Sodium in PDB 1bw9: Phenylalanine Dehydrogenase Structure in Ternary Complex with Nad+ and Phenylpyruvate

All present enzymatic activity of Phenylalanine Dehydrogenase Structure in Ternary Complex with Nad+ and Phenylpyruvate:
1.4.1.20;

The structure of Phenylalanine Dehydrogenase Structure in Ternary Complex with Nad+ and Phenylpyruvate, PDB code: 1bw9 was solved by J.L.Vanhooke, J.B.Thoden, N.M.W.Brunhuber, J.L.Blanchard, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.300, 110.200, 113.400, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of Phenylalanine Dehydrogenase Structure in Ternary Complex with Nad+ and Phenylpyruvate also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Sodium atom in the Phenylalanine Dehydrogenase Structure in Ternary Complex with Nad+ and Phenylpyruvate (pdb code 1bw9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Phenylalanine Dehydrogenase Structure in Ternary Complex with Nad+ and Phenylpyruvate, PDB code: 1bw9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Phenylalanine Dehydrogenase Structure in Ternary Complex with Nad+ and Phenylpyruvate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Phenylalanine Dehydrogenase Structure in Ternary Complex with Nad+ and Phenylpyruvate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na851 b:12.1 occ:1.00 O B:HOH1319 2.3 49.3 1.0 O B:ASP409 2.6 9.7 1.0 O B:HOH1100 2.7 15.6 1.0 O B:HOH1227 2.9 24.1 1.0 C B:ASP409 3.6 8.2 1.0 O B:HOH924 3.8 13.7 1.0 CB B:ASP409 4.1 12.4 1.0 O B:HOH1249 4.1 32.2 1.0 CA B:ASP409 4.1 6.9 1.0 O B:GLY410 4.4 7.7 1.0 N B:GLY410 4.7 8.5 1.0 O B:HOH1114 4.7 13.7 1.0 C B:GLY410 4.7 7.6 1.0 CG B:ASP409 5.0 0.0 1.0

Sodium binding site 2 out of 2 in the Phenylalanine Dehydrogenase Structure in Ternary Complex with Nad+ and Phenylpyruvate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Phenylalanine Dehydrogenase Structure in Ternary Complex with Nad+ and Phenylpyruvate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na852 b:9.0 occ:1.00 O B:GLY618 2.6 19.5 1.0 O B:HOH1008 2.6 15.1 1.0 O B:HOH1083 2.7 14.8 1.0 O B:HOH1326 2.7 48.7 1.0 NE2 B:GLN600 2.9 33.6 1.0 C B:GLY618 3.7 14.1 1.0 CD B:GLN600 3.9 38.4 1.0 O B:HOH1286 4.1 46.4 1.0 CA B:HIS619 4.2 14.0 1.0 OE1 B:GLN600 4.4 39.9 1.0 O B:HOH971 4.4 22.7 1.0 N B:HIS619 4.4 11.9 1.0 O B:HOH1300 4.4 45.7 1.0 OG1 B:THR620 4.5 15.0 1.0 ND1 B:HIS619 4.6 20.7 1.0 O B:HOH1314 4.7 42.4 1.0 C B:HIS619 4.7 14.5 1.0 N B:LEU601 4.7 7.0 1.0 CA B:GLY618 4.7 20.1 1.0 O B:LEU601 4.7 8.9 1.0 CA B:GLN600 4.8 7.3 1.0 CB B:GLN600 4.9 12.5 1.0 N B:THR620 4.9 9.2 1.0

J.L.Vanhooke, J.B.Thoden, N.M.Brunhuber, J.S.Blanchard, H.M.Holden. Phenylalanine Dehydrogenase From Rhodococcus Sp. M4: High-Resolution X-Ray Analyses of Inhibitory Ternary Complexes Reveal Key Features in the Oxidative Deamination Mechanism. Biochemistry V. 38 2326 1999.
ISSN: ISSN 0006-2960
PubMed: 10029526
DOI: 10.1021/BI982244Q