Magnesium 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:

Sodium

(Na)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 24 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 24 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 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-Ketohexanoic Acid and Nad+ (1.35 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg408 b:7.1 occ:1.00 O A:HOH595 2.0 7.7 1.0 O A:HOH543 2.1 8.4 1.0 OE2 A:GLU211 2.1 7.2 1.0 O C:HOH589 2.1 7.6 1.0 O C:HOH687 2.1 7.7 1.0 O C:HOH556 2.1 7.1 1.0 CD A:GLU211 3.1 5.5 1.0 OE1 A:GLU211 3.5 6.5 1.0 O C:GLU204 3.7 6.7 1.0 O C:HOH862 3.8 23.3 1.0 NE2 A:HIS184 3.9 7.7 1.0 O C:GLU202 4.0 7.7 1.0 O A:MET206 4.0 6.9 1.0 O C:HOH632 4.3 19.0 1.0 O A:HOH938 4.4 19.4 1.0 CG A:GLU211 4.4 6.9 1.0 O C:ASP201 4.5 8.3 1.0 C2 C:EDO406 4.5 16.1 1.0 CB A:PRO210 4.7 7.9 1.0 O A:HOH740 4.8 27.5 1.0 C1 C:EDO406 4.8 19.1 1.0 CE1 A:HIS184 4.8 8.8 1.0 CG A:PRO210 4.8 9.7 1.0 C C:GLU202 4.8 7.8 1.0 CD2 A:HIS184 4.8 7.7 1.0 C C:GLU204 4.9 5.8 1.0

Magnesium binding site 2 out of 24 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 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-Ketohexanoic Acid and Nad+ (1.35 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg409 b:14.2 occ:1.00 O A:HOH572 2.0 12.6 1.0 O A:HOH516 2.0 26.2 1.0 O A:HOH949 2.1 23.6 1.0 O A:HOH560 2.1 14.5 1.0 O A:HOH564 2.1 12.4 1.0 O A:HOH511 2.1 18.6 1.0 NH1 A:ARG126 3.7 24.8 1.0 OE2 A:GLU267 4.0 15.0 1.0 OE1 A:GLU267 4.1 15.0 1.0 O A:HOH946 4.1 10.6 0.5 OE2 A:GLU129 4.2 12.2 1.0 O A:HOH586 4.2 13.9 1.0 OE1 A:GLU129 4.3 9.2 1.0 O A:HOH567 4.3 19.6 1.0 NH2 A:ARG109 4.5 10.0 1.0 CD A:GLU267 4.5 14.8 1.0 CD A:GLU129 4.6 9.3 1.0 O A:HOH714 4.6 11.1 1.0 CZ A:ARG126 4.9 15.9 1.0

Magnesium binding site 3 out of 24 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 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-Ketohexanoic Acid and Nad+ (1.35 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg410 b:16.0 occ:0.50 O A:HOH937 2.0 29.2 1.0 O A:HOH930 2.0 23.9 1.0 O A:HOH964 2.0 38.8 1.0 O A:HOH888 2.1 40.5 1.0 O A:HOH912 4.1 34.2 1.0 O A:HOH591 4.1 28.8 1.0 O A:HOH862 4.2 26.0 1.0 CD A:ARG148 4.3 13.1 1.0 O A:HOH810 4.3 19.7 1.0 O A:HOH616 4.5 11.9 1.0 O A:HOH617 4.7 20.3 1.0 O A:HOH908 4.9 17.4 1.0 O A:HOH960 4.9 36.3 1.0

Magnesium binding site 4 out of 24 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 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-Ketohexanoic Acid and Nad+ (1.35 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg411 b:31.0 occ:1.00 O A:HOH557 2.0 15.1 1.0 OG1 A:THR132 2.0 10.0 1.0 O A:ALA134 2.2 7.9 1.0 O A:HOH786 2.3 31.3 1.0 O A:THR132 2.6 7.4 1.0 O A:HOH904 3.2 18.5 1.0 CB A:THR132 3.3 7.9 1.0 C A:THR132 3.3 5.9 1.0 C A:ALA134 3.4 6.7 1.0 CA A:THR132 3.6 6.9 1.0 N A:THR132 3.7 6.0 1.0 O A:HOH598 3.8 18.2 1.0 N A:ALA134 4.1 5.4 1.0 O A:HOH910 4.2 17.0 1.0 CG A:GLU136 4.2 9.6 1.0 CA A:ALA134 4.2 7.2 1.0 OE2 A:GLU136 4.3 20.6 1.0 C A:LEU133 4.3 5.8 1.0 CG2 A:THR132 4.4 9.2 1.0 N A:GLY135 4.4 6.9 1.0 N A:LEU133 4.4 5.5 1.0 O A:HOH902 4.4 42.6 1.0 CA A:GLY135 4.5 8.4 1.0 N A:GLU136 4.6 6.5 1.0 CB A:ALA134 4.6 10.4 1.0 O A:LEU133 4.7 6.6 1.0 C A:GLY135 4.8 10.3 1.0 CD A:GLU136 4.8 14.9 1.0 CA A:LEU133 4.8 5.8 1.0 O B:HOH893 4.8 42.1 1.0 C A:PHE131 4.9 6.2 1.0

