Magnesium in PDB 8qzb: D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution)

The structure of D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution), PDB code: 8qzb was solved by P.J.Baker, J.R.Barrett, A.A.A.B.Dakhil, J.Domenech, C.Bisson, N.Pramanpol, J.Ferrer, D.W.Rice, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.63 / 1.16
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	66.182, 74.777, 78.172, 109.07, 107.88, 95.56
R / Rfree (%)	13.5 / 16.5

The structure of D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution) also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Sodium	(Na)	12 atoms

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>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Magnesium atom in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution) (pdb code 8qzb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 19 binding sites of Magnesium where determined in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution), PDB code: 8qzb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 19 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 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 (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:10.0 occ:1.00 O A:HOH555 2.0 12.4 1.0 O A:HOH578 2.0 12.9 1.0 O A:HOH730 2.0 11.1 1.0 OE2 A:GLU211 2.1 9.0 1.0 O A:HOH772 2.1 10.2 1.0 O A:HOH857 2.1 12.4 1.0 CD A:GLU211 3.1 8.5 1.0 OE1 A:GLU211 3.4 9.0 1.0 O A:HOH818 3.9 26.6 1.0 O A:MET206 4.0 9.6 1.0 NE2 A:HIS184 4.0 9.9 1.0 O A:HOH507 4.1 23.8 1.0 O A:HOH847 4.1 43.9 1.0 O A:HOH883 4.3 26.5 1.0 CG A:GLU211 4.4 8.2 1.0 CB A:PRO210 4.8 11.1 1.0 CE1 A:HIS184 4.8 11.1 1.0 CG A:PRO210 4.9 11.6 1.0 CD2 A:HIS184 5.0 10.2 1.0

Magnesium binding site 2 out of 19 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 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 (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:15.3 occ:1.00 O B:HOH673 2.0 20.8 1.0 OD1 B:ASP265 2.0 15.4 1.0 O A:HOH561 2.1 18.0 1.0 O A:HOH723 2.1 15.9 1.0 NE2 A:HIS120 2.1 13.8 1.0 O B:HOH748 2.1 17.4 1.0 CE1 A:HIS120 3.1 13.5 1.0 CD2 A:HIS120 3.1 13.3 1.0 CG B:ASP265 3.2 17.6 1.0 OD2 B:ASP265 4.0 19.0 1.0 ND1 A:HIS120 4.2 13.8 1.0 CB B:ASP265 4.2 13.2 1.0 CG A:HIS120 4.3 11.6 1.0 O A:HIS118 4.3 13.1 1.0 O B:HOH647 4.3 28.1 1.0 CA B:ASP265 4.3 11.2 1.0 O A:HOH655 4.4 25.8 1.0 O B:HOH804 4.5 24.4 0.5 O A:GLN117 4.7 9.8 1.0 N B:ASP265 4.8 10.6 1.0 O B:TRP264 4.8 11.8 1.0 CB B:TRP264 4.9 10.7 1.0 C B:TRP264 4.9 10.4 1.0 C A:HIS118 5.0 10.2 1.0

Magnesium binding site 3 out of 19 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 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 (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:27.7 occ:1.00 O A:HOH669 1.9 24.2 1.0 O A:HOH534 2.1 31.1 1.0 O A:HOH887 2.1 25.9 1.0 O A:HOH504 2.1 22.6 1.0 O A:HOH750 2.1 19.8 0.5 O A:HOH634 2.2 25.2 1.0 OE2 A:GLU129 3.8 25.0 1.0 OE1 A:GLU267 4.1 23.8 1.0 O A:HOH530 4.1 26.1 1.0 O A:HOH852 4.1 26.7 1.0 OE1 A:GLU129 4.2 16.4 1.0 OE2 A:GLU267 4.2 22.1 1.0 CD A:GLU129 4.3 19.3 1.0 NE A:ARG126 4.5 26.4 1.0 NH2 A:ARG109 4.5 15.5 1.0 CD A:GLU267 4.5 21.5 1.0 O A:HOH594 4.7 19.2 1.0 O A:HOH586 4.7 36.2 1.0 O A:HOH903 4.8 47.3 1.0 NH2 A:ARG126 4.8 31.9 1.0

Magnesium binding site 4 out of 19 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 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 (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:34.1 occ:1.00 O A:HOH520 1.9 30.7 1.0 O A:HOH638 2.0 44.7 1.0 O A:HOH892 2.0 41.6 1.0 O A:HOH901 2.1 37.0 1.0 O A:HOH549 2.4 50.3 1.0 OE1 A:GLU10 3.7 37.9 1.0 OE2 A:GLU37 4.2 46.7 1.0 OE2 A:GLU10 4.4 35.1 1.0 CD A:GLU10 4.5 27.9 1.0

Magnesium binding site 5 out of 19 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 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 (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg408 b:24.4 occ:1.00 O A:HOH874 2.0 36.8 1.0 O A:HOH846 2.0 35.2 1.0 O A:HOH551 2.0 19.6 1.0 O A:HOH897 2.1 35.1 1.0 O A:HOH902 2.1 34.8 1.0 O A:HOH827 2.3 42.2 1.0 O A:HOH797 3.9 41.3 1.0 O A:HOH714 4.2 27.2 1.0 OD2 A:ASP268 4.3 11.9 1.0 O A:ALA245 4.3 10.9 1.0 O A:HOH599 4.4 16.1 1.0 O A:HOH552 4.5 21.5 1.0 CA A:ALA245 4.8 9.0 1.0 CB A:ALA245 4.9 11.9 1.0 O A:HOH872 5.0 54.6 1.0

