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Magnesium in PDB 9ibe: D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with Potassium, 2-Ketohexanoic Acid, Nadp+ and Chloride

Protein crystallography data

The structure of D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with Potassium, 2-Ketohexanoic Acid, Nadp+ and Chloride, PDB code: 9ibe 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) 52.28 / 1.26
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 66.633, 75.34, 78.234, 108.84, 108.08, 95.53
R / Rfree (%) 15.2 / 18.8

Other elements in 9ibe:

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

Potassium (K) 24 atoms
Chlorine (Cl) 5 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with Potassium, 2-Ketohexanoic Acid, Nadp+ and Chloride (pdb code 9ibe). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with Potassium, 2-Ketohexanoic Acid, Nadp+ and Chloride, PDB code: 9ibe:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 9ibe

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Magnesium binding site 1 out of 12 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with Potassium, 2-Ketohexanoic Acid, Nadp+ and Chloride


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 Potassium, 2-Ketohexanoic Acid, Nadp+ and Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg410

b:10.1
occ:1.00
 O A:HOH561 2.0 10.8 1.0
O A:HOH573 2.0 10.9 1.0
O A:HOH743 2.1 10.2 1.0
O A:HOH845 2.1 11.3 1.0
O A:HOH746 2.1 10.5 1.0
OE2 A:GLU211 2.1 9.9 1.0
CD A:GLU211 3.1 10.5 1.0
OE1 A:GLU211 3.4 10.0 1.0
K A:K409 3.8 17.5 1.0
O A:MET206 4.0 10.0 1.0
NE2 A:HIS184 4.0 10.5 1.0
O A:HOH807 4.3 26.7 1.0
O A:HOH860 4.3 23.8 1.0
CG A:GLU211 4.4 9.1 1.0
CB A:PRO210 4.8 11.2 1.0
CE1 A:HIS184 4.9 11.8 1.0
CG A:PRO210 4.9 10.8 1.0
CD2 A:HIS184 5.0 11.3 1.0
C A:MET206 5.0 9.2 1.0

Magnesium binding site 2 out of 12 in 9ibe

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Magnesium binding site 2 out of 12 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with Potassium, 2-Ketohexanoic Acid, Nadp+ and Chloride


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 Potassium, 2-Ketohexanoic Acid, Nadp+ and Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg411

b:23.9
occ:1.00
 OD1 B:ASP265 2.0 31.1 1.0
O B:HOH825 2.1 32.6 1.0
O B:HOH570 2.1 27.4 1.0
NE2 A:HIS120 2.2 16.2 1.0
O D:HOH505 2.3 25.1 1.0
O A:HOH669 2.3 22.9 1.0
CD2 A:HIS120 3.1 14.4 1.0
CE1 A:HIS120 3.2 15.5 1.0
CG B:ASP265 3.2 26.4 1.0
OD1 D:ASP172 3.8 20.9 1.0
CA B:ASP265 4.0 16.0 1.0
CB B:ASP265 4.0 18.6 1.0
OD2 B:ASP265 4.1 31.5 1.0
O B:HOH523 4.2 33.0 1.0
ND1 A:HIS120 4.3 15.4 1.0
CG A:HIS120 4.3 14.3 1.0
O A:HOH508 4.3 38.6 1.0
O B:HOH828 4.4 50.3 1.0
N B:ASP265 4.5 13.6 1.0
O B:TRP264 4.5 14.3 1.0
O A:HIS118 4.5 14.7 1.0
C B:TRP264 4.5 13.8 1.0
CB B:TRP264 4.6 12.9 1.0
CG D:ASP172 4.6 19.0 1.0
O A:GLN117 4.8 11.7 1.0
O D:HOH530 4.8 31.6 1.0
CA D:ASP172 4.9 17.8 1.0
O D:HOH508 4.9 38.1 1.0

Magnesium binding site 3 out of 12 in 9ibe

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Magnesium binding site 3 out of 12 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with Potassium, 2-Ketohexanoic Acid, Nadp+ and Chloride


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 Potassium, 2-Ketohexanoic Acid, Nadp+ and Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg408

b:9.8
occ:1.00
 O B:HOH604 2.0 9.9 1.0
OE2 B:GLU211 2.1 9.7 1.0
O B:HOH555 2.1 9.9 1.0
CD B:GLU211 3.1 10.0 1.0
OE1 B:GLU211 3.4 10.4 1.0
NE2 B:HIS184 4.0 10.5 1.0
O B:MET206 4.0 10.1 1.0
O B:HOH904 4.3 19.5 1.0
CG B:GLU211 4.4 10.8 1.0
CB B:PRO210 4.7 9.7 1.0
CE1 B:HIS184 4.8 11.3 1.0
CG B:PRO210 4.9 10.1 1.0
CD2 B:HIS184 4.9 10.4 1.0

Magnesium binding site 4 out of 12 in 9ibe

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Magnesium binding site 4 out of 12 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with Potassium, 2-Ketohexanoic Acid, Nadp+ and Chloride


