Sodium in PDB 1c1d: L-Phenylalanine Dehydrogenase Structure in Ternary Complex with Nadh and L-Phenylalanine

The structure of L-Phenylalanine Dehydrogenase Structure in Ternary Complex with Nadh and L-Phenylalanine, PDB code: 1c1d was solved by J.L.Vanhooke, J.B.Thoden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.800, 110.600, 113.300, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of L-Phenylalanine Dehydrogenase Structure in Ternary Complex with Nadh and L-Phenylalanine also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Sodium atom in the L-Phenylalanine Dehydrogenase Structure in Ternary Complex with Nadh and L-Phenylalanine (pdb code 1c1d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the L-Phenylalanine Dehydrogenase Structure in Ternary Complex with Nadh and L-Phenylalanine, PDB code: 1c1d:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the L-Phenylalanine Dehydrogenase Structure in Ternary Complex with Nadh and L-Phenylalanine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of L-Phenylalanine Dehydrogenase Structure in Ternary Complex with Nadh and L-Phenylalanine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na854 b:14.4 occ:1.00 O B:ASP30 2.6 10.4 1.0 O B:HOH1094 2.6 19.7 1.0 O B:HOH1140 2.9 21.9 1.0 O B:HOH1156 3.1 20.7 1.0 O B:HOH1228 3.4 27.9 1.0 O B:HOH1312 3.6 32.6 1.0 C B:ASP30 3.8 8.6 1.0 O B:HOH1422 3.9 31.6 1.0 O B:ASP9 3.9 13.9 1.0 CG B:GLU11 4.0 9.0 1.0 CA B:GLY10 4.1 9.2 1.0 N B:GLU11 4.1 8.0 1.0 C B:GLY10 4.3 10.8 1.0 O B:HOH1523 4.3 37.2 1.0 O B:HOH1482 4.3 35.7 1.0 CB B:SER31 4.4 10.4 1.0 CA B:SER31 4.4 8.5 1.0 OD2 B:ASP30 4.5 11.3 1.0 OE1 B:GLU11 4.5 11.4 1.0 N B:SER31 4.6 7.8 1.0 CG B:ASP30 4.6 13.4 1.0 OD1 B:ASP30 4.7 14.2 1.0 O B:HOH1182 4.7 22.3 1.0 CD B:GLU11 4.8 11.9 1.0 C B:ASP9 4.8 13.9 1.0 CA B:ASP30 4.9 8.6 1.0 N B:GLY10 4.9 11.7 1.0 OG B:SER31 4.9 11.0 1.0 CA B:GLU11 4.9 8.5 1.0 CB B:GLU11 5.0 9.1 1.0

Sodium binding site 2 out of 2 in the L-Phenylalanine Dehydrogenase Structure in Ternary Complex with Nadh and L-Phenylalanine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of L-Phenylalanine Dehydrogenase Structure in Ternary Complex with Nadh and L-Phenylalanine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na855 b:15.4 occ:1.00 O B:HOH1754 2.2 62.9 1.0 O B:HOH1067 2.6 19.3 1.0 ND1 B:HIS219 2.8 22.5 1.0 N B:LEU201 2.9 14.1 1.0 O B:HOH1219 3.5 23.2 1.0 CE1 B:HIS219 3.6 28.3 1.0 CA B:GLN200 3.7 13.0 1.0 CB B:LEU201 3.7 15.9 1.0 C B:GLN200 3.8 17.7 1.0 CA B:LEU201 3.8 16.5 1.0 CG B:HIS219 4.0 21.4 1.0 O B:LEU201 4.0 16.5 1.0 CA B:HIS219 4.0 25.7 1.0 O B:GLY218 4.1 26.1 1.0 O B:ALA199 4.1 15.6 1.0 NE2 B:GLN200 4.2 57.9 1.0 CB B:HIS219 4.4 19.2 1.0 CD1 B:LEU201 4.4 20.9 1.0 C B:LEU201 4.4 17.4 1.0 CD B:GLN200 4.4 70.1 1.0 C B:GLY218 4.4 28.7 1.0 N B:HIS219 4.4 22.2 1.0 OE1 B:GLN200 4.5 39.4 1.0 CB B:GLN200 4.5 17.4 1.0 CG B:LEU201 4.6 20.6 1.0 N B:GLN200 4.8 14.7 1.0 NE2 B:HIS219 4.8 21.4 1.0 CD2 B:LEU201 4.8 31.5 1.0 C B:ALA199 4.9 14.7 1.0 O B:GLN200 5.0 17.9 1.0 CD2 B:HIS219 5.0 25.7 1.0

N.M.Brunhuber, J.B.Thoden, J.S.Blanchard, J.L.Vanhooke. Rhodococcus L-Phenylalanine Dehydrogenase: Kinetics, Mechanism, and Structural Basis For Catalytic Specificity. Biochemistry V. 39 9174 2000.
ISSN: ISSN 0006-2960
PubMed: 10924111
DOI: 10.1021/BI000494C