Magnesium binding site 6 out of 19 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 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 Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg405 b:8.6 occ:1.00 O B:HOH605 2.1 10.2 1.0 O B:HOH777 2.1 8.9 1.0 OE2 B:GLU211 2.1 8.9 1.0 O B:HOH795 2.1 9.4 1.0 O B:HOH901 2.1 9.9 1.0 O B:HOH553 2.1 10.3 1.0 CD B:GLU211 3.1 8.7 1.0 OE1 B:GLU211 3.4 9.1 1.0 O B:HOH867 3.8 26.8 1.0 NE2 B:HIS184 3.9 9.7 1.0 O B:MET206 4.0 9.4 1.0 O B:HOH931 4.3 25.0 1.0 CG B:GLU211 4.4 8.9 1.0 CB B:PRO210 4.7 8.5 1.0 CE1 B:HIS184 4.8 10.2 1.0 CG B:PRO210 4.9 9.1 1.0 CD2 B:HIS184 4.9 9.6 1.0

Magnesium binding site 7 out of 19 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 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 Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg406 b:17.0 occ:1.00 OD1 A:ASP265 1.9 16.0 1.0 O A:HOH608 2.1 23.5 1.0 O B:HOH569 2.1 18.4 1.0 O A:HOH713 2.1 18.3 1.0 NE2 B:HIS120 2.1 11.6 1.0 O A:HOH744 2.2 17.6 1.0 CD2 B:HIS120 3.1 12.0 1.0 CG A:ASP265 3.1 12.4 1.0 CE1 B:HIS120 3.1 11.6 1.0 OD2 A:ASP265 3.8 16.9 1.0 O B:HOH833 4.1 44.1 1.0 CB A:ASP265 4.1 10.8 1.0 ND1 B:HIS120 4.2 11.9 1.0 CG B:HIS120 4.2 10.7 1.0 CA A:ASP265 4.3 10.4 1.0 O B:HIS118 4.3 11.8 1.0 O A:HOH616 4.4 39.7 1.0 CB A:TRP264 4.6 9.4 1.0 N A:ASP265 4.7 8.8 1.0 O A:TRP264 4.7 10.8 1.0 O B:GLN117 4.7 10.2 1.0 C A:TRP264 4.8 9.0 1.0

Magnesium binding site 8 out of 19 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 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 Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg407 b:20.5 occ:1.00 O B:HOH851 1.9 17.6 1.0 O B:HOH557 2.0 18.1 1.0 O B:HOH674 2.1 29.4 1.0 O B:HOH680 2.1 14.8 1.0 O B:HOH940 2.1 24.9 1.0 O B:HOH527 2.2 23.1 1.0 O B:HOH666 3.9 17.9 1.0 OE2 B:GLU267 4.0 22.4 1.0 O B:HOH908 4.0 23.8 1.0 NH1 B:ARG126 4.1 18.8 1.0 O B:HOH775 4.1 19.5 1.0 O B:HOH914 4.2 41.2 1.0 OE2 B:GLU129 4.2 17.7 1.0 OE1 B:GLU267 4.3 19.3 1.0 O B:HOH934 4.3 29.4 1.0 O B:HOH821 4.3 44.2 1.0 OE1 B:GLU129 4.5 10.8 1.0 CD B:GLU267 4.5 19.3 1.0 O B:HOH669 4.5 20.6 1.0 NH2 B:ARG109 4.6 11.7 1.0 O B:HOH738 4.7 11.0 1.0 CD B:GLU129 4.8 11.0 1.0 O B:HOH566 4.8 18.8 1.0 O B:HOH885 4.9 25.1 1.0

Magnesium binding site 9 out of 19 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 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 Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg408 b:23.0 occ:1.00 OD2 B:ASP301 2.0 26.3 1.0 O B:HOH604 2.0 20.6 1.0 O B:HOH890 2.0 25.3 1.0 O B:HOH544 2.0 21.1 1.0 O B:HOH598 2.1 27.6 1.0 O B:HOH726 2.2 33.9 1.0 CG B:ASP301 3.0 23.1 1.0 OD1 B:ASP301 3.5 25.2 1.0 OE1 B:GLU295 4.1 15.9 1.0 OE2 B:GLU295 4.1 15.9 1.0 OG1 B:THR299 4.2 18.3 1.0 NZ B:LYS296 4.2 24.4 1.0 CB B:ASP301 4.3 20.8 1.0 CD B:GLU295 4.6 14.9 1.0 CD B:LYS296 4.8 24.6 1.0

Magnesium binding site 10 out of 19 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 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 Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with 2-Ketohexanoic Acid, Nad+ and Chloride (1.16 A Resolution) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg409 b:34.5 occ:1.00 O B:HOH848 1.9 44.2 1.0 O B:HOH884 1.9 45.3 1.0 O B:HOH586 2.0 20.0 1.0 O B:HOH949 2.1 39.5 1.0 O B:HOH877 2.2 36.5 1.0 O B:HOH915 2.6 39.8 1.0 O B:GLU217 4.2 12.6 1.0 O B:HOH631 4.2 20.6 1.0 CA B:GLY242 4.4 13.8 1.0 O B:HOH906 4.4 33.6 1.0 O B:GLY242 4.4 14.8 1.0 O B:HOH536 4.7 29.4 1.0 CA B:ALA245 4.7 9.9 1.0 O B:ILE244 4.7 11.7 1.0 C B:GLY242 4.9 13.0 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. Ternary Complexes of Haloferax Mediterranei D-2-Hydroxyacid Dehydrogenase Provide Insights Into Halophilicity and the Chiral Specificity of Its Reaction Mechanism. To Be Published.