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 Potassium, 2-Ketohexanoic Acid, Nadp+ and Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg409

b:16.5
occ:1.00
 OD1 A:ASP265 1.9 16.3 1.0
O C:HOH604 2.1 20.0 1.0
O B:HOH564 2.1 18.9 1.0
O A:HOH685 2.1 23.7 1.0
O B:HOH767 2.1 17.1 1.0
NE2 B:HIS120 2.1 13.6 1.0
CD2 B:HIS120 3.1 12.4 1.0
CG A:ASP265 3.1 15.8 1.0
CE1 B:HIS120 3.2 12.8 1.0
OD2 A:ASP265 3.9 19.4 1.0
O C:HOH564 3.9 26.9 1.0
OD1 C:ASP172 4.1 19.0 1.0
O C:HOH566 4.1 24.7 1.0
CB A:ASP265 4.2 13.1 1.0
O B:HIS118 4.3 14.4 1.0
CG B:HIS120 4.3 11.4 1.0
O B:HOH750 4.3 31.5 1.0
ND1 B:HIS120 4.3 13.1 1.0
CA A:ASP265 4.4 11.5 1.0
O A:HOH644 4.4 30.9 1.0
CB A:TRP264 4.6 11.1 1.0
O A:TRP264 4.6 11.7 1.0
O B:GLN117 4.7 10.8 1.0
C A:TRP264 4.7 10.2 1.0
N A:ASP265 4.7 10.5 1.0
C B:HIS118 5.0 12.8 1.0
CG C:ASP172 5.0 15.6 1.0

Magnesium binding site 5 out of 12 in 9ibe

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Magnesium binding site 5 out of 12 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with Potassium, 2-Ketohexanoic Acid, Nadp+ and Chloride


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 Potassium, 2-Ketohexanoic Acid, Nadp+ and Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg410

b:19.6
occ:1.00
 O B:HOH829 2.0 18.0 1.0
O B:HOH614 2.0 18.9 1.0
O B:HOH526 2.0 19.9 1.0
O B:HOH600 2.1 24.2 1.0
O B:HOH654 2.1 14.3 1.0
O B:HOH917 2.2 22.8 1.0
O B:HOH689 4.0 18.9 1.0
NH1 B:ARG126 4.1 18.7 1.0
OE2 B:GLU267 4.1 21.4 1.0
O B:HOH881 4.1 28.2 1.0
OE2 B:GLU129 4.1 20.7 1.0
O B:HOH764 4.2 17.9 1.0
O B:HOH903 4.3 31.7 1.0
OE1 B:GLU267 4.3 21.7 1.0
O B:HOH915 4.3 35.3 1.0
OE1 B:GLU129 4.4 13.3 1.0
O B:HOH635 4.6 23.7 1.0
CD B:GLU267 4.6 22.7 1.0
NH1 B:ARG109 4.6 12.7 1.0
O B:HOH713 4.6 13.9 1.0
CD B:GLU129 4.7 11.8 1.0
O B:HOH861 4.9 25.9 1.0
O B:HOH545 5.0 18.6 1.0

Magnesium binding site 6 out of 12 in 9ibe

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Magnesium binding site 6 out of 12 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with Potassium, 2-Ketohexanoic Acid, Nadp+ and Chloride


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 Potassium, 2-Ketohexanoic Acid, Nadp+ and Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg411

b:32.1
occ:1.00
 OD2 B:ASP301 1.8 34.7 1.0
O B:HOH580 2.0 24.6 1.0
O B:HOH609 2.1 24.0 1.0
O B:HOH863 2.1 32.6 1.0
O B:HOH728 2.2 38.2 1.0
O B:HOH615 2.3 33.6 1.0
CG B:ASP301 3.0 31.4 1.0
OD1 B:ASP301 3.5 31.1 1.0
O B:HOH911 3.9 37.8 1.0
OE1 B:GLU295 4.0 18.3 1.0
OG1 B:THR299 4.1 20.9 1.0
OE2 B:GLU295 4.1 18.9 1.0
NZ B:LYS296 4.2 27.7 1.0
CB B:ASP301 4.2 25.8 1.0
CD B:GLU295 4.5 19.4 1.0
CB B:THR299 4.9 22.1 1.0

Magnesium binding site 7 out of 12 in 9ibe

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Magnesium binding site 7 out of 12 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with Potassium, 2-Ketohexanoic Acid, Nadp+ and Chloride


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 Potassium, 2-Ketohexanoic Acid, Nadp+ and Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg410

b:9.6
occ:1.00
 O C:HOH563 2.1 10.0 1.0
O C:HOH537 2.1 10.0 1.0
OE2 C:GLU211 2.1 9.8 1.0
CD C:GLU211 3.1 10.9 1.0
OE1 C:GLU211 3.4 9.6 1.0
K C:K409 3.8 21.1 1.0
NE2 C:HIS184 4.0 10.2 1.0
O C:MET206 4.0 9.8 1.0
O C:HOH885 4.3 22.5 1.0
CG C:GLU211 4.4 10.0 1.0
O C:HOH859 4.5 10.7 0.5
CB C:PRO210 4.7 11.5 1.0
O C:HOH859 4.8 15.0 0.5
CE1 C:HIS184 4.8 10.0 1.0
CG C:PRO210 4.9 10.8 1.0
CD2 C:HIS184 4.9 11.1 1.0

