Sodium in PDB 8qza: D-2-Hydroxyacid Dehydrogenase (D2-Hdh) From Haloferax Mediterranei Apo-Enzyme (2.25 A Resolution)

The structure of D-2-Hydroxyacid Dehydrogenase (D2-Hdh) From Haloferax Mediterranei Apo-Enzyme (2.25 A Resolution), PDB code: 8qza was solved by P.J.Baker, J.R.Barrett, A.A.A.B.Dakhil, J.Domenech, C.Bisson, N.Pramanpol, S.E.Sedelnikova, J.Ferrer, D.W.Rice, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.45 / 2.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.352, 75.986, 74.589, 90, 93.99, 90
R / Rfree (%)	19 / 25.1

The structure of D-2-Hydroxyacid Dehydrogenase (D2-Hdh) From Haloferax Mediterranei Apo-Enzyme (2.25 A Resolution) also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Sodium atom in the D-2-Hydroxyacid Dehydrogenase (D2-Hdh) From Haloferax Mediterranei Apo-Enzyme (2.25 A Resolution) (pdb code 8qza). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the D-2-Hydroxyacid Dehydrogenase (D2-Hdh) From Haloferax Mediterranei Apo-Enzyme (2.25 A Resolution), PDB code: 8qza:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the D-2-Hydroxyacid Dehydrogenase (D2-Hdh) From Haloferax Mediterranei Apo-Enzyme (2.25 A Resolution)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of D-2-Hydroxyacid Dehydrogenase (D2-Hdh) From Haloferax Mediterranei Apo-Enzyme (2.25 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:48.3 occ:1.00 O A:ASP243 2.3 47.8 1.0 O A:PHE212 2.4 49.0 1.0 O A:MET215 2.4 43.4 1.0 O A:GLU213 2.8 39.6 1.0 C A:ASP243 3.3 49.7 1.0 C A:GLU213 3.5 42.9 1.0 C A:PHE212 3.5 50.3 1.0 C A:MET215 3.5 41.9 1.0 CA A:GLU213 3.7 52.5 1.0 CA A:ASP243 3.7 53.7 1.0 N A:MET215 3.9 40.8 1.0 CB A:ASP243 3.9 56.8 1.0 N A:GLU213 4.1 47.1 1.0 CA A:MET215 4.2 43.6 1.0 OD1 A:ASP243 4.2 52.4 1.0 CG A:GLU217 4.3 59.0 1.0 C A:ARG216 4.3 41.0 1.0 N A:GLU217 4.4 47.4 1.0 N A:ILE244 4.4 45.7 1.0 C A:THR214 4.4 40.6 1.0 CB A:MET215 4.4 39.5 1.0 CG2 A:ILE244 4.4 39.2 1.0 O A:ARG216 4.5 45.2 1.0 N A:THR214 4.5 41.2 1.0 N A:ARG216 4.5 44.7 1.0 CG A:ASP243 4.6 66.9 1.0 CA A:GLU217 4.6 48.8 1.0 CA A:PHE212 4.7 41.1 1.0 CA A:ARG216 4.8 45.2 1.0 O A:THR214 4.9 42.4 1.0 CA A:ILE244 5.0 49.5 1.0

Sodium binding site 2 out of 2 in the D-2-Hydroxyacid Dehydrogenase (D2-Hdh) From Haloferax Mediterranei Apo-Enzyme (2.25 A Resolution)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of D-2-Hydroxyacid Dehydrogenase (D2-Hdh) From Haloferax Mediterranei Apo-Enzyme (2.25 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:47.3 occ:1.00 O B:MET215 2.1 41.1 1.0 O B:PHE212 2.3 50.6 1.0 O B:ASP243 2.4 47.6 1.0 O B:HOH517 2.4 48.5 1.0 O B:GLU213 2.9 40.4 1.0 C B:MET215 3.2 40.7 1.0 C B:PHE212 3.5 53.2 1.0 C B:ASP243 3.5 49.7 1.0 C B:GLU213 3.5 37.8 1.0 N B:MET215 3.7 40.0 1.0 CA B:GLU213 3.7 43.2 1.0 CA B:MET215 3.9 42.5 1.0 CA B:ASP243 4.0 44.9 1.0 N B:GLU213 4.0 40.8 1.0 CB B:ASP243 4.1 62.5 1.0 C B:ARG216 4.2 39.0 1.0 C B:THR214 4.2 41.5 1.0 CB B:MET215 4.2 38.4 1.0 O B:ARG216 4.3 46.4 1.0 N B:ARG216 4.3 37.8 1.0 N B:GLU217 4.3 45.1 1.0 CG B:GLU217 4.4 79.0 1.0 N B:THR214 4.4 38.7 1.0 CG2 B:ILE244 4.4 38.7 1.0 OD1 B:ASP243 4.5 53.1 1.0 CA B:ARG216 4.6 38.6 1.0 N B:ILE244 4.6 41.4 1.0 O B:THR214 4.6 46.1 1.0 OE2 B:GLU217 4.6 98.4 1.0 CA B:PHE212 4.7 46.1 1.0 CA B:GLU217 4.7 49.9 1.0 CG B:ASP243 4.8 68.2 1.0 CA B:THR214 4.8 38.6 1.0 OE2 B:GLU213 5.0 87.0 1.0

J.Domenech, N.Pramanpol, C.Bisson, S.E.Sedelnikova, J.R.Barrett, A.A.A.B.Dakhil, A.S.Abdelhameed, S.E.Harding, D.W.Rice, P.J.Baker, J.Ferrer. D-2-Hydroxyacid Dehydrogenase (D2-Hdh) From Haloferax Mediterranei in Complex with 2-Keto-Hexanoic Acid and Nad+ (1.16 A Resolution) To Be Published.