Sodium in PDB 2yxt: Human Pyridoxal Kinase

All present enzymatic activity of Human Pyridoxal Kinase:
2.7.1.35;

The structure of Human Pyridoxal Kinase, PDB code: 2yxt 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 / 2.00
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.630, 115.286, 172.403, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 24.5

The binding sites of Sodium atom in the Human Pyridoxal Kinase (pdb code 2yxt). 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: 2yxt:
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:Na1314 b:61.7 occ:1.00 O A:HOH1324 1.9 55.9 1.0 O A:HOH1320 1.9 42.9 1.0 O A:HOH1322 2.1 56.1 1.0 O A:HOH1323 2.3 39.2 1.0 O A:HOH1321 2.4 34.8 1.0 OD1 A:ASP113 3.6 33.9 1.0 OG1 A:THR186 3.8 36.3 1.0 OE1 A:GLU153 3.9 27.3 1.0 O A:THR148 3.9 26.5 1.0 OD2 A:ASP113 4.2 39.7 1.0 CG A:ASP113 4.4 33.1 1.0 CB A:ASN150 4.4 23.4 1.0 O A:HOH1344 4.5 31.3 1.0 OE2 A:GLU153 4.5 39.6 1.0 N A:ASN150 4.5 27.6 1.0 CD A:GLU153 4.6 39.6 1.0 CA A:GLY234 4.8 24.6 1.0 CG A:ASN150 4.9 31.6 1.0 C A:PRO149 5.0 35.6 1.0 OD1 A:ASN150 5.0 40.9 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:Na1316 b:62.9 occ:1.00 O B:HOH1350 2.0 33.3 1.0 O B:HOH1352 2.3 44.8 1.0 O B:HOH1353 2.7 48.5 1.0 O B:HOH1351 3.0 40.3 1.0 OG1 B:THR186 3.5 54.9 1.0 O B:THR148 3.9 28.7 1.0 OE1 B:GLU153 4.0 38.7 1.0 OD1 B:ASP113 4.2 37.0 1.0 CB B:ASN150 4.2 25.4 1.0 N B:ASN150 4.2 26.3 1.0 O B:HOH1423 4.3 23.3 1.0 ND2 B:ASN150 4.4 36.7 1.0 CG B:ASN150 4.6 25.8 1.0 CA B:ASN150 4.6 27.6 1.0 CB B:THR186 4.6 39.6 1.0 CG2 B:THR186 4.6 45.4 1.0 C B:PRO149 4.7 32.6 1.0 OD2 B:ASP113 4.8 29.4 1.0 C5 B:MPD1023 4.8 57.9 1.0 CD B:GLU153 4.8 37.1 1.0 CA B:GLY234 4.8 17.8 1.0 CG B:ASP113 4.9 32.9 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