Magnesium in PDB 5mha: D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with A Mixture of 2-Ketohexanoic Acid and 2-Hydroxyhexanoic Acid, and Nadph (1.57 A Resolution)

The structure of D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with A Mixture of 2-Ketohexanoic Acid and 2-Hydroxyhexanoic Acid, and Nadph (1.57 A Resolution), PDB code: 5mha 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)	38.15 / 1.57
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.540, 76.300, 66.990, 90.00, 97.04, 90.00
R / Rfree (%)	17.4 / 21.6

The binding sites of Magnesium atom in the D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with A Mixture of 2-Ketohexanoic Acid and 2-Hydroxyhexanoic Acid, and Nadph (1.57 A Resolution) (pdb code 5mha). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with A Mixture of 2-Ketohexanoic Acid and 2-Hydroxyhexanoic Acid, and Nadph (1.57 A Resolution), PDB code: 5mha:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with A Mixture of 2-Ketohexanoic Acid and 2-Hydroxyhexanoic Acid, and Nadph (1.57 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 Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with A Mixture of 2-Ketohexanoic Acid and 2-Hydroxyhexanoic Acid, and Nadph (1.57 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:15.4 occ:1.00 O A:HOH590 2.0 20.6 1.0 O A:HOH647 2.1 18.4 1.0 O A:HOH563 2.1 15.2 1.0 O A:GLU204 3.8 17.6 1.0 O A:GLU202 4.0 20.7 1.0 O A:HOH673 4.4 30.2 1.0 O A:ASP201 4.5 20.6 1.0 O A:HOH518 4.5 41.1 1.0 O A:HOH548 4.7 30.9 1.0 C A:GLU202 4.8 13.9 1.0

Magnesium binding site 2 out of 7 in the D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with A Mixture of 2-Ketohexanoic Acid and 2-Hydroxyhexanoic Acid, and Nadph (1.57 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 Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with A Mixture of 2-Ketohexanoic Acid and 2-Hydroxyhexanoic Acid, and Nadph (1.57 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:17.6 occ:1.00 OE2 A:GLU211 2.1 16.7 1.0 O A:HOH529 2.1 19.9 1.0 O A:HOH545 2.1 18.1 1.0 CD A:GLU211 3.1 15.2 1.0 OE1 A:GLU211 3.5 14.5 1.0 NE2 A:HIS184 4.0 17.0 1.0 O A:MET206 4.1 18.1 1.0 O A:HOH507 4.2 37.9 1.0 CG A:GLU211 4.4 18.7 1.0 CB A:PRO210 4.7 18.8 1.0 CG A:PRO210 4.7 21.0 1.0 CD2 A:HIS184 4.9 18.1 1.0 CE1 A:HIS184 4.9 24.8 1.0

Magnesium binding site 3 out of 7 in the D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with A Mixture of 2-Ketohexanoic Acid and 2-Hydroxyhexanoic Acid, and Nadph (1.57 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 Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with A Mixture of 2-Ketohexanoic Acid and 2-Hydroxyhexanoic Acid, and Nadph (1.57 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:36.1 occ:1.00 O A:HOH532 1.9 39.4 1.0 OD1 A:ASP265 2.0 33.3 1.0 O A:HOH624 2.3 31.9 1.0 O A:HOH608 2.3 44.5 1.0 NE2 B:HIS120 2.4 27.9 1.0 CG A:ASP265 3.2 35.7 1.0 CD2 B:HIS120 3.3 28.9 1.0 CE1 B:HIS120 3.5 28.6 1.0 OD2 A:ASP265 4.0 35.0 1.0 O B:HIS118 4.1 26.8 1.0 CB A:ASP265 4.3 33.7 1.0 CA A:ASP265 4.4 23.8 1.0 CG B:HIS120 4.5 20.2 1.0 ND1 B:HIS120 4.6 23.1 1.0 O B:GLN117 4.7 23.0 1.0 O A:TRP264 4.7 24.5 1.0 N A:ASP265 4.8 26.9 1.0 C A:TRP264 4.8 24.8 1.0 C B:HIS118 4.9 20.0 1.0 CB A:TRP264 4.9 23.1 1.0

Magnesium binding site 4 out of 7 in the D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with A Mixture of 2-Ketohexanoic Acid and 2-Hydroxyhexanoic Acid, and Nadph (1.57 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 Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with A Mixture of 2-Ketohexanoic Acid and 2-Hydroxyhexanoic Acid, and Nadph (1.57 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:20.8 occ:1.00 O A:HOH526 2.0 24.1 1.0 O A:HOH559 2.1 24.1 1.0 O A:HOH541 2.1 25.7 1.0 O A:HOH520 2.1 22.5 1.0 OE1 A:GLU267 4.1 27.0 1.0 OE2 A:GLU267 4.1 27.6 1.0 O A:HOH554 4.1 25.2 1.0 OE2 A:GLU129 4.2 28.0 1.0 OE1 A:GLU129 4.3 22.2 1.0 O A:HOH692 4.3 42.3 1.0 O A:HOH512 4.3 28.0 1.0 NH2 A:ARG109 4.4 22.1 1.0 CD A:GLU267 4.5 25.6 1.0 O A:HOH631 4.5 19.1 1.0 CD A:GLU129 4.6 21.0 1.0 O A:HOH686 4.7 35.6 1.0

