Sodium in PDB 1omo: Alanine Dehydrogenase Dimer W/Bound Nad (Archaeal)

All present enzymatic activity of Alanine Dehydrogenase Dimer W/Bound Nad (Archaeal):
1.4.1.1;

The structure of Alanine Dehydrogenase Dimer W/Bound Nad (Archaeal), PDB code: 1omo was solved by D.T.Gallagher, N.N.Smith, M.J.Holden, I.Schroeder, H.G.Monbouquette, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.32
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	108.700, 55.500, 131.300, 90.00, 111.10, 90.00
R / Rfree (%)	20.3 / 26.2

The binding sites of Sodium atom in the Alanine Dehydrogenase Dimer W/Bound Nad (Archaeal) (pdb code 1omo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Alanine Dehydrogenase Dimer W/Bound Nad (Archaeal), PDB code: 1omo:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Alanine Dehydrogenase Dimer W/Bound Nad (Archaeal)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Alanine Dehydrogenase Dimer W/Bound Nad (Archaeal) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na900 b:19.6 occ:1.00 OE1 A:GLU225 2.4 25.8 1.0 OE1 A:GLU249 2.8 16.1 1.0 N A:ALA218 2.9 21.1 1.0 CB A:ALA218 3.1 21.6 1.0 CD A:GLU225 3.3 24.4 1.0 O A:HOH504 3.4 8.8 1.0 CB A:GLU249 3.5 18.7 1.0 CG A:GLU225 3.5 23.2 1.0 N A:GLY217 3.6 17.4 1.0 CA A:ALA218 3.6 23.8 1.0 C A:ALA215 3.7 16.6 1.0 CD A:GLU249 3.7 16.8 1.0 CB A:ALA215 3.8 14.5 1.0 N A:ILE216 3.9 17.3 1.0 C A:GLY217 3.9 19.2 1.0 CG A:GLU249 3.9 16.9 1.0 O A:ALA215 3.9 15.0 1.0 CA A:GLY217 4.0 15.8 1.0 CB A:GLU225 4.0 19.8 1.0 C A:ILE216 4.0 18.2 1.0 CA A:ALA215 4.1 14.3 1.0 OG1 A:THR193 4.1 14.8 1.0 CA A:GLU249 4.1 19.5 1.0 CA A:ILE216 4.5 16.3 1.0 OE2 A:GLU225 4.5 25.7 1.0 N A:GLU225 4.5 21.3 1.0 N A:GLU249 4.5 19.7 1.0 O A:ALA218 4.6 28.1 1.0 C A:ALA218 4.6 27.2 1.0 O A:ILE216 4.7 17.5 1.0 O A:HOH552 4.8 29.9 1.0 OE2 A:GLU249 4.9 14.0 1.0 O A:THR193 4.9 19.0 1.0 CA A:GLU225 4.9 21.4 1.0

Sodium binding site 2 out of 2 in the Alanine Dehydrogenase Dimer W/Bound Nad (Archaeal)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Alanine Dehydrogenase Dimer W/Bound Nad (Archaeal) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na901 b:23.0 occ:1.00 OE1 B:GLU225 2.5 44.0 1.0 OE1 B:GLU249 2.7 45.7 1.0 N B:ALA218 2.8 43.1 1.0 CB B:ALA218 3.1 41.0 1.0 O B:HOH516 3.1 32.2 1.0 O B:ALA215 3.4 43.9 1.0 CD B:GLU225 3.4 46.1 1.0 C B:ALA215 3.4 42.6 1.0 N B:GLY217 3.4 43.7 1.0 CA B:ALA218 3.5 41.4 1.0 CB B:ALA215 3.6 42.6 1.0 C B:GLY217 3.7 43.4 1.0 CG B:GLU225 3.7 46.0 1.0 CA B:ALA215 3.8 43.1 1.0 CD B:GLU249 3.8 46.8 1.0 CA B:GLY217 3.8 43.2 1.0 N B:ILE216 3.9 42.4 1.0 CB B:GLU225 4.0 48.0 1.0 C B:ILE216 4.1 42.8 1.0 OG1 B:THR193 4.1 47.7 1.0 CB B:GLU249 4.1 43.5 1.0 CG B:GLU249 4.3 44.8 1.0 CA B:ILE216 4.5 41.7 1.0 OE2 B:GLU225 4.5 44.6 1.0 CA B:GLU249 4.6 42.6 1.0 C B:ALA218 4.6 40.1 1.0 N B:GLU225 4.7 48.0 1.0 O B:THR193 4.7 45.4 1.0 O B:ALA218 4.7 41.7 1.0 N B:GLU249 4.8 41.3 1.0 O B:ILE216 4.8 43.5 1.0 OE2 B:GLU249 4.8 48.6 1.0 O B:GLY217 4.9 44.3 1.0 CA B:GLU225 5.0 48.4 1.0

D.T.Gallagher, H.G.Monbouquette, I.Schroeder, H.Robinson, M.J.Holden, N.N.Smith. Structure of Alanine Dehydrogenase From Archaeoglobus: Active Site Analysis and Relation to Bacterial Cyclodeaminases and Mammalian Mu Crystallin. J.Mol.Biol. V. 342 119 2004.
ISSN: ISSN 0022-2836
PubMed: 15313611
DOI: 10.1016/J.JMB.2004.06.090