Sodium in PDB 3fhy: Crystal Structure of D235N Mutant of Human Pyridoxal Kinase

All present enzymatic activity of Crystal Structure of D235N Mutant of Human Pyridoxal Kinase:
2.7.1.35;

The structure of Crystal Structure of D235N Mutant of Human Pyridoxal Kinase, PDB code: 3fhy was solved by M.K.Safo, A.K.Gandhi, F.N.Musayev, M.Ghatge, M.L.Di Salvo, V.Schirch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.36 / 2.30
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	91.110, 114.643, 169.681, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 26.1

The structure of Crystal Structure of D235N Mutant of Human Pyridoxal Kinase also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of D235N Mutant of Human Pyridoxal Kinase (pdb code 3fhy). 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 D235N Mutant of Human Pyridoxal Kinase, PDB code: 3fhy:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of D235N Mutant of 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 Crystal Structure of D235N Mutant of Human Pyridoxal Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:28.7 occ:1.00 O A:THR148 2.4 30.3 1.0 O3B A:ATP409 2.4 41.5 1.0 OG1 A:THR186 2.6 36.2 1.0 O A:HOH419 2.7 50.9 1.0 OD1 A:ASP113 3.3 42.5 1.0 O1G A:ATP409 3.3 45.2 1.0 PG A:ATP409 3.4 80.1 1.0 N A:ASN150 3.5 28.4 1.0 O1B A:ATP409 3.5 35.4 1.0 C A:THR148 3.6 32.8 1.0 C A:PRO149 3.6 38.7 1.0 PB A:ATP409 3.6 32.0 1.0 OE1 A:GLU153 3.7 41.7 1.0 CB A:THR186 3.7 39.4 1.0 O2G A:ATP409 3.8 36.5 1.0 CA A:PRO149 3.8 36.0 1.0 CG2 A:THR186 3.8 20.8 1.0 O A:PRO149 4.1 34.5 1.0 CA A:ASN150 4.2 34.1 1.0 CG A:ASP113 4.2 34.0 1.0 N A:PRO149 4.2 38.7 1.0 CB A:ASN150 4.3 38.8 1.0 OG1 A:THR148 4.4 17.9 1.0 OD2 A:ASP113 4.4 34.7 1.0 CB A:THR148 4.5 29.3 1.0 O3A A:ATP409 4.5 51.0 1.0 O2B A:ATP409 4.7 37.8 1.0 CA A:THR148 4.7 23.1 1.0 O3G A:ATP409 4.8 59.6 1.0 CD A:GLU153 4.8 44.5 1.0 CA A:THR186 4.9 30.1 1.0 CA A:GLY234 5.0 25.5 1.0 CG A:ASN150 5.0 37.0 1.0 N A:THR186 5.0 29.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of D235N Mutant of 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 Crystal Structure of D235N Mutant of Human Pyridoxal Kinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na406 b:33.5 occ:1.00 O B:THR148 2.3 29.4 1.0 O3B B:ATP407 2.5 35.6 1.0 OG1 B:THR186 2.6 33.8 1.0 O B:HOH418 2.6 28.2 1.0 O2G B:ATP407 3.2 54.7 1.0 OD1 B:ASP113 3.3 42.8 1.0 PG B:ATP407 3.4 69.3 1.0 CG2 B:THR186 3.5 29.8 1.0 C B:THR148 3.5 30.5 1.0 CB B:THR186 3.5 32.9 1.0 N B:ASN150 3.7 29.9 1.0 PB B:ATP407 3.7 39.0 1.0 O1B B:ATP407 3.7 38.6 1.0 C B:PRO149 3.8 31.4 1.0 OG1 B:THR148 4.0 30.6 1.0 OE1 B:GLU153 4.0 30.5 1.0 O3G B:ATP407 4.0 47.5 1.0 CA B:PRO149 4.0 19.4 1.0 CG B:ASP113 4.1 33.7 1.0 O B:PRO149 4.2 30.1 1.0 OD2 B:ASP113 4.2 33.8 1.0 N B:PRO149 4.3 29.3 1.0 CB B:THR148 4.3 31.6 1.0 CA B:ASN150 4.3 31.0 1.0 CB B:ASN150 4.4 39.8 1.0 O3A B:ATP407 4.5 27.8 1.0 CA B:THR148 4.6 26.8 1.0 O1G B:ATP407 4.7 58.6 1.0 O2B B:ATP407 4.8 39.3 1.0 CA B:THR186 4.8 29.3 1.0 N B:THR186 4.9 32.3 1.0 ND2 B:ASN150 4.9 39.1 1.0 CG B:ASN150 5.0 39.7 1.0 CA B:GLY234 5.0 28.1 1.0

A.K.Gandhi, M.S.Ghatge, F.N.Musayev, A.Sease, S.O.Aboagye, M.L.Di Salvo, V.Schirch, M.K.Safo. Kinetic and Structural Studies of the Role of the Active Site Residue ASP235 of Human Pyridoxal Kinase. Biochem.Biophys.Res.Commun. V. 381 12 2009.
ISSN: ISSN 0006-291X
PubMed: 19351586
DOI: 10.1016/J.BBRC.2009.01.170