Iron in PDB 4eht: Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp

The structure of Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp, PDB code: 4eht was solved by S.H.Knauer, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.70 / 1.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	66.154, 161.005, 63.576, 90.00, 110.75, 90.00
R / Rfree (%)	17.6 / 20.5

The structure of Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Iron atom in the Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp (pdb code 4eht). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp, PDB code: 4eht:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:23.6 occ:1.00 FE1 A:SF4301 0.0 23.6 1.0 S2 A:SF4301 2.2 26.5 1.0 S3 A:SF4301 2.2 24.2 1.0 S4 A:SF4301 2.2 23.8 1.0 SG B:CYS125 2.3 24.0 1.0 FE3 A:SF4301 2.8 20.5 1.0 FE4 A:SF4301 2.8 25.0 1.0 FE2 A:SF4301 2.9 21.5 1.0 HB2 B:CYS125 3.2 26.4 1.0 CB B:CYS125 3.3 22.1 1.0 HA B:CYS125 3.4 27.9 1.0 H B:ALA127 3.5 26.3 1.0 H B:ALA126 3.6 26.4 1.0 CA B:CYS125 3.8 23.3 1.0 S1 A:SF4301 3.9 26.6 1.0 HA B:CYS164 3.9 27.6 1.0 N B:ALA126 4.1 22.1 1.0 HB3 B:CYS125 4.1 26.4 1.0 H B:THR165 4.2 25.2 1.0 HB3 B:ALA127 4.2 26.0 1.0 HB2 B:ALA127 4.2 26.0 1.0 O A:HOH569 4.2 35.8 0.5 C B:CYS125 4.3 26.0 1.0 N B:ALA127 4.4 22.0 1.0 SG A:CYS164 4.5 26.0 1.0 HG1 B:THR165 4.5 26.7 1.0 CB B:ALA127 4.6 21.8 1.0 HB2 A:CYS164 4.7 22.9 1.0 CA B:CYS164 4.8 23.1 1.0 O A:HOH569 4.9 41.8 0.5 HB2 A:CYS125 4.9 28.4 1.0 HB3 B:ALA126 4.9 27.2 1.0 O B:HOH438 4.9 36.1 1.0 SG B:CYS164 4.9 24.0 1.0 N B:THR165 5.0 21.1 1.0 SG A:CYS125 5.0 24.2 1.0

Iron binding site 2 out of 4 in the Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:21.5 occ:1.00 FE2 A:SF4301 0.0 21.5 1.0 S4 A:SF4301 2.2 23.8 1.0 S1 A:SF4301 2.2 26.6 1.0 S3 A:SF4301 2.3 24.2 1.0 SG A:CYS125 2.3 24.2 1.0 FE4 A:SF4301 2.7 25.0 1.0 FE3 A:SF4301 2.8 20.5 1.0 FE1 A:SF4301 2.9 23.6 1.0 HB2 A:CYS125 3.2 28.4 1.0 CB A:CYS125 3.3 23.8 1.0 HA A:CYS125 3.5 34.7 1.0 H A:ALA127 3.6 30.7 1.0 H A:ALA126 3.7 29.1 1.0 S2 A:SF4301 3.8 26.5 1.0 HA A:CYS164 3.8 28.4 1.0 CA A:CYS125 3.9 29.0 1.0 O A:HOH569 4.1 41.8 0.5 N A:ALA126 4.1 24.3 1.0 HB3 A:CYS125 4.1 28.4 1.0 H A:THR165 4.1 34.8 1.0 HB3 A:ALA127 4.1 25.0 1.0 HB2 A:ALA127 4.1 25.0 1.0 C A:CYS125 4.3 30.8 1.0 N A:ALA127 4.4 25.7 1.0 SG B:CYS164 4.4 24.0 1.0 HG1 A:THR165 4.4 24.1 1.0 CB A:ALA127 4.6 20.9 1.0 O A:HOH569 4.7 35.8 0.5 CA A:CYS164 4.8 23.7 1.0 SG A:CYS164 4.9 26.0 1.0 HB2 B:CYS164 4.9 20.7 1.0 HB2 A:CYS164 4.9 22.9 1.0 N A:THR165 4.9 29.0 1.0 HB2 B:CYS125 5.0 26.4 1.0 SG B:CYS125 5.0 24.0 1.0

