Potassium in PDB 9j3u: Crystal Structure of Tyrosine Phenol-Lyase in Complex with 3,5- Dihydroxybenzoic Acid

All present enzymatic activity of Crystal Structure of Tyrosine Phenol-Lyase in Complex with 3,5- Dihydroxybenzoic Acid:
4.1.99.2;

The structure of Crystal Structure of Tyrosine Phenol-Lyase in Complex with 3,5- Dihydroxybenzoic Acid, PDB code: 9j3u was solved by K.Hara, T.Kobayashi, S.Ohishi, H.Hashimoto, K.Watanabe, N.Miyoshi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.94 / 1.83
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	111.422, 155.664, 58.919, 90, 90, 90
R / Rfree (%)	15.1 / 18.2

The binding sites of Potassium atom in the Crystal Structure of Tyrosine Phenol-Lyase in Complex with 3,5- Dihydroxybenzoic Acid (pdb code 9j3u). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of Tyrosine Phenol-Lyase in Complex with 3,5- Dihydroxybenzoic Acid, PDB code: 9j3u:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Crystal Structure of Tyrosine Phenol-Lyase in Complex with 3,5- Dihydroxybenzoic Acid


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Tyrosine Phenol-Lyase in Complex with 3,5- Dihydroxybenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:K503 b:19.2 occ:1.00 OE1 B:GLU69 2.7 15.9 1.0 O A:GLY52 2.7 15.3 1.0 O B:HOH703 2.8 19.2 1.0 O B:HOH694 2.8 21.2 1.0 O A:ASN262 2.9 17.4 1.0 HB3 B:GLU69 3.0 20.1 1.0 HB3 A:ASN262 3.0 17.8 1.0 O A:HOH763 3.0 20.5 1.0 HA3 A:GLY52 3.3 21.4 1.0 HA B:ALA295 3.3 18.8 1.0 O B:GLU69 3.4 18.4 1.0 C A:GLY52 3.5 17.9 1.0 HA B:GLU69 3.6 18.2 1.0 H B:GLY296 3.7 19.2 1.0 CB B:GLU69 3.8 16.8 1.0 CD B:GLU69 3.8 15.9 1.0 HA A:ASN262 3.8 18.8 1.0 CA A:GLY52 3.9 17.9 1.0 C A:ASN262 3.9 18.2 1.0 CB A:ASN262 3.9 14.9 1.0 CA B:GLU69 4.0 15.2 1.0 HE3 A:LYS256 4.1 25.3 1.0 CA A:ASN262 4.1 15.7 1.0 C B:GLU69 4.1 20.0 1.0 HA2 A:GLY52 4.2 21.4 1.0 HD22 A:ASN262 4.3 20.8 1.0 CA B:ALA295 4.3 15.6 1.0 CG B:GLU69 4.3 15.7 1.0 O B:HOH734 4.3 18.3 1.0 HB2 A:ASN262 4.4 17.8 1.0 N B:GLY296 4.5 16.0 1.0 HG3 B:GLU69 4.5 18.8 1.0 HB2 B:GLU69 4.5 20.1 1.0 HB1 B:ALA295 4.5 17.2 1.0 HA A:THR53 4.6 19.7 1.0 N A:THR53 4.7 16.1 1.0 HB2 B:ALA295 4.7 17.2 1.0 HZ3 A:LYS256 4.8 27.6 1.0 CB B:ALA295 4.8 14.3 1.0 ND2 A:ASN262 4.8 17.4 1.0 O B:LEU294 4.8 18.8 1.0 CG A:ASN262 4.9 17.1 1.0 O A:SER51 4.9 19.1 1.0 OE2 B:GLU69 4.9 16.6 1.0 HB A:ILE263 4.9 25.9 1.0 CE A:LYS256 4.9 21.1 1.0 C B:ALA295 4.9 15.6 1.0

Potassium binding site 2 out of 2 in the Crystal Structure of Tyrosine Phenol-Lyase in Complex with 3,5- Dihydroxybenzoic Acid


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Tyrosine Phenol-Lyase in Complex with 3,5- Dihydroxybenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:K501 b:18.9 occ:1.00 OE1 A:GLU69 2.7 16.9 1.0 O B:GLY52 2.8 15.7 1.0 O A:HOH676 2.8 19.1 1.0 O B:HOH666 2.9 18.7 1.0 O B:ASN262 2.9 17.5 1.0 HB3 A:GLU69 2.9 18.8 1.0 HB3 B:ASN262 3.0 18.0 1.0 O B:HOH797 3.0 21.6 1.0 HA3 B:GLY52 3.3 18.8 1.0 HA A:ALA295 3.3 18.3 1.0 O A:GLU69 3.5 18.9 1.0 C B:GLY52 3.6 16.8 1.0 HA A:GLU69 3.7 15.6 1.0 CB A:GLU69 3.8 15.6 1.0 H A:GLY296 3.8 17.6 1.0 HA B:ASN262 3.8 18.1 1.0 CD A:GLU69 3.8 18.6 1.0 C B:ASN262 3.9 14.8 1.0 CA B:GLY52 3.9 15.7 1.0 CB B:ASN262 3.9 15.0 1.0 HE3 B:LYS256 4.0 26.8 1.0 CA A:GLU69 4.1 13.0 1.0 CA B:ASN262 4.1 15.1 1.0 HA2 B:GLY52 4.2 18.8 1.0 C A:GLU69 4.2 17.6 1.0 CA A:ALA295 4.3 15.3 1.0 CG A:GLU69 4.3 16.9 1.0 HD22 B:ASN262 4.3 18.6 1.0 O A:HOH756 4.3 16.9 1.0 HB2 B:ASN262 4.4 18.0 1.0 HG3 A:GLU69 4.5 20.2 1.0 HB1 A:ALA295 4.5 19.7 1.0 N A:GLY296 4.5 14.6 1.0 HB2 A:GLU69 4.5 18.8 1.0 HA B:THR53 4.6 19.6 1.0 HB2 A:ALA295 4.7 19.7 1.0 N B:THR53 4.7 14.5 1.0 CB A:ALA295 4.7 16.4 1.0 HZ3 B:LYS256 4.8 25.2 1.0 O A:LEU294 4.8 19.0 1.0 CE B:LYS256 4.8 22.3 1.0 O B:SER51 4.8 18.0 1.0 ND2 B:ASN262 4.9 15.5 1.0 CG B:ASN262 4.9 16.2 1.0 HE2 B:LYS256 4.9 26.8 1.0 OE2 A:GLU69 4.9 16.9 1.0 HB B:ILE263 4.9 21.2 1.0 C A:ALA295 4.9 15.1 1.0

T.Kobayashi, S.Oishi, K.Hara, M.Matsui, P.Mena, H.Hashimoto, K.Watanabe, N.Miyoshi. 3,5-Dihydroxybenzoic Acid As A Potent Inhibitor of Tyrosine Phenol-Lyase Decreases Fecal Phenol Levels in Mice. J.Med.Chem. 2025.
ISSN: ISSN 0022-2623
PubMed: 40173106
DOI: 10.1021/ACS.JMEDCHEM.5C00418