Magnesium binding site 5 out of 24 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 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-Ketohexanoic Acid and Nad+ (1.35 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg412 b:25.8 occ:1.00 O A:HOH924 2.0 32.1 1.0 O A:HOH913 2.1 33.5 1.0 O A:HOH965 2.1 26.5 1.0 O A:HOH633 2.2 18.0 1.0 O A:HOH890 2.2 39.1 1.0 O A:HOH873 4.0 40.4 1.0 O A:HOH565 4.2 13.9 1.0 O A:HOH660 4.3 14.5 1.0 CA A:GLY242 4.3 12.6 1.0 O A:HOH951 4.3 42.8 1.0 O A:GLU217 4.5 12.6 1.0 O A:GLY242 4.5 12.2 1.0 O A:HOH891 4.5 51.3 1.0 CA A:ALA245 4.7 9.0 1.0 O A:ILE244 4.8 9.9 1.0 C A:GLY242 4.9 9.2 1.0

Magnesium binding site 6 out of 24 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 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-Ketohexanoic Acid and Nad+ (1.35 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg413 b:11.1 occ:1.00 O A:MET215 2.2 10.0 1.0 O A:HOH832 2.3 19.3 1.0 O A:PHE212 2.3 9.9 1.0 O A:ASP243 2.4 7.9 1.0 O A:HOH844 2.7 35.1 1.0 O A:GLU213 2.7 10.9 1.0 C A:GLU213 3.3 8.3 1.0 C A:ASP243 3.3 8.6 1.0 C A:MET215 3.4 9.7 1.0 C A:PHE212 3.5 9.4 1.0 CA A:GLU213 3.6 11.4 1.0 CA A:ASP243 3.8 12.0 1.0 O A:HOH785 3.9 16.9 0.5 N A:MET215 3.9 6.8 1.0 CB A:ASP243 3.9 11.0 1.0 N A:GLU213 4.0 8.4 1.0 CA A:MET215 4.0 7.8 1.0 C A:THR214 4.3 8.3 1.0 C A:ARG216 4.3 9.6 1.0 N A:THR214 4.3 8.5 1.0 CG A:GLU217 4.3 20.6 1.0 CB A:MET215 4.4 7.2 1.0 N A:GLU217 4.4 10.7 1.0 O A:ARG216 4.4 8.9 1.0 N A:ARG216 4.4 8.9 1.0 CG2 A:ILE244 4.5 9.9 1.0 N A:ILE244 4.5 9.2 1.0 O A:THR214 4.7 9.3 1.0 CA A:ARG216 4.7 9.8 1.0 CA A:PHE212 4.7 7.6 1.0 CG A:ASP243 4.8 24.9 1.0 CA A:GLU217 4.8 10.2 1.0 OD1 A:ASP243 4.8 24.8 1.0 O A:HOH785 4.8 28.6 0.5 CA A:THR214 4.8 7.5 1.0

Magnesium binding site 7 out of 24 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 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-Ketohexanoic Acid and Nad+ (1.35 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg414 b:33.3 occ:1.00 OG A:SER253 1.9 24.9 1.0 O A:HOH816 2.5 22.4 1.0 O A:VAL230 2.8 8.8 1.0 O A:HOH601 2.8 17.2 1.0 O A:GLY227 2.8 6.5 1.0 C A:GLY227 3.2 6.2 1.0 CB A:SER253 3.2 20.6 1.0 OE1 A:GLU232 3.3 20.4 1.0 CB A:GLU232 3.4 15.8 1.0 CA A:PRO228 3.6 5.8 1.0 N A:PRO228 3.6 5.2 1.0 N A:GLU232 3.7 10.5 1.0 C A:VAL230 3.9 8.1 1.0 N A:SER253 3.9 11.8 1.0 CA A:GLU232 4.0 10.4 1.0 CA A:SER253 4.0 13.2 1.0 CA A:GLY227 4.0 6.5 1.0 CD A:GLU232 4.0 18.1 1.0 CG A:GLU232 4.1 16.6 1.0 CD A:PRO228 4.5 6.2 1.0 C A:PRO228 4.5 6.0 1.0 O A:HOH735 4.5 15.9 1.0 CB A:PRO228 4.6 8.2 1.0 C A:VAL231 4.6 8.5 1.0 CG A:PRO228 4.6 8.9 1.0 CA A:VAL230 4.7 6.9 1.0 N A:VAL230 4.7 6.1 1.0 CB A:VAL230 4.7 7.7 1.0 N A:VAL231 4.8 7.3 1.0 CA A:VAL231 4.8 6.5 1.0 C A:PHE252 4.9 10.7 1.0 O A:PRO228 5.0 7.8 1.0

