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Potassium 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:

Chlorine (Cl) 5 atoms
Magnesium (Mg) 12 atoms

Potassium Binding Sites:

Pages:

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

Binding sites:

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

Potassium binding site 1 out of 24 in 9ibe

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Potassium binding site 1 out of 24 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 Potassium with other atoms in the K 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:K403

b:13.1
occ:1.00
 O A:MET215 2.6 12.4 1.0
O A:ASP243 2.7 11.6 1.0
O A:PHE212 2.7 12.3 1.0
O A:HOH603 2.7 20.8 1.0
O A:HOH794 2.8 24.7 1.0
O A:GLU213 2.9 11.9 1.0
C A:GLU213 3.5 11.3 1.0
C A:ASP243 3.7 10.9 1.0
C A:MET215 3.7 10.9 1.0
CA A:GLU213 3.8 12.7 1.0
C A:PHE212 3.8 10.8 1.0
K A:K404 3.9 23.0 1.0
CA A:ASP243 4.1 14.4 1.0
CG A:GLU217 4.1 21.3 1.0
CB A:ASP243 4.2 18.0 1.0
N A:GLU213 4.3 11.2 1.0
C A:ARG216 4.3 11.8 1.0
N A:GLU217 4.3 11.7 1.0
N A:MET215 4.3 11.0 1.0
CA A:MET215 4.5 11.4 1.0
N A:THR214 4.5 11.2 1.0
O A:HOH586 4.6 35.6 1.0
O A:ARG216 4.6 11.1 1.0
CA A:GLU217 4.6 13.6 1.0
C A:THR214 4.6 12.4 1.0
N A:ARG216 4.7 11.3 1.0
OE1 A:GLU213 4.7 25.8 1.0
CG2 A:ILE244 4.8 12.3 1.0
CA A:ARG216 4.8 11.4 1.0
OD1 A:ASP243 4.8 24.0 1.0
CB A:MET215 4.8 9.7 1.0
N A:ILE244 4.8 12.6 1.0
CD A:GLU213 4.9 27.6 1.0
CG A:ASP243 4.9 23.8 1.0

Potassium binding site 2 out of 24 in 9ibe

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Potassium binding site 2 out of 24 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 Potassium with other atoms in the K 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:K404

b:23.0
occ:1.00
 O A:HOH586 2.4 35.6 1.0
O A:HOH794 2.7 24.7 1.0
O A:GLU213 2.9 11.9 1.0
O A:THR214 2.9 13.0 1.0
O A:MET215 2.9 12.4 1.0
O A:HOH531 3.0 22.3 1.0
O A:HOH631 3.3 27.6 1.0
C A:THR214 3.4 12.4 1.0
O A:HOH872 3.7 56.3 1.0
C A:MET215 3.7 10.9 1.0
K A:K403 3.9 13.1 1.0
C A:GLU213 4.0 11.3 1.0
CA A:THR214 4.0 10.8 1.0
N A:MET215 4.2 11.0 1.0
N A:ARG216 4.4 11.3 1.0
O A:HOH763 4.4 16.9 1.0
N A:THR214 4.4 11.2 1.0
CA A:ARG216 4.5 11.4 1.0
CA A:MET215 4.5 11.4 1.0
O A:HOH844 4.6 40.5 1.0
OE2 A:GLU213 4.9 29.5 1.0

Potassium binding site 3 out of 24 in 9ibe

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Potassium binding site 3 out of 24 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 Potassium with other atoms in the K 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
A:K405

b:19.9
occ:1.00
 O1A A:NAP401 2.7 12.1 1.0
OG1 A:THR88 2.7 16.8 1.0
O A:HOH812 2.7 29.7 1.0
OG1 A:THR145 2.7 12.4 1.0
O A:HOH700 2.9 33.2 1.0
O A:HOH728 3.6 32.5 1.0
CB A:THR88 3.9 13.5 1.0
CB A:THR145 3.9 11.1 1.0
PA A:NAP401 3.9 11.7 1.0
CG2 A:THR88 3.9 13.9 1.0
N A:GLY89 4.0 11.1 1.0
N A:THR145 4.1 9.8 1.0
O2A A:NAP401 4.2 14.2 1.0
C A:THR88 4.3 11.7 1.0
O A:HOH781 4.3 26.4 1.0
O2N A:NAP401 4.4 10.0 1.0
CA A:GLY89 4.4 11.8 1.0
CA A:THR145 4.5 10.6 1.0
O A:HOH690 4.6 26.2 1.0
O3 A:NAP401 4.6 11.7 1.0
CA A:THR88 4.7 13.2 1.0
O A:HOH837 4.7 43.4 1.0
O A:THR88 4.9 13.9 1.0
PN A:NAP401 5.0 10.8 1.0

