Magnesium 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:

Sodium

(Na)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 5 binding sites of Magnesium where determined in the D-2-Hydroxyacid Dehydrogenase (D2-Hdh) From Haloferax Mediterranei Apo-Enzyme (2.25 A Resolution), PDB code: 8qza:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 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 Magnesium with other atoms in the Mg 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:Mg401 b:39.8 occ:1.00 O A:HOH509 1.8 30.1 1.0 O A:HOH524 2.1 36.9 1.0 OE2 A:GLU211 2.2 34.2 1.0 CD A:GLU211 3.1 39.0 1.0 OE1 A:GLU211 3.4 36.6 1.0 CE1 A:HIS184 4.0 40.4 1.0 O A:MET206 4.2 47.7 1.0 CG A:GLU211 4.5 37.2 1.0 NE2 A:HIS184 4.7 41.5 1.0 CB A:PRO210 4.7 45.0 1.0 CG A:PRO210 5.0 42.8 1.0

Magnesium binding site 2 out of 5 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 Magnesium with other atoms in the Mg 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 A:Mg402 b:67.7 occ:1.00 OD1 B:ASP265 2.4 55.0 1.0 NE2 A:HIS120 3.0 48.1 1.0 O A:HIS118 3.7 60.7 1.0 CG B:ASP265 3.7 54.3 1.0 CD2 A:HIS120 3.8 50.1 1.0 CE1 A:HIS120 4.2 52.0 1.0 OD2 B:ASP265 4.6 56.9 1.0 CB B:ASP265 4.6 44.6 1.0 C A:HIS118 4.6 48.8 1.0 CA B:ASP265 4.9 45.5 1.0 CA A:HIS118 4.9 51.5 1.0 O A:GLN117 5.0 51.6 1.0

Magnesium binding site 3 out of 5 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 Magnesium with other atoms in the Mg binding site number 3 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:Mg403 b:67.5 occ:1.00 OD1 A:ASP265 2.2 74.8 1.0 NE2 B:HIS120 2.5 55.5 1.0 CD2 B:HIS120 3.4 53.5 1.0 CG A:ASP265 3.4 57.9 1.0 CE1 B:HIS120 3.5 53.8 1.0 O B:HIS118 3.8 44.8 1.0 OD2 A:ASP265 4.0 80.2 1.0 CB A:ASP265 4.5 54.0 1.0 CG B:HIS120 4.6 52.2 1.0 ND1 B:HIS120 4.6 52.3 1.0 C B:HIS118 4.8 52.8 1.0 CA A:ASP265 4.9 51.3 1.0

Magnesium binding site 4 out of 5 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 Magnesium with other atoms in the Mg binding site number 4 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:Mg401 b:35.6 occ:1.00 O B:HOH505 1.9 34.7 1.0 O B:HOH509 2.1 38.2 1.0 OE2 B:GLU211 2.3 34.3 1.0 CD B:GLU211 3.1 38.8 1.0 OE1 B:GLU211 3.4 33.6 1.0 O B:MET206 4.0 42.6 1.0 NE2 B:HIS184 4.0 40.6 1.0 CG B:GLU211 4.5 41.3 1.0 CD2 B:HIS184 4.9 40.6 1.0 CG B:PRO210 4.9 35.3 1.0 C B:MET206 4.9 38.7 1.0 CE1 B:HIS184 4.9 39.7 1.0

Magnesium binding site 5 out of 5 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 Magnesium with other atoms in the Mg binding site number 5 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:Mg402 b:62.6 occ:1.00 O B:HOH502 2.0 52.4 1.0 O B:HOH535 2.0 50.9 1.0 OD2 B:ASP169 3.8 53.1 1.0 OD1 B:ASP169 4.0 53.1 1.0 CG B:ASP169 4.3 60.4 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.