Sodium in PDB 5mh6: D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid and Nad+ (1.35 A Resolution)

The structure of D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid and Nad+ (1.35 A Resolution), PDB code: 5mh6 was solved by C.Bisson, P.J.Baker, J.Domenech Perez, N.Pramanpol, S.E.Harding, D.W.Rice, J.Ferrer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.54 / 1.35
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	66.455, 75.008, 77.555, 109.11, 107.55, 95.91
R / Rfree (%)	12.6 / 16.2

The structure of D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid and Nad+ (1.35 A Resolution) also contains other interesting chemical elements:

Magnesium

(Mg)

24 atoms

The binding sites of Sodium atom in the D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid and Nad+ (1.35 A Resolution) (pdb code 5mh6). 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 Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid and Nad+ (1.35 A Resolution), PDB code: 5mh6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid and Nad+ (1.35 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 Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid and Nad+ (1.35 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na401 b:31.1 occ:1.00 O2A C:NAD415 2.3 10.8 1.0 OG1 C:THR145 2.4 11.0 1.0 O C:HOH676 2.5 33.9 1.0 O C:HOH861 2.6 41.9 1.0 OG1 C:THR88 2.6 16.0 0.5 O C:HOH927 3.0 51.0 1.0 CB C:THR145 3.6 7.5 1.0 PA C:NAD415 3.6 10.9 1.0 N C:THR145 3.8 5.7 1.0 CB C:THR88 3.9 10.3 0.5 CB C:THR88 3.9 13.2 0.5 N C:GLY89 4.0 7.2 1.0 CG2 C:THR88 4.1 17.8 0.5 O1A C:NAD415 4.1 12.5 1.0 OG1 C:THR88 4.2 14.8 0.5 CA C:THR145 4.2 6.6 1.0 O C:HOH855 4.2 25.5 1.0 CA C:GLY89 4.3 6.4 1.0 C C:THR88 4.4 8.9 1.0 O1N C:NAD415 4.4 9.4 1.0 O3 C:NAD415 4.4 9.5 1.0 O C:HOH761 4.4 23.9 1.0 O C:HOH532 4.6 36.5 1.0 O C:HOH693 4.6 45.6 1.0 CA C:THR88 4.7 8.9 0.5 CA C:THR88 4.7 8.9 0.5 O5B C:NAD415 4.7 11.0 1.0 CG2 C:THR145 4.7 7.1 1.0 CG2 C:THR88 4.8 9.1 0.5 PN C:NAD415 4.8 7.8 1.0 C C:GLY144 4.8 5.3 1.0 O C:THR88 4.9 9.7 1.0 CA C:GLY144 5.0 7.1 1.0

Sodium binding site 2 out of 2 in the D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid and Nad+ (1.35 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 Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid and Nad+ (1.35 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na401 b:27.2 occ:1.00 O D:HOH770 2.2 44.8 1.0 O D:HOH798 2.3 44.1 1.0 O2A D:NAD412 2.3 11.8 1.0 OG1 D:THR88 2.5 10.5 0.5 OG1 D:THR145 2.5 11.6 1.0 PA D:NAD412 3.6 10.1 1.0 CB D:THR145 3.6 8.7 1.0 CB D:THR88 3.6 11.4 0.5 CB D:THR88 3.7 9.1 0.5 CG2 D:THR88 3.8 8.7 0.5 N D:THR145 3.8 5.9 1.0 N D:GLY89 3.9 8.6 1.0 OG1 D:THR88 3.9 15.6 0.5 O1A D:NAD412 4.0 11.7 1.0 O1N D:NAD412 4.1 8.2 1.0 C D:THR88 4.3 9.0 1.0 CA D:THR145 4.3 7.1 1.0 CA D:GLY89 4.3 9.0 1.0 O3 D:NAD412 4.3 8.5 1.0 O D:HOH817 4.4 34.4 1.0 O D:HOH686 4.5 25.0 1.0 CG2 D:THR88 4.5 15.8 0.5 CA D:THR88 4.5 7.5 0.5 CA D:THR88 4.5 7.7 0.5 O D:HOH561 4.6 26.4 1.0 PN D:NAD412 4.7 7.6 1.0 O5B D:NAD412 4.8 9.7 1.0 CG2 D:THR145 4.8 8.4 1.0 C D:GLY144 4.8 6.9 1.0 O D:THR88 4.9 10.2 1.0 O D:HOH860 4.9 45.6 1.0 O D:HOH748 4.9 31.8 1.0 O2N D:NAD412 5.0 7.7 1.0 CA D:GLY144 5.0 7.6 1.0

J.Domenech Perez, N.Pramanpol, P.J.Baker, C.Bisson, S.E.Harding, D.W.Rice, J.Ferrer. Productive Ternary Complexes of D-2-Hydroxyacid Dehydrogenase Provide Insights Into the Chiral Specificity of Its Reaction Mechanism To Be Published.