Sodium in PDB 1ebf: Homoserine Dehydrogenase From S. Cerevisiae Complex with Nad+

All present enzymatic activity of Homoserine Dehydrogenase From S. Cerevisiae Complex with Nad+:
1.1.1.3;

The structure of Homoserine Dehydrogenase From S. Cerevisiae Complex with Nad+, PDB code: 1ebf was solved by B.Delabarre, P.R.Thompson, G.D.Wright, A.M.Berghuis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.96 / 2.30
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	80.396, 80.396, 250.165, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 26.9

The binding sites of Sodium atom in the Homoserine Dehydrogenase From S. Cerevisiae Complex with Nad+ (pdb code 1ebf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Homoserine Dehydrogenase From S. Cerevisiae Complex with Nad+, PDB code: 1ebf:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Homoserine Dehydrogenase From S. Cerevisiae Complex with Nad+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Homoserine Dehydrogenase From S. Cerevisiae Complex with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2104 b:29.4 occ:1.00 O A:GLU143 2.7 13.2 1.0 O A:LEU150 2.8 15.8 1.0 O A:ALA148 2.8 15.8 1.0 O A:VAL146 2.9 17.5 1.0 OE2 A:GLU143 2.9 18.4 1.0 C A:GLY147 3.5 16.0 1.0 O A:GLY147 3.5 15.9 1.0 CG A:GLU143 3.6 16.7 1.0 C A:ALA148 3.6 15.6 1.0 C A:GLU143 3.6 13.9 1.0 CD A:GLU143 3.7 18.5 1.0 N A:LEU150 3.7 14.3 1.0 C A:VAL146 3.8 16.6 1.0 C A:LEU150 3.8 14.7 1.0 N A:ALA148 3.9 16.2 1.0 CA A:GLY147 3.9 16.4 1.0 CA A:LEU150 4.2 14.1 1.0 N A:GLY147 4.2 15.8 1.0 C A:GLY149 4.2 14.2 1.0 N A:GLY149 4.3 15.1 1.0 CB A:ILE152 4.3 11.5 1.0 CA A:ALA148 4.3 14.8 1.0 CD1 A:ILE152 4.4 10.8 1.0 N A:ALA144 4.4 12.4 1.0 CA A:GLY149 4.4 14.4 1.0 CA A:GLU143 4.4 14.4 1.0 N A:ILE152 4.4 13.2 1.0 CG1 A:ILE152 4.5 11.7 1.0 CA A:ALA144 4.5 11.8 1.0 CB A:LEU150 4.5 12.3 1.0 CB A:GLU143 4.6 15.1 1.0 N A:VAL146 4.8 14.8 1.0 OE1 A:GLU143 4.9 19.4 1.0 CA A:VAL146 4.9 16.1 1.0 N A:PRO151 4.9 13.1 1.0 N A:ILE153 5.0 11.2 1.0 CA A:ILE152 5.0 12.5 1.0

Sodium binding site 2 out of 2 in the Homoserine Dehydrogenase From S. Cerevisiae Complex with Nad+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Homoserine Dehydrogenase From S. Cerevisiae Complex with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2114 b:35.7 occ:1.00 O B:VAL146 2.6 17.9 1.0 O B:ALA148 2.7 16.0 1.0 OE2 B:GLU143 2.7 12.7 1.0 O B:LEU150 2.8 12.0 1.0 O B:GLU143 2.8 16.7 1.0 O B:GLY147 3.4 15.2 1.0 C B:ALA148 3.5 14.9 1.0 C B:GLY147 3.5 14.6 1.0 CD B:GLU143 3.5 16.2 1.0 CG B:GLU143 3.5 14.5 1.0 C B:VAL146 3.6 16.8 1.0 C B:GLU143 3.6 16.0 1.0 N B:LEU150 3.8 13.6 1.0 C B:LEU150 3.8 13.6 1.0 N B:ALA148 3.9 14.3 1.0 CA B:GLY147 4.0 15.0 1.0 C B:GLY149 4.1 14.1 1.0 N B:GLY149 4.2 14.7 1.0 N B:GLY147 4.2 15.5 1.0 CA B:LEU150 4.2 13.5 1.0 CA B:ALA148 4.3 15.3 1.0 N B:ALA144 4.3 15.7 1.0 CB B:ILE152 4.3 14.3 1.0 CA B:GLY149 4.4 13.5 1.0 CA B:ALA144 4.4 16.5 1.0 N B:ILE152 4.4 15.8 1.0 CB B:LEU150 4.5 14.3 1.0 CA B:GLU143 4.5 14.7 1.0 CG1 B:ILE152 4.5 14.4 1.0 CB B:GLU143 4.6 13.9 1.0 CD1 B:ILE152 4.6 16.8 1.0 N B:VAL146 4.7 16.1 1.0 CA B:VAL146 4.7 17.1 1.0 OE1 B:GLU143 4.7 17.2 1.0 O B:GLY149 4.8 12.3 1.0 N B:PRO151 5.0 15.4 1.0 CA B:ILE152 5.0 15.8 1.0 C B:ALA144 5.0 17.4 1.0

B.Delabarre, P.R.Thompson, G.D.Wright, A.M.Berghuis. Crystal Structures of Homoserine Dehydrogenase Suggest A Novel Catalytic Mechanism For Oxidoreductases. Nat.Struct.Biol. V. 7 238 2000.
ISSN: ISSN 1072-8368
PubMed: 10700284
DOI: 10.1038/73359