL336 4.2 27.7 1.0 HB2 B:ASN299 4.2 35.4 1.0 N B:LYS300 4.3 37.8 1.0 C B:ASN299 4.3 40.1 1.0 CB B:VAL336 4.4 30.9 1.0 CB B:ASN299 4.5 29.5 1.0 NH1 B:ARG198 4.5 81.5 1.0 O B:VAL336 4.5 47.3 1.0 HH22 B:ARG198 4.6 75.7 1.0 HG12 B:VAL336 4.7 49.0 1.0 HB3 B:ASN299 4.7 35.4 1.0 HB3 B:LYS300 4.7 38.8 1.0 C B:VAL298 4.7 40.8 1.0 HG11 B:VAL336 4.7 49.0 1.0 HG23 B:VAL336 4.7 33.2 1.0 N B:ASN299 4.8 44.1 1.0 HG21 B:VAL336 4.8 33.2 1.0 C B:VAL336 4.8 33.6 1.0 O B:HOH627 4.9 48.3 1.0 HH11 B:ARG198 4.9 97.8 1.0 O B:ALA335 5.0 30.4 1.0 CA B:ASN339 5.0 32.2 1.0 OD1 B:ASN339 5.0 32.9 1.0 N B:VAL336 5.0 27.0 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