Iron binding site 3 out of 4 in the Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:20.5 occ:1.00 FE3 A:SF4301 0.0 20.5 1.0 S4 A:SF4301 2.2 23.8 1.0 S1 A:SF4301 2.2 26.6 1.0 S2 A:SF4301 2.2 26.5 1.0 SG A:CYS164 2.2 26.0 1.0 FE4 A:SF4301 2.8 25.0 1.0 FE1 A:SF4301 2.8 23.6 1.0 FE2 A:SF4301 2.8 21.5 1.0 HA A:CYS164 3.0 28.4 1.0 H A:THR165 3.1 34.8 1.0 CB A:CYS164 3.2 19.1 1.0 HB2 A:CYS164 3.3 22.9 1.0 H B:ALA126 3.3 26.4 1.0 CA A:CYS164 3.5 23.7 1.0 H A:VAL166 3.5 26.0 1.0 N A:THR165 3.6 29.0 1.0 HA B:CYS125 3.7 27.9 1.0 S3 A:SF4301 3.8 24.2 1.0 HG23 A:VAL166 3.9 38.4 1.0 C A:CYS164 3.9 28.3 1.0 HB3 A:CYS164 4.1 22.9 1.0 HB3 B:ALA126 4.1 27.2 1.0 N B:ALA126 4.1 22.1 1.0 HB A:THR165 4.2 22.7 1.0 HG1 A:THR165 4.3 24.1 1.0 N A:VAL166 4.4 21.7 1.0 HB A:VAL166 4.5 34.3 1.0 HG23 B:VAL166 4.5 33.8 1.0 CA B:CYS125 4.6 23.3 1.0 SG B:CYS125 4.6 24.0 1.0 HB2 B:ALA126 4.6 27.2 1.0 CA A:THR165 4.7 27.9 1.0 CG2 A:VAL166 4.7 32.1 1.0 H B:ALA127 4.7 26.3 1.0 H B:THR165 4.7 25.2 1.0 HB B:THR165 4.7 34.5 1.0 CB B:ALA126 4.7 22.8 1.0 CB A:THR165 4.8 19.0 1.0 HG21 A:VAL166 4.9 38.4 1.0 SG B:CYS164 4.9 24.0 1.0 C B:CYS125 4.9 26.0 1.0 N A:CYS164 4.9 25.9 1.0 HB2 B:CYS125 4.9 26.4 1.0 SG A:CYS125 4.9 24.2 1.0 HG1 B:THR165 4.9 26.7 1.0 CB B:CYS125 5.0 22.1 1.0 OG1 A:THR165 5.0 20.2 1.0 O A:CYS164 5.0 27.0 1.0 H A:PHE167 5.0 32.7 1.0

Iron binding site 4 out of 4 in the Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:25.0 occ:1.00 FE4 A:SF4301 0.0 25.0 1.0 S3 A:SF4301 2.2 24.2 1.0 S2 A:SF4301 2.2 26.5 1.0 S1 A:SF4301 2.3 26.6 1.0 SG B:CYS164 2.3 24.0 1.0 FE2 A:SF4301 2.7 21.5 1.0 FE3 A:SF4301 2.8 20.5 1.0 FE1 A:SF4301 2.8 23.6 1.0 HA B:CYS164 3.0 27.6 1.0 H B:THR165 3.1 25.2 1.0 CB B:CYS164 3.3 17.3 1.0 H A:ALA126 3.3 29.1 1.0 HB2 B:CYS164 3.4 20.7 1.0 CA B:CYS164 3.5 23.1 1.0 H B:VAL166 3.5 28.3 1.0 N B:THR165 3.6 21.1 1.0 S4 A:SF4301 3.7 23.8 1.0 HA A:CYS125 3.7 34.7 1.0 HG23 B:VAL166 3.8 33.8 1.0 C B:CYS164 4.0 25.3 1.0 HB3 B:CYS164 4.2 20.7 1.0 N A:ALA126 4.2 24.3 1.0 HB B:THR165 4.2 34.5 1.0 HB3 A:ALA126 4.3 25.3 1.0 HB B:VAL166 4.4 30.7 1.0 N B:VAL166 4.4 23.7 1.0 HG1 B:THR165 4.5 26.7 1.0 SG A:CYS125 4.5 24.2 1.0 CA A:CYS125 4.5 29.0 1.0 CG2 B:VAL166 4.6 28.2 1.0 HG23 A:VAL166 4.7 38.4 1.0 CA B:THR165 4.7 25.8 1.0 HG21 B:VAL166 4.7 33.8 1.0 H A:ALA127 4.7 30.7 1.0 H A:THR165 4.7 34.8 1.0 HB2 A:CYS125 4.7 28.4 1.0 HB A:THR165 4.8 22.7 1.0 CB B:THR165 4.8 28.8 1.0 HB2 A:ALA126 4.8 25.3 1.0 CB A:CYS125 4.8 23.8 1.0 SG A:CYS164 4.9 26.0 1.0 HG1 A:THR165 4.9 24.1 1.0 C A:CYS125 4.9 30.8 1.0 N B:CYS164 4.9 25.9 1.0 CB A:ALA126 4.9 21.2 1.0 SG B:CYS125 5.0 24.0 1.0 CB B:VAL166 5.0 25.7 1.0

S.H.Knauer, W.Buckel, H.Dobbek. On the Atp-Dependent Activation of the Radical Enzyme (R)-2-Hydroxyisocaproyl-Coa Dehydratase. Biochemistry V. 51 6609 2012.
ISSN: ISSN 0006-2960
PubMed: 22827463
DOI: 10.1021/BI300571Z