Potassium binding site 4 out of 24 in 9ibe

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Potassium binding site 4 out of 24 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 Potassium with other atoms in the K 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
A:K406

b:36.3
occ:1.00
 O A:ALA59 2.7 28.6 1.0
O A:LEU57 2.7 29.5 1.0
O A:HOH567 2.7 42.1 1.0
O A:ALA80 2.8 37.6 1.0
OG1 A:THR82 2.9 31.9 1.0
O A:HOH509 3.1 44.5 1.0
O A:GLY81 3.6 37.7 1.0
C A:ALA59 3.8 28.2 1.0
C A:LEU57 3.9 28.8 1.0
C A:ALA80 3.9 35.5 1.0
C A:GLY81 3.9 36.5 1.0
C A:ASP58 4.1 29.2 1.0
N A:THR82 4.1 32.3 1.0
CB A:THR82 4.2 27.8 1.0
O A:ASP58 4.3 29.1 1.0
CA A:ASP58 4.4 28.9 1.0
CA A:THR82 4.4 27.7 1.0
N A:ALA59 4.4 31.5 1.0
OD1 A:ASP60 4.5 34.4 1.0
CA A:GLY81 4.5 39.9 1.0
N A:ASP58 4.5 28.9 1.0
CB A:ALA80 4.6 37.3 1.0
N A:ASP60 4.6 25.3 1.0
CA A:ASP60 4.6 26.6 1.0
N A:GLY81 4.6 37.3 1.0
CA A:ALA59 4.7 29.1 1.0
CA A:ALA80 4.8 36.2 1.0
CA A:LEU57 4.9 31.5 1.0

Potassium binding site 5 out of 24 in 9ibe

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Potassium binding site 5 out of 24 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 Potassium with other atoms in the K 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
A:K407

b:15.9
occ:1.00
 O A:HOH782 2.7 40.2 1.0
O A:VAL174 2.7 12.6 1.0
O A:HOH720 2.8 17.8 1.0
O A:VAL171 2.8 9.9 1.0
O A:HOH674 2.9 14.5 1.0
C A:VAL171 3.7 9.7 1.0
C A:VAL174 3.8 11.1 1.0
N A:VAL174 4.0 9.6 1.0
O A:HOH825 4.0 21.0 1.0
N A:ASN173 4.1 10.9 1.0
CA A:ASP172 4.2 11.6 1.0
N A:VAL171 4.3 11.1 1.0
N A:ASP172 4.3 11.2 1.0
C A:ASP172 4.4 10.1 1.0
CA A:VAL174 4.4 10.2 1.0
CA A:VAL171 4.7 10.1 1.0
N A:SER175 4.7 10.7 1.0
CA A:SER175 4.8 12.1 0.5
C A:ASN173 4.8 12.1 1.0
CA A:SER175 4.9 12.2 0.5
CB A:VAL174 4.9 9.9 1.0
CA A:ASN173 4.9 11.7 1.0
CB A:PRO170 5.0 15.3 1.0

Potassium binding site 6 out of 24 in 9ibe

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Potassium binding site 6 out of 24 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 Potassium with other atoms in the K 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
A:K408

b:29.6
occ:0.50
 O A:GLU23 2.7 17.0 1.0
OG A:SER26 2.9 24.5 1.0
O A:HOH792 3.2 25.0 1.0
C A:GLU23 3.8 17.3 1.0
CB A:SER26 4.0 21.4 1.0
CA A:ALA24 4.2 14.5 1.0
O A:ALA24 4.2 16.0 1.0
C A:ALA24 4.3 15.1 1.0
N A:SER26 4.4 15.1 1.0
N A:ALA24 4.4 15.5 1.0
O A:HOH515 4.6 41.7 1.0
CA A:SER26 4.8 18.2 1.0
CA A:GLU23 4.9 17.0 1.0
N A:LEU25 5.0 14.8 1.0

Potassium binding site 7 out of 24 in 9ibe

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Potassium binding site 7 out of 24 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 Potassium with other atoms in the K 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
A:K409

b:17.5
occ:1.00
 O A:HOH845 2.9 11.3 1.0
O A:HOH724 2.9 11.4 1.0
O A:GLY205 3.1 11.9 1.0
O A:HOH573 3.2 10.9 1.0
O A:HOH561 3.4 10.8 1.0
MG A:MG410 3.8 10.1 1.0
C A:GLY205 4.0 9.9 1.0
O A:HOH797 4.1 22.1 1.0
CA A:MET206 4.6 9.4 1.0
O A:HOH610 4.7 16.8 1.0
N A:MET206 4.7 8.9 1.0
O A:MET206 4.7 10.0 1.0
O A:HOH860 4.8 23.8 1.0
C A:MET206 4.9 9.2 1.0
O A:GLU204 5.0 11.7 1.0
CA A:GLY205 5.0 10.8 1.0

