Potassium 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:

Sodium

(Na)

2 atoms

The binding sites of Potassium 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 Potassium atom.
In total 4 binding sites of Potassium where determined in the L-Phenylalanine Dehydrogenase Structure in Ternary Complex with Nadh and L-Phenylalanine, PDB code: 1c1d:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the L-Phenylalanine Dehydrogenase Structure in Ternary Complex with Nadh and L-Phenylalanine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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 A:K850 b:24.2 occ:1.00 O A:THR121 2.6 15.5 1.0 O A:ASP118 2.7 12.8 1.0 O A:HOH1493 2.8 30.7 1.0 O A:HOH1602 3.0 44.0 1.0 O A:HOH1082 3.3 17.4 1.0 O A:HOH1488 3.5 34.4 1.0 C A:ASP118 3.7 14.3 1.0 C A:THR121 3.8 22.4 1.0 O A:HOH1766 3.9 43.2 1.0 N A:THR121 4.2 11.6 1.0 N A:ASP118 4.3 13.2 1.0 N A:ASN120 4.4 14.8 1.0 CB A:PRO117 4.5 17.6 1.0 CA A:ASP118 4.5 12.5 1.0 N A:VAL119 4.5 12.3 1.0 CA A:VAL119 4.5 12.4 1.0 O1N A:NAI360 4.6 17.2 1.0 CA A:THR121 4.6 13.7 1.0 N A:ASN122 4.7 15.4 1.0 CA A:ASN122 4.7 12.1 1.0 C A:VAL119 4.7 15.8 1.0 C A:PRO117 5.0 14.9 1.0

Potassium binding site 2 out of 4 in the L-Phenylalanine Dehydrogenase Structure in Ternary Complex with Nadh and L-Phenylalanine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K 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 A:K853 b:33.6 occ:1.00 OE2 A:GLU299 2.5 18.7 1.0 O A:VAL136 2.8 15.5 1.0 NE A:ARG139 2.9 16.2 1.0 N A:ARG139 3.0 13.2 1.0 CG A:ARG139 3.2 20.4 1.0 N A:GLY138 3.2 13.3 1.0 CA A:PHE137 3.3 14.2 1.0 CD A:GLU299 3.3 19.4 1.0 C A:PHE137 3.4 11.9 1.0 CB A:ARG139 3.4 12.6 1.0 OE1 A:GLU299 3.4 19.2 1.0 CD A:ARG139 3.5 20.9 1.0 CA A:GLY145 3.5 18.9 1.0 O A:HOH1266 3.6 30.8 1.0 O A:HOH1972 3.6 69.5 1.0 C A:VAL136 3.7 18.2 1.0 CA A:ARG139 3.8 11.7 1.0 CZ A:ARG139 3.9 18.5 1.0 N A:PHE137 3.9 13.8 1.0 O A:HOH1823 4.0 40.4 1.0 NH2 A:ARG139 4.0 17.3 1.0 C A:GLY138 4.1 15.0 1.0 CA A:GLY138 4.1 12.7 1.0 O A:PHE137 4.2 12.0 1.0 N A:GLY145 4.3 18.3 1.0 CB A:PHE137 4.6 13.7 1.0 O A:HOH1971 4.7 66.7 1.0 C A:GLY145 4.7 31.5 1.0 N A:ALA146 4.7 16.4 1.0 CG A:GLU299 4.7 15.9 1.0 C A:ARG139 4.8 18.9 1.0 O A:GLY144 4.8 19.7 1.0 O A:ARG139 4.8 17.3 1.0 C A:GLY144 4.9 19.7 1.0 CG1 A:VAL136 4.9 15.7 1.0 CD1 A:PHE137 5.0 15.7 1.0 CA A:VAL136 5.0 12.3 1.0

Potassium binding site 3 out of 4 in the L-Phenylalanine Dehydrogenase Structure in Ternary Complex with Nadh and L-Phenylalanine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 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:K851 b:21.6 occ:1.00 O B:SER172 2.6 14.2 1.0 O B:HOH1194 2.6 21.5 1.0 O B:ASP174 2.7 19.4 1.0 O B:HOH1421 2.9 29.4 1.0 O B:LEU170 3.1 12.9 1.0 CD2 B:LEU176 3.6 10.5 1.0 C B:SER172 3.7 12.2 1.0 N B:SER172 3.8 13.9 1.0 C B:ASP174 3.8 15.2 1.0 CG B:LEU176 3.9 13.9 1.0 O B:HOH1456 4.0 48.6 1.0 N B:ASP174 4.3 15.8 1.0 CA B:SER172 4.3 13.1 1.0 OG B:SER172 4.3 26.4 1.0 C B:LEU170 4.3 11.3 1.0 O B:HOH1648 4.3 53.6 1.0 C B:LEU173 4.5 15.9 1.0 CA B:ASP174 4.6 15.1 1.0 O B:HOH1614 4.6 49.5 1.0 CD1 B:LEU176 4.6 13.3 1.0 C B:GLY171 4.7 14.7 1.0 N B:LEU173 4.7 12.5 1.0 N B:GLY175 4.8 17.8 1.0 C B:GLY175 4.8 35.0 1.0 CA B:GLY171 4.8 11.6 1.0 N B:LEU176 4.9 17.7 1.0 CB B:SER172 4.9 19.4 1.0 CB B:ASP174 4.9 11.7 0.5 CA B:GLY175 4.9 20.9 1.0 O B:LEU173 5.0 13.0 1.0 CA B:LEU173 5.0 13.6 1.0

Potassium binding site 4 out of 4 in the L-Phenylalanine Dehydrogenase Structure in Ternary Complex with Nadh and L-Phenylalanine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 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:K852 b:21.9 occ:1.00 O B:THR121 2.6 14.2 1.0 O B:HOH1746 2.7 34.8 1.0 O B:ASP118 2.7 12.9 1.0 O B:HOH1667 2.7 46.7 1.0 O B:HOH1452 2.8 32.2 1.0 O B:HOH1320 2.9 32.4 1.0 O B:HOH1300 3.3 39.9 1.0 O B:HOH1200 3.3 20.7 1.0 C B:ASP118 3.7 12.4 1.0 C B:THR121 3.8 12.2 1.0 O B:HOH1214 4.0 27.5 1.0 N B:THR121 4.2 9.5 1.0 N B:ASP118 4.3 11.8 1.0 N B:ASN120 4.4 11.1 1.0 CA B:ASP118 4.4 10.4 1.0 CB B:PRO117 4.4 10.1 1.0 N B:VAL119 4.6 11.5 1.0 O B:HOH1380 4.6 36.2 1.0 CA B:VAL119 4.6 12.8 1.0 CA B:THR121 4.7 10.9 1.0 CA B:ASN122 4.7 9.4 1.0 N B:ASN122 4.7 10.3 1.0 O2N B:NAI760 4.8 18.9 1.0 C B:VAL119 4.8 10.6 1.0 O B:HOH1644 4.9 54.3 1.0 C B:PRO117 4.9 13.3 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