Magnesium binding site 8 out of 24 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 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-Ketohexanoic Acid and Nad+ (1.35 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg417 b:26.0 occ:1.00 OD1 A:ASP265 1.8 17.8 1.0 O A:HOH850 2.2 35.6 1.0 O A:HOH716 2.4 23.9 1.0 NE2 B:HIS120 2.4 12.1 1.0 O B:HOH528 2.5 31.4 1.0 CG A:ASP265 3.0 25.4 1.0 CE1 B:HIS120 3.3 12.1 1.0 CD2 B:HIS120 3.4 14.4 1.0 CB A:ASP265 3.8 14.4 1.0 O A:HOH763 3.9 39.9 1.0 CA A:ASP265 3.9 14.3 1.0 OD2 A:ASP265 3.9 21.2 1.0 O A:HOH540 4.1 20.9 1.0 ND1 B:HIS120 4.4 11.5 1.0 N A:ASP265 4.4 11.2 1.0 O B:HIS118 4.5 11.9 1.0 CG B:HIS120 4.5 10.2 1.0 O B:HOH562 4.6 45.4 1.0 O2 A:EDO401 4.6 34.0 1.0 O A:TRP264 4.6 9.6 1.0 C A:TRP264 4.6 9.6 1.0 CB A:TRP264 4.8 9.6 1.0 O B:GLN117 5.0 8.0 1.0

Magnesium binding site 9 out of 24 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 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-Ketohexanoic Acid and Nad+ (1.35 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg408 b:8.4 occ:1.00 O B:HOH581 2.0 10.6 1.0 OE2 B:GLU211 2.1 7.8 1.0 O B:HOH735 2.1 9.3 1.0 O B:HOH537 2.1 10.4 1.0 O B:HOH761 2.1 8.2 1.0 CD B:GLU211 3.1 7.1 1.0 OE1 B:GLU211 3.4 6.1 1.0 O B:HOH506 3.9 24.2 1.0 NE2 B:HIS184 4.0 7.9 1.0 O B:MET206 4.0 8.6 1.0 O B:HOH846 4.2 25.5 1.0 O1 B:EDO405 4.3 24.4 1.0 O B:HOH884 4.4 26.4 1.0 CG B:GLU211 4.4 6.3 1.0 CB B:PRO210 4.8 7.3 1.0 CE1 B:HIS184 4.8 10.4 1.0 CD2 B:HIS184 4.9 9.0 1.0 CG B:PRO210 4.9 8.2 1.0

Magnesium binding site 10 out of 24 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 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-Ketohexanoic Acid and Nad+ (1.35 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg409 b:9.0 occ:0.50 O B:HOH617 2.0 18.1 1.0 O B:HOH569 2.1 18.0 1.0 O B:HOH549 2.1 18.4 1.0 O B:HOH514 2.1 16.3 1.0 O B:HOH902 2.1 21.9 1.0 O B:HOH757 2.2 24.7 1.0 O B:HOH867 4.0 26.7 1.0 O B:HOH560 4.0 16.0 1.0 OE2 B:GLU129 4.1 16.8 1.0 OE1 B:GLU267 4.2 16.5 1.0 OE1 B:GLU129 4.2 11.9 1.0 OE2 B:GLU267 4.2 17.4 1.0 O B:HOH887 4.3 14.1 0.5 NE B:ARG126 4.4 19.5 1.0 NH1 B:ARG109 4.5 13.8 1.0 CD B:GLU129 4.5 14.3 1.0 CD B:GLU267 4.6 15.7 1.0 NH2 B:ARG126 4.7 23.2 1.0 O B:HOH650 4.7 15.0 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.