Potassium binding site 8 out of 24 in 9ibe

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Potassium binding site 8 out of 24 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 Potassium with other atoms in the K 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
B:K403

b:13.7
occ:1.00
 O B:MET215 2.6 13.5 1.0
O B:HOH504 2.6 32.6 1.0
O B:ASP243 2.7 12.0 1.0
O B:PHE212 2.7 13.3 1.0
O B:HOH833 2.8 32.1 1.0
O B:GLU213 2.9 14.6 1.0
C B:GLU213 3.5 11.5 1.0
C B:ASP243 3.7 13.1 1.0
C B:MET215 3.7 13.4 1.0
C B:PHE212 3.8 12.2 1.0
CA B:GLU213 3.8 12.9 1.0
K B:K404 3.9 26.0 1.0
CA B:ASP243 4.1 14.7 1.0
CG B:GLU217 4.1 25.6 1.0
CB B:ASP243 4.2 16.6 1.0
N B:GLU213 4.3 12.5 1.0
N B:MET215 4.3 11.2 1.0
N B:GLU217 4.3 12.5 1.0
O B:HOH516 4.3 33.1 1.0
C B:ARG216 4.3 11.8 1.0
CA B:MET215 4.4 11.2 1.0
N B:THR214 4.5 11.8 1.0
O B:ARG216 4.5 11.2 1.0
CA B:GLU217 4.6 13.3 1.0
C B:THR214 4.6 12.7 1.0
OE1 B:GLU213 4.6 37.6 1.0
N B:ARG216 4.7 13.3 1.0
CB B:MET215 4.8 9.7 1.0
CG2 B:ILE244 4.8 12.8 1.0
OD1 B:ASP243 4.8 28.8 1.0
CG B:ASP243 4.8 30.3 1.0
N B:ILE244 4.8 13.2 1.0
CA B:ARG216 4.8 12.7 1.0
CD B:GLU213 5.0 29.7 1.0

Potassium binding site 9 out of 24 in 9ibe

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Potassium binding site 9 out of 24 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 Potassium with other atoms in the K 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
B:K404

b:26.0
occ:1.00
 O B:HOH516 2.5 33.1 1.0
O B:HOH833 2.8 32.1 1.0
O B:HOH637 2.9 23.0 1.0
O B:MET215 2.9 13.5 1.0
O B:THR214 2.9 13.4 1.0
O B:GLU213 3.0 14.6 1.0
O B:HOH636 3.3 32.5 1.0
C B:THR214 3.4 12.7 1.0
C B:MET215 3.7 13.4 1.0
K B:K403 3.9 13.7 1.0
CA B:THR214 4.0 11.3 1.0
C B:GLU213 4.1 11.5 1.0
O B:HOH798 4.2 18.8 1.0
O B:HOH923 4.2 49.0 1.0
N B:MET215 4.2 11.2 1.0
N B:ARG216 4.3 13.3 1.0
CA B:ARG216 4.5 12.7 1.0
N B:THR214 4.5 11.8 1.0
CA B:MET215 4.6 11.2 1.0
OE2 B:GLU213 4.8 31.6 1.0

Potassium binding site 10 out of 24 in 9ibe

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Potassium binding site 10 out of 24 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 Potassium with other atoms in the K 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
B:K405

b:15.9
occ:1.00
 OG1 B:THR88 2.7 12.9 1.0
O B:HOH842 2.7 29.6 1.0
O1A B:NAP401 2.7 12.0 1.0
OG1 B:THR145 2.7 12.7 1.0
O B:HOH862 2.8 26.8 1.0
O B:HOH782 2.9 25.5 1.0
O B:HOH762 3.7 27.6 1.0
CG2 B:THR88 3.8 12.7 1.0
CB B:THR88 3.8 12.2 1.0
PA B:NAP401 3.9 11.3 1.0
CB B:THR145 3.9 10.6 1.0
N B:GLY89 4.0 11.3 1.0
N B:THR145 4.1 9.6 1.0
O B:HOH927 4.2 41.1 1.0
O2A B:NAP401 4.2 11.7 1.0
O2N B:NAP401 4.3 10.1 1.0
C B:THR88 4.3 11.3 1.0
CA B:GLY89 4.3 11.4 1.0
O B:HOH691 4.6 23.0 1.0
CA B:THR145 4.6 9.9 1.0
O3 B:NAP401 4.6 10.2 1.0
CA B:THR88 4.6 10.5 1.0
O B:HOH890 4.6 30.2 1.0
O B:HOH811 4.8 26.0 1.0
O B:THR88 4.8 13.5 1.0
PN B:NAP401 4.9 10.0 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 20:47:08 2025

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