Magnesium binding site 5 out of 7 in the D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with A Mixture of 2-Ketohexanoic Acid and 2-Hydroxyhexanoic Acid, and Nadph (1.57 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 Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with A Mixture of 2-Ketohexanoic Acid and 2-Hydroxyhexanoic Acid, and Nadph (1.57 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:39.0 occ:1.00 O A:ALA134 2.1 16.1 1.0 O A:HOH556 2.2 30.0 1.0 OG1 A:THR132 2.2 17.7 1.0 O A:THR132 2.5 12.8 1.0 C A:THR132 3.2 14.7 1.0 C A:ALA134 3.3 17.4 1.0 CB A:THR132 3.4 18.5 1.0 CA A:THR132 3.6 13.8 1.0 N A:THR132 3.8 13.3 1.0 N A:ALA134 4.0 12.5 1.0 CG A:GLU136 4.0 21.1 1.0 O A:HOH592 4.1 25.2 1.0 CA A:ALA134 4.1 15.7 1.0 C A:LEU133 4.1 13.5 1.0 OE2 A:GLU136 4.2 30.0 1.0 N A:LEU133 4.3 13.3 1.0 N A:GLY135 4.3 18.6 1.0 CA A:GLY135 4.4 27.6 1.0 O A:LEU133 4.5 15.3 1.0 N A:GLU136 4.5 17.6 1.0 CB A:ALA134 4.6 17.3 1.0 CG2 A:THR132 4.6 18.5 1.0 CD A:GLU136 4.6 28.5 1.0 C A:GLY135 4.6 34.2 1.0 CA A:LEU133 4.7 9.2 1.0 O A:HOH693 4.7 35.5 1.0

Magnesium binding site 6 out of 7 in the D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with A Mixture of 2-Ketohexanoic Acid and 2-Hydroxyhexanoic Acid, and Nadph (1.57 A Resolution)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with A Mixture of 2-Ketohexanoic Acid and 2-Hydroxyhexanoic Acid, and Nadph (1.57 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:21.9 occ:1.00 O B:PHE212 2.2 16.4 1.0 O B:MET215 2.2 18.8 1.0 O B:ASP243 2.3 20.3 1.0 O B:HOH699 2.4 25.9 1.0 O B:GLU213 2.9 16.9 1.0 C B:ASP243 3.3 13.1 1.0 C B:GLU213 3.3 23.0 1.0 C B:MET215 3.3 19.4 1.0 C B:PHE212 3.4 16.1 1.0 CA B:GLU213 3.6 25.4 1.0 CA B:ASP243 3.8 17.6 1.0 N B:MET215 3.9 18.8 1.0 CB B:ASP243 3.9 17.2 1.0 N B:GLU213 3.9 21.4 1.0 O B:HOH674 4.0 37.0 1.0 CA B:MET215 4.0 15.1 1.0 C B:ARG216 4.2 20.6 1.0 C B:THR214 4.3 21.0 1.0 N B:THR214 4.3 16.3 1.0 CB B:MET215 4.3 20.6 1.0 O B:ARG216 4.3 17.3 1.0 CG2 B:ILE244 4.4 15.5 1.0 N B:GLU217 4.4 16.3 1.0 N B:ARG216 4.4 18.8 1.0 N B:ILE244 4.5 21.0 1.0 O B:HOH505 4.6 44.5 1.0 CA B:PHE212 4.6 13.9 1.0 O B:THR214 4.7 17.3 1.0 CA B:ARG216 4.7 18.9 1.0 CA B:GLU217 4.7 17.2 1.0 CG B:ASP243 4.7 35.8 1.0 CG B:GLU217 4.8 56.0 1.0 CA B:THR214 4.9 16.0 1.0 OD1 B:ASP243 4.9 26.1 1.0

Magnesium binding site 7 out of 7 in the D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with A Mixture of 2-Ketohexanoic Acid and 2-Hydroxyhexanoic Acid, and Nadph (1.57 A Resolution)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with A Mixture of 2-Ketohexanoic Acid and 2-Hydroxyhexanoic Acid, and Nadph (1.57 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:33.2 occ:1.00 O B:HOH617 1.9 37.8 1.0 O B:HOH513 2.0 26.4 1.0 O B:HOH547 2.1 31.8 1.0 O B:HOH706 2.1 43.0 1.0 O B:HOH540 2.2 23.8 1.0 O2 B:EDO403 2.2 26.5 1.0 C2 B:EDO403 3.0 0.0 1.0 C1 B:EDO403 3.8 31.9 1.0 OE2 B:GLU129 4.0 27.4 1.0 O B:HOH581 4.1 35.0 1.0 OE1 B:GLU267 4.2 29.0 1.0 NH1 B:ARG126 4.2 22.5 0.5 OE2 B:GLU267 4.2 27.0 1.0 OE1 B:GLU129 4.2 23.2 1.0 O B:HOH549 4.3 29.3 1.0 NH1 B:ARG109 4.5 23.3 1.0 NH2 B:ARG126 4.5 26.1 0.5 CD B:GLU129 4.5 23.0 1.0 CD B:GLU267 4.6 33.7 1.0 O B:HOH627 4.7 24.0 1.0 O1 B:EDO403 4.9 44.3 1.0 NE B:ARG126 4.9 64.4 0.5

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.