Sodium in PDB 5hxi: 2-Methyl-3-Hydroxypyridine-5-Carboxylic Acid Oxygenase, 5HN Bound

The structure of 2-Methyl-3-Hydroxypyridine-5-Carboxylic Acid Oxygenase, 5HN Bound, PDB code: 5hxi was solved by J.Kobayashi, B.Mikami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.50
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	49.338, 131.140, 132.282, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 17.4

The binding sites of Sodium atom in the 2-Methyl-3-Hydroxypyridine-5-Carboxylic Acid Oxygenase, 5HN Bound (pdb code 5hxi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the 2-Methyl-3-Hydroxypyridine-5-Carboxylic Acid Oxygenase, 5HN Bound, PDB code: 5hxi:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the 2-Methyl-3-Hydroxypyridine-5-Carboxylic Acid Oxygenase, 5HN Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2-Methyl-3-Hydroxypyridine-5-Carboxylic Acid Oxygenase, 5HN Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:13.8 occ:0.75 SD A:MET293 1.9 11.9 0.8 SG A:CYS339 2.4 11.0 1.0 O A:HOH827 2.7 15.6 1.0 OG A:SER343 3.1 9.6 0.4 NA A:NA405 3.2 15.5 0.8 CE A:MET293 3.3 10.8 1.0 CG A:MET293 3.5 10.7 1.0 CB A:GLN299 3.5 11.2 1.0 O A:CYS339 3.6 10.2 1.0 CB A:CYS339 3.6 10.9 1.0 C A:CYS339 3.6 10.5 1.0 N A:GLN340 3.9 10.7 1.0 CB A:SER343 4.1 9.5 0.4 CB A:SER343 4.1 9.5 0.6 C A:GLN299 4.1 10.6 1.0 CA A:CYS339 4.2 10.8 1.0 CA A:GLN299 4.3 10.9 1.0 O A:GLN299 4.3 10.8 1.0 CA A:GLN340 4.3 10.7 1.0 CB A:MET293 4.4 10.9 1.0 OG A:SER343 4.5 9.6 0.6 N A:GLY300 4.5 10.6 1.0 CB A:LEU297 4.6 11.3 1.0 N A:GLN299 4.6 10.9 1.0 SG A:CYS303 4.6 12.3 1.0 O A:CYS294 4.7 11.1 1.0 CG A:GLN299 4.7 11.4 1.0 CD1 A:LEU297 4.9 11.7 1.0

Sodium binding site 2 out of 2 in the 2-Methyl-3-Hydroxypyridine-5-Carboxylic Acid Oxygenase, 5HN Bound


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 2-Methyl-3-Hydroxypyridine-5-Carboxylic Acid Oxygenase, 5HN Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:15.5 occ:0.75 SG A:CYS303 1.7 12.3 1.0 SG A:CYS339 2.5 11.0 1.0 CB A:CYS339 3.1 10.9 1.0 NA A:NA404 3.2 13.8 0.8 CB A:CYS303 3.3 11.1 1.0 CB A:GLN299 3.4 11.2 1.0 O A:GLN299 3.4 10.8 1.0 CB A:ALA365 3.7 11.1 1.0 OE1 A:GLN299 3.8 11.7 1.0 CE A:MET293 3.9 10.8 1.0 SD A:MET293 3.9 11.9 0.8 C A:GLN299 4.1 10.6 1.0 CG A:GLN299 4.1 11.4 1.0 CA A:CYS303 4.3 10.2 1.0 CD A:GLN299 4.3 11.3 1.0 CA A:GLN299 4.3 10.9 1.0 N A:CYS303 4.4 10.0 1.0 CA A:CYS339 4.5 10.8 1.0 O A:HOH887 4.7 13.7 1.0 CA A:THR336 4.8 11.1 1.0 O A:ILE335 4.9 12.1 1.0 C A:CYS339 4.9 10.5 1.0

J.Kobayashi, H.Yoshida, T.Yagi, S.Kamitori, H.Hayashi, K.Mizutani, N.Takahashi, B.Mikami. Role of the TYR270 Residue in 2-Methyl-3-Hydroxypyridine-5-Carboxylic Acid Oxygenase From Mesorhizobium Loti J. Biosci. Bioeng. V. 123 154 2017.
ISSN: ISSN 1347-4421
PubMed: 27568368
DOI: 10.1016/J.JBIOSC.2016.07.022