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Chlorine 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
Magnesium (Mg) 12 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 5 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 9ibe

Go back to Chlorine Binding Sites List in 9ibe
Chlorine binding site 1 out of 5 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 Chlorine with other atoms in the Cl 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:Cl412

b:24.5
occ:1.00
 NE A:ARG20 3.1 22.1 1.0
NH1 A:ARG20 3.4 22.1 1.0
CZ A:ARG20 3.7 19.8 1.0
CB A:PRO17 3.7 16.7 1.0
CB A:ARG20 3.9 16.2 1.0
CG A:PRO17 4.0 18.3 1.0
CD A:ARG20 4.1 17.1 1.0
N A:ARG20 4.3 14.8 1.0
CA A:ARG20 4.5 14.3 1.0
CG A:ARG20 4.5 19.4 1.0
O A:HOH766 4.8 25.1 1.0
CB A:GLN19 5.0 15.5 1.0

Chlorine binding site 2 out of 5 in 9ibe

Go back to Chlorine Binding Sites List in 9ibe
Chlorine binding site 2 out of 5 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 Chlorine with other atoms in the Cl 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:Cl413

b:35.2
occ:1.00
 O A:HOH734 3.0 32.9 1.0
OG A:SER253 3.0 16.6 0.5
O A:HOH715 3.1 18.9 1.0
N A:GLU232 3.3 10.4 1.0
O A:VAL230 3.4 10.6 1.0
O A:HOH627 3.5 19.0 1.0
CB A:SER253 3.6 14.0 0.5
OG A:SER253 3.8 13.9 0.5
CA A:VAL231 3.8 10.1 1.0
CB A:SER253 4.0 12.0 0.5
CB A:GLU232 4.0 10.2 1.0
C A:VAL231 4.1 8.9 1.0
CA A:GLU232 4.3 10.6 1.0
O A:HOH646 4.3 30.9 1.0
C A:VAL230 4.4 10.8 1.0
N A:VAL231 4.6 10.2 1.0
CG1 A:VAL231 4.7 12.2 1.0
CB A:VAL231 4.8 9.5 1.0
CA A:PRO228 4.9 9.2 1.0
CA A:SER253 5.0 12.3 0.5

Chlorine binding site 3 out of 5 in 9ibe

Go back to Chlorine Binding Sites List in 9ibe
Chlorine binding site 3 out of 5 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 Chlorine with other atoms in the Cl 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:Cl412

b:17.7
occ:1.00
 O B:HOH932 3.1 35.1 1.0
O B:HOH738 3.2 19.2 1.0
OG B:SER253 3.2 21.3 1.0
O B:HOH672 3.3 13.1 1.0
N B:GLU232 3.3 10.5 1.0
O B:VAL230 3.5 10.5 1.0
CB B:SER253 3.7 18.5 1.0
CA B:VAL231 3.8 8.7 1.0
C B:VAL231 4.1 8.8 1.0
CB B:GLU232 4.1 11.0 1.0
O B:HOH655 4.1 20.0 1.0
CA B:GLU232 4.3 10.3 1.0
C B:VAL230 4.5 9.4 1.0
O B:HOH922 4.6 36.9 1.0
CG1 B:VAL231 4.6 13.1 1.0
N B:VAL231 4.7 9.2 1.0
CB B:VAL231 4.8 10.1 1.0
O B:HOH906 4.8 41.7 1.0
CA B:PRO228 4.9 9.3 1.0
O B:HOH660 5.0 20.6 1.0

Chlorine binding site 4 out of 5 in 9ibe

Go back to Chlorine Binding Sites List in 9ibe
Chlorine binding site 4 out of 5 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 Chlorine with other atoms in the Cl 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
C:Cl413

b:17.1
occ:1.00
 O C:HOH730 3.1 16.9 1.0
OG C:SER253 3.2 21.9 1.0
O C:HOH906 3.2 33.2 1.0
O C:HOH656 3.3 12.9 1.0
N C:GLU232 3.3 9.7 1.0
O C:VAL230 3.6 11.2 1.0
CB C:SER253 3.7 20.5 1.0
CA C:VAL231 3.8 9.4 1.0
C C:VAL231 4.1 8.8 1.0
CB C:GLU232 4.1 11.4 1.0
O C:HOH669 4.1 19.5 1.0
CA C:GLU232 4.3 10.3 1.0
C C:VAL230 4.5 9.5 1.0
O C:HOH892 4.5 36.2 1.0
O C:HOH898 4.6 40.9 1.0
CG1 C:VAL231 4.6 12.3 1.0
N C:VAL231 4.7 9.1 1.0
O C:HOH913 4.7 43.9 1.0
CB C:VAL231 4.8 10.4 1.0
O C:HOH545 5.0 22.5 1.0
CA C:PRO228 5.0 8.7 1.0

Chlorine binding site 5 out of 5 in 9ibe

Go back to Chlorine Binding Sites List in 9ibe
Chlorine binding site 5 out of 5 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 Chlorine with other atoms in the Cl 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
D:Cl410

b:33.0
occ:1.00
 O D:HOH708 2.9 31.9 1.0
O D:HOH718 3.1 20.6 1.0
OG D:SER253 3.1 17.4 0.5
N D:GLU232 3.2 11.0 1.0
O D:VAL230 3.4 11.4 1.0
O D:HOH669 3.5 21.1 1.0
CB D:SER253 3.6 17.1 0.5
CA D:VAL231 3.7 10.9 1.0
CB D:GLU232 3.9 12.3 1.0
OG D:SER253 3.9 18.8 0.5
C D:VAL231 4.0 11.1 1.0
CB D:SER253 4.0 17.2 0.5
CA D:GLU232 4.2 12.9 1.0
O D:HOH674 4.2 28.8 1.0
C D:VAL230 4.4 9.2 1.0
N D:VAL231 4.6 10.6 1.0
CG1 D:VAL231 4.6 13.9 1.0
CB D:VAL231 4.7 12.0 1.0
CA D:PRO228 4.9 10.1 1.0
N D:SER233 5.0 14.8 1.0
O D:HOH503 5.0 38.2 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 20:07:30 2025

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