Sodium in PDB 8wr2: Crystal Structure of Human Pyridoxal Kinase with Bound Luteolin

The structure of Crystal Structure of Human Pyridoxal Kinase with Bound Luteolin, PDB code: 8wr2 was solved by J.Fan, Y.Zhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.48 / 1.94
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	94.54, 116.11, 169.08, 90, 90, 90
R / Rfree (%)	18.4 / 20.9

The binding sites of Sodium atom in the Crystal Structure of Human Pyridoxal Kinase with Bound Luteolin (pdb code 8wr2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human Pyridoxal Kinase with Bound Luteolin, PDB code: 8wr2:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Pyridoxal Kinase with Bound Luteolin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Pyridoxal Kinase with Bound Luteolin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:51.2 occ:1.00 O6 B:LU2402 2.5 45.6 0.9 O B:HOH614 2.5 44.8 1.0 O B:HOH659 2.7 36.3 1.0 O B:THR148 2.8 37.5 1.0 O B:HOH618 3.0 50.4 1.0 C14 B:LU2402 3.3 41.9 0.9 C13 B:LU2402 3.3 43.3 0.9 OD1 B:ASP113 3.6 40.2 1.0 O B:HOH727 3.9 56.1 1.0 C B:THR148 4.0 39.6 1.0 OD2 B:ASP113 4.0 40.3 1.0 OG1 B:THR186 4.0 44.9 1.0 OG1 B:THR148 4.0 39.1 1.0 CG B:ASP113 4.1 40.6 1.0 N B:ASN150 4.1 35.2 1.0 CB B:THR148 4.3 38.4 1.0 C B:PRO149 4.3 38.1 1.0 CA B:GLY234 4.4 38.4 1.0 O B:HOH688 4.6 50.2 1.0 C15 B:LU2402 4.6 39.4 0.9 OE1 B:GLU153 4.6 38.6 1.0 C12 B:LU2402 4.6 44.2 0.9 O B:PRO149 4.7 38.9 1.0 CB B:ASN150 4.7 37.2 1.0 CA B:ASN150 4.8 37.7 1.0 CA B:PRO149 4.8 35.4 1.0 CA B:THR148 4.8 35.5 1.0 CD2 B:PHE237 4.8 37.5 1.0 O B:HOH691 4.8 52.1 1.0 N B:PRO149 4.9 36.2 1.0 O B:GLY234 4.9 35.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Pyridoxal Kinase with Bound Luteolin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human Pyridoxal Kinase with Bound Luteolin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:54.7 occ:1.00 O6 A:LU2402 2.4 56.8 0.8 O A:HOH504 2.6 47.5 1.0 OG1 A:THR186 2.9 55.7 1.0 O A:HOH541 2.9 38.2 1.0 O A:THR148 2.9 42.5 1.0 C14 A:LU2402 3.1 51.7 0.8 C13 A:LU2402 3.1 55.9 0.8 CG2 A:THR186 3.4 48.8 1.0 OD1 A:ASP113 3.6 46.7 1.0 CB A:THR186 3.6 51.6 1.0 O A:HOH507 3.8 56.4 1.0 OD2 A:ASP113 4.0 45.3 1.0 CG A:ASP113 4.1 45.7 1.0 C A:THR148 4.1 38.7 1.0 OG1 A:THR148 4.2 38.4 1.0 N A:ASN150 4.2 41.2 1.0 CA A:GLY234 4.3 40.7 1.0 O A:HOH513 4.3 63.1 1.0 C15 A:LU2402 4.4 51.7 0.8 C A:PRO149 4.4 38.7 1.0 CB A:THR148 4.4 41.2 1.0 O A:HOH542 4.5 53.4 1.0 C12 A:LU2402 4.5 57.1 0.8 OE1 A:GLU153 4.7 43.8 1.0 O A:PRO149 4.8 42.7 1.0 O A:GLY234 4.9 37.9 1.0 CB A:ASN150 4.9 45.3 1.0 CA A:ASN150 4.9 45.0 1.0 CA A:PRO149 4.9 41.9 1.0 CA A:THR148 4.9 39.2 1.0 N A:PRO149 5.0 43.1 1.0

Y.Zhu, G.Bao, G.Zhu, K.Zhang, S.Zhu, J.Hu, J.He, W.Jiang, J.Fan, Y.Dang. Discovery and Characterization of Natural Product Luteolin As An Effective Inhibitor of Human Pyridoxal Kinase. Bioorg.Chem. V. 143 07057 2024.
ISSN: ISSN 0045-2068
PubMed: 38150934
DOI: 10.1016/J.BIOORG.2023.107057