Magnesium in PDB 5mh5: D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with 2-Keto-Hexanoic Acid and Nadp+ (1.4 A Resolution)

The structure of D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with 2-Keto-Hexanoic Acid and Nadp+ (1.4 A Resolution), PDB code: 5mh5 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)	52.51 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.530, 87.400, 66.100, 90.00, 96.34, 90.00
R / Rfree (%)	13.6 / 16.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Magnesium atom in the D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with 2-Keto-Hexanoic Acid and Nadp+ (1.4 A Resolution) (pdb code 5mh5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 21 binding sites of Magnesium where determined in the D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with 2-Keto-Hexanoic Acid and Nadp+ (1.4 A Resolution), PDB code: 5mh5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 21 in the D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with 2-Keto-Hexanoic Acid and Nadp+ (1.4 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 2-Keto-Hexanoic Acid and Nadp+ (1.4 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:9.4 occ:1.00 O A:HOH659 2.0 11.0 1.0 O A:HOH734 2.0 13.0 1.0 O A:GLU204 3.8 9.8 1.0 O A:HOH753 3.8 24.8 1.0 O A:GLU202 4.0 13.2 1.0 O A:HOH509 4.3 27.5 1.0 O A:HOH756 4.4 31.2 1.0 O A:ASP201 4.4 14.3 1.0 MG A:MG405 4.6 55.6 1.0 C A:GLU202 4.8 11.7 1.0

Magnesium binding site 2 out of 21 in the D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with 2-Keto-Hexanoic Acid and Nadp+ (1.4 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 2-Keto-Hexanoic Acid and Nadp+ (1.4 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:33.5 occ:1.00 O A:HOH562 1.9 21.0 1.0 O A:HOH569 2.1 30.7 1.0 O A:HOH827 2.1 46.0 1.0 O A:HOH582 2.1 19.2 1.0 O A:HOH806 2.2 47.4 1.0 O A:HOH814 2.3 31.9 1.0 O A:HOH679 3.9 21.8 1.0 O2A A:NAP414 4.2 11.4 1.0 O2X A:NAP414 4.2 10.6 1.0 O1X A:NAP414 4.3 13.2 1.0 O A:HOH512 4.6 21.4 1.0 P2B A:NAP414 4.8 9.6 1.0 NH1 A:ARG166 4.9 24.9 0.5 C3B A:NAP414 5.0 8.5 1.0

Magnesium binding site 3 out of 21 in the D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with 2-Keto-Hexanoic Acid and Nadp+ (1.4 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 2-Keto-Hexanoic Acid and Nadp+ (1.4 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:33.9 occ:1.00 O A:HOH546 2.0 32.3 1.0 O A:HOH710 2.0 21.6 1.0 O A:HOH794 2.0 27.4 1.0 O A:HOH811 2.1 36.8 1.0 O A:HOH747 2.2 40.5 1.0 O A:HOH625 3.9 12.2 1.0 OD2 A:ASP152 4.1 11.8 1.0 OD2 A:ASP172 4.1 28.9 1.0 CB A:ASP172 4.2 12.1 1.0 O A:HOH805 4.2 35.8 1.0 O A:HOH693 4.4 20.1 1.0 OD1 A:ASP152 4.5 11.5 1.0 CG A:ASP152 4.7 8.8 1.0 CG A:ASP172 4.7 13.8 1.0

Magnesium binding site 4 out of 21 in the D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with 2-Keto-Hexanoic Acid and Nadp+ (1.4 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 2-Keto-Hexanoic Acid and Nadp+ (1.4 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:35.7 occ:1.00 O A:HOH594 2.0 16.7 1.0 O A:HOH630 2.1 27.4 1.0 OG1 A:THR132 2.2 11.9 1.0 O A:ALA134 2.4 10.5 1.0 O A:THR132 2.5 8.9 1.0 O A:HOH773 3.1 29.7 1.0 C A:THR132 3.3 6.4 1.0 CB A:THR132 3.4 8.9 1.0 C A:ALA134 3.6 9.3 1.0 CA A:THR132 3.6 7.3 1.0 N A:THR132 3.7 7.2 1.0 OE2 A:GLU136 4.0 21.7 1.0 O A:HOH656 4.0 20.4 1.0 CG A:GLU136 4.0 9.7 1.0 N A:ALA134 4.2 6.7 1.0 C A:LEU133 4.3 6.2 1.0 N A:LEU133 4.4 6.3 1.0 O A:HOH795 4.4 19.7 1.0 CA A:ALA134 4.4 8.2 1.0 CD A:GLU136 4.5 16.1 1.0 CG2 A:THR132 4.5 12.5 1.0 N A:GLY135 4.6 11.5 1.0 O A:LEU133 4.6 7.1 1.0 N A:GLU136 4.7 7.9 1.0 CA A:GLY135 4.7 10.4 1.0 CB A:ALA134 4.8 12.1 1.0 CA A:LEU133 4.8 6.2 1.0 C A:GLY135 4.9 11.1 1.0

Magnesium binding site 5 out of 21 in the D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with 2-Keto-Hexanoic Acid and Nadp+ (1.4 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 2-Keto-Hexanoic Acid and Nadp+ (1.4 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:55.6 occ:1.00 OE1 A:GLU202 2.3 24.0 1.0 O A:HOH631 2.6 41.1 1.0 O A:HOH659 3.0 11.0 1.0 CD A:GLU202 3.4 18.6 1.0 OE2 A:GLU202 3.9 13.8 1.0 O A:HOH813 4.4 23.6 1.0 O A:HOH748 4.5 31.8 1.0 MG A:MG401 4.6 9.4 1.0 CG A:GLU202 4.7 18.4 1.0 O A:HOH509 4.7 27.5 1.0 O A:GLU202 4.8 13.2 1.0 O A:HOH711 4.9 16.2 1.0 CB A:GLU202 5.0 14.0 1.0

