Sodium in PDB 2yxu: Human Pyridoxal Kinase

All present enzymatic activity of Human Pyridoxal Kinase:
2.7.1.35;

The structure of Human Pyridoxal Kinase, PDB code: 2yxu was solved by M.K.Safo, F.N.Musayev, T.P.Ko, V.Schirch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.20
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.462, 115.119, 170.201, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 24.3

The structure of Human Pyridoxal Kinase also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

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

Sodium binding site 1 out of 2 in the Human Pyridoxal Kinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Pyridoxal Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1406 b:22.9 occ:1.00 O A:HOH1508 2.3 33.8 1.0 OG1 A:THR186 2.4 28.6 1.0 O A:THR148 2.5 34.3 1.0 O3B A:ATP1410 2.5 33.5 1.0 O2G A:ATP1410 2.7 47.4 1.0 PG A:ATP1410 3.0 60.5 1.0 OD1 A:ASP113 3.4 37.3 1.0 CB A:THR186 3.5 31.8 1.0 O2B A:ATP1410 3.5 32.2 1.0 O1G A:ATP1410 3.6 39.9 1.0 C A:THR148 3.6 30.6 1.0 PB A:ATP1410 3.6 34.8 1.0 CG2 A:THR186 3.7 20.5 1.0 N A:ASN150 3.8 30.5 1.0 C A:PRO149 3.9 28.9 1.0 OD2 A:ASP113 4.1 38.2 1.0 CG A:ASP113 4.1 35.9 1.0 CA A:PRO149 4.1 25.7 1.0 OG1 A:THR148 4.2 24.7 1.0 OE1 A:GLU153 4.2 31.9 1.0 CB A:THR148 4.3 26.3 1.0 N A:PRO149 4.4 32.3 1.0 O3A A:ATP1410 4.4 38.8 1.0 O3G A:ATP1410 4.5 41.7 1.0 O A:PRO149 4.5 33.0 1.0 CA A:ASN150 4.5 27.2 1.0 CB A:ASN150 4.5 25.2 1.0 CA A:THR148 4.6 29.8 1.0 CA A:GLY234 4.7 24.0 1.0 CA A:THR186 4.7 23.6 1.0 O1B A:ATP1410 4.7 31.6 1.0 N A:THR186 4.9 28.5 1.0 O A:GLY234 4.9 26.5 1.0

Sodium binding site 2 out of 2 in the Human Pyridoxal Kinase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Pyridoxal Kinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2406 b:24.9 occ:1.00 OG1 B:THR186 2.1 32.9 1.0 O B:THR148 2.4 30.2 1.0 O B:HOH2413 2.4 21.9 1.0 O1G B:ATP2410 2.5 44.0 1.0 O3B B:ATP2410 2.5 28.3 1.0 PG B:ATP2410 3.1 60.4 1.0 CB B:THR186 3.2 29.4 1.0 O2B B:ATP2410 3.3 28.1 1.0 CG2 B:THR186 3.3 32.2 1.0 PB B:ATP2410 3.5 32.9 1.0 C B:THR148 3.5 28.2 1.0 C B:PRO149 3.7 27.9 1.0 N B:ASN150 3.7 25.7 1.0 OD2 B:ASP113 3.9 35.7 1.0 O3G B:ATP2410 3.9 46.1 1.0 O B:PRO149 4.0 24.9 1.0 OG1 B:THR148 4.1 18.6 1.0 CA B:PRO149 4.1 23.3 1.0 OE1 B:GLU153 4.1 27.4 1.0 N B:PRO149 4.2 27.4 1.0 CA B:ASN150 4.3 25.4 1.0 CB B:THR148 4.3 20.4 1.0 O3A B:ATP2410 4.4 28.0 1.0 OD1 B:ASP113 4.4 23.4 1.0 CB B:ASN150 4.4 20.9 1.0 O2G B:ATP2410 4.4 45.0 1.0 CG B:ASP113 4.5 25.0 1.0 CA B:THR186 4.5 29.2 1.0 CA B:THR148 4.6 25.4 1.0 O1B B:ATP2410 4.6 35.4 1.0 N B:THR186 4.6 26.5 1.0

F.N.Musayev, M.L.Di Salvo, T.P.Ko, A.K.Gandhi, A.Goswami, V.Schirch, M.K.Safo. Crystal Structure of Human Pyridoxal Kinase: Structural Basis of M(+) and M(2+) Activation. Protein Sci. V. 16 2184 2007.
ISSN: ISSN 0961-8368
PubMed: 17766369
DOI: 10.1110/PS.073022107