Magnesium binding site 8 out of 12 in 9ibe

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Magnesium binding site 8 out of 12 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with Potassium, 2-Ketohexanoic Acid, Nadp+ and Chloride


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 Potassium, 2-Ketohexanoic Acid, Nadp+ and Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg411

b:17.6
occ:1.00
 O D:HOH722 2.0 23.2 1.0
O D:HOH653 2.0 19.2 1.0
OD1 D:ASP265 2.1 20.7 1.0
O C:HOH726 2.1 17.1 1.0
NE2 C:HIS120 2.2 14.2 1.0
CD2 C:HIS120 3.2 13.7 1.0
CE1 C:HIS120 3.2 13.1 1.0
CG D:ASP265 3.3 23.0 1.0
OD2 D:ASP265 4.2 26.3 1.0
CA D:ASP265 4.2 13.3 1.0
CB D:ASP265 4.2 14.4 1.0
O C:HOH532 4.2 33.0 1.0
O C:HIS118 4.3 13.1 1.0
ND1 C:HIS120 4.3 12.3 1.0
O D:HOH575 4.3 36.3 1.0
CG C:HIS120 4.3 13.2 1.0
O D:TRP264 4.5 12.2 1.0
O C:GLN117 4.7 12.1 1.0
N D:ASP265 4.7 13.6 1.0
C D:TRP264 4.7 12.2 1.0
CB D:TRP264 4.7 12.3 1.0
C C:HIS118 5.0 12.8 1.0

Magnesium binding site 9 out of 12 in 9ibe

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Magnesium binding site 9 out of 12 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with Potassium, 2-Ketohexanoic Acid, Nadp+ and Chloride


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 Potassium, 2-Ketohexanoic Acid, Nadp+ and Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg412

b:25.0
occ:1.00
 O C:HOH808 2.0 19.2 1.0
O C:HOH652 2.0 26.4 1.0
O C:HOH716 2.0 28.8 1.0
O C:HOH677 2.0 34.1 1.0
O C:HOH670 2.1 18.3 1.0
O C:HOH663 2.2 23.0 1.0
O C:HOH529 3.8 27.9 1.0
OE2 C:GLU267 4.0 28.3 1.0
O C:HOH896 4.1 39.0 1.0
NH1 C:ARG126 4.2 21.9 1.0
O C:HOH873 4.2 37.9 1.0
O C:HOH755 4.2 21.3 1.0
OE2 C:GLU129 4.3 21.6 1.0
OE1 C:GLU267 4.3 27.8 1.0
O C:HOH501 4.3 17.4 0.5
OE1 C:GLU129 4.4 15.5 1.0
CD C:GLU267 4.5 22.2 1.0
OD2 C:ASP123 4.6 23.7 0.5
O C:HOH744 4.6 14.1 1.0
O C:HOH698 4.7 25.9 1.0
O C:HOH796 4.7 28.7 1.0
NH2 C:ARG109 4.7 12.3 1.0
CD C:GLU129 4.8 18.4 1.0

Magnesium binding site 10 out of 12 in 9ibe

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Magnesium binding site 10 out of 12 in the D-2-Hydroxyacid Dehydrogenase (D2HDH) From Haloferax Mediterranei in Complex with Potassium, 2-Ketohexanoic Acid, Nadp+ and Chloride


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 Potassium, 2-Ketohexanoic Acid, Nadp+ and Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg407

b:11.2
occ:1.00
 O D:HOH578 2.1 12.3 1.0
O D:HOH591 2.1 12.7 1.0
OE2 D:GLU211 2.1 11.1 1.0
CD D:GLU211 3.1 11.2 1.0
OE1 D:GLU211 3.4 10.1 1.0
O D:MET206 4.0 11.6 1.0
NE2 D:HIS184 4.0 10.8 1.0
O D:HOH817 4.3 23.4 1.0
O D:HOH769 4.4 40.1 1.0
CG D:GLU211 4.4 10.4 1.0
CB D:PRO210 4.7 11.5 1.0
CE1 D:HIS184 4.9 13.7 1.0
CG D:PRO210 4.9 12.2 1.0
CD2 D:HIS184 5.0 11.3 1.0

Reference:

J.Domenech, N.Pramanpol, C.Bisson, S.E.Sedelnikova, J.R.Barrett, A.A.A.B.Dakhil, V.Mykhaylyk, A.S.Abdelhameed, S.E.Harding, D.W.Rice, P.J.Baker, J.Ferrer. Potassium Binding By Carbonyl Clusters, Halophilic Adaptation and Catalysis of Haloferax Mediterranei D-2-Hydroxyacid Dehydrogenase. Commun Biol V. 8 1170 2025.
ISSN: ESSN 2399-3642
PubMed: 40770045
DOI: 10.1038/S42003-025-08587-7
Page generated: Tue Aug 26 21:11:39 2025

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