Magnesium binding site 6 out of 21 in the D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with 2-Keto-Hexanoic Acid and Nadp+ (1.4 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 2-Keto-Hexanoic Acid and Nadp+ (1.4 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:43.4 occ:1.00 O A:HOH829 2.1 43.7 1.0 O A:HOH537 2.3 23.7 1.0 O A:HOH781 2.5 41.3 1.0 O A:HOH818 2.7 49.0 1.0 OD2 A:ASP268 4.2 14.2 1.0 O A:HOH591 4.4 21.3 1.0 O A:ALA245 4.5 10.8 1.0 O A:HOH765 4.7 25.5 1.0 O A:HOH697 4.9 14.6 1.0 O A:HOH766 4.9 46.5 1.0 O A:HOH533 4.9 44.0 1.0 O A:HOH559 5.0 20.2 1.0

Magnesium binding site 7 out of 21 in the D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with 2-Keto-Hexanoic Acid and Nadp+ (1.4 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 2-Keto-Hexanoic Acid and Nadp+ (1.4 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:32.8 occ:1.00 O A:HOH502 1.9 43.5 1.0 O A:HOH762 2.2 33.2 1.0 O A:HOH722 2.7 37.6 1.0 OE2 A:GLU302 3.2 0.5 1.0 CD A:GLU302 4.1 62.1 1.0 OE1 A:GLU302 4.2 64.7 1.0

Magnesium binding site 8 out of 21 in the D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with 2-Keto-Hexanoic Acid and Nadp+ (1.4 A Resolution)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with 2-Keto-Hexanoic Acid and Nadp+ (1.4 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg408 b:33.4 occ:1.00 O A:HOH799 2.0 44.3 1.0 O A:HOH538 2.0 35.4 1.0 O A:HOH676 2.1 37.4 1.0 OD1 A:ASP172 2.2 17.5 1.0 CG A:ASP172 3.3 13.8 1.0 OD2 A:ASP172 3.7 28.9 1.0 O A:HOH687 3.9 35.4 1.0 OD1 A:ASN173 4.1 15.2 1.0 N A:ASN173 4.6 11.1 1.0 CB A:ASP172 4.6 12.1 1.0 CG A:ASN173 4.8 10.3 1.0

Magnesium binding site 9 out of 21 in the D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with 2-Keto-Hexanoic Acid and Nadp+ (1.4 A Resolution)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with 2-Keto-Hexanoic Acid and Nadp+ (1.4 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg409 b:10.3 occ:1.00 O A:HOH613 2.0 11.8 1.0 OE2 A:GLU211 2.1 10.4 1.0 O A:HOH540 2.1 12.3 1.0 CD A:GLU211 3.1 8.3 1.0 OE1 A:GLU211 3.4 8.8 1.0 O A:HOH753 3.8 24.8 1.0 NE2 A:HIS184 4.0 10.7 1.0 O A:MET206 4.1 9.8 0.5 O A:MET206 4.1 9.3 0.5 O A:HOH813 4.3 23.6 1.0 O A:HOH817 4.4 34.5 1.0 O A:HOH761 4.4 31.2 1.0 CG A:GLU211 4.4 8.3 1.0 CB A:PRO210 4.8 9.6 1.0 CG A:PRO210 4.9 11.1 1.0 CD2 A:HIS184 4.9 9.6 1.0 CE1 A:HIS184 4.9 11.9 1.0

Magnesium binding site 10 out of 21 in the D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with 2-Keto-Hexanoic Acid and Nadp+ (1.4 A Resolution)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of D-2-Hydroxyacid Dehydrogenases (D2-Hdh) From Haloferax Mediterranei in Complex with 2-Keto-Hexanoic Acid and Nadp+ (1.4 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg410 b:12.3 occ:1.00 O A:MET215 2.3 9.9 1.0 O A:HOH745 2.3 21.0 1.0 O A:PHE212 2.3 9.8 1.0 O A:ASP243 2.3 11.2 1.0 O A:GLU213 2.8 12.6 1.0 C A:ASP243 3.3 10.5 1.0 C A:GLU213 3.3 9.7 1.0 C A:MET215 3.4 10.1 1.0 C A:PHE212 3.4 9.5 1.0 CA A:GLU213 3.6 10.3 1.0 O A:HOH690 3.7 34.1 1.0 CA A:ASP243 3.8 13.3 1.0 N A:MET215 3.9 8.4 1.0 CB A:ASP243 4.0 11.5 1.0 N A:GLU213 4.0 8.7 1.0 CG A:GLU217 4.0 18.6 1.0 CA A:MET215 4.0 8.2 1.0 C A:ARG216 4.2 10.2 1.0 N A:GLU217 4.3 11.8 1.0 N A:THR214 4.3 9.1 1.0 C A:THR214 4.3 9.2 1.0 CB A:MET215 4.3 8.6 1.0 O A:ARG216 4.3 10.0 1.0 N A:ARG216 4.4 9.7 1.0 N A:ILE244 4.5 8.3 1.0 CG2 A:ILE244 4.5 11.1 1.0 CA A:GLU217 4.6 10.7 1.0 CA A:ARG216 4.7 10.9 1.0 CA A:PHE212 4.7 9.3 1.0 O A:THR214 4.8 11.8 1.0 OE2 A:GLU217 4.8 38.8 1.0 CG A:ASP243 4.8 22.3 1.0 OE1 A:GLU213 4.8 43.0 1.0 CA A:THR214 4.9 9.3 1.0 CD A:GLU217 5.0 34.3 1.0 OD1 A:ASP243 5.0 24.5 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.