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

The structure of Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adpnp, PDB code: 4ehu 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)	25.17 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	66.105, 158.259, 62.988, 90.00, 111.97, 90.00
R / Rfree (%)	17.1 / 19.7

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

Magnesium	(Mg)	2 atoms
Sodium	(Na)	3 atoms

The binding sites of Iron atom in the Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adpnp (pdb code 4ehu). 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 Adpnp, PDB code: 4ehu:
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 Adpnp


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 Adpnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:15.9 occ:1.00 FE1 A:SF4301 0.0 15.9 1.0 S2 A:SF4301 2.2 16.2 1.0 S3 A:SF4301 2.2 16.0 1.0 S4 A:SF4301 2.3 15.4 1.0 SG A:CYS164 2.3 20.4 1.0 FE3 A:SF4301 2.6 17.3 1.0 FE2 A:SF4301 2.6 17.1 1.0 FE4 A:SF4301 2.7 17.9 1.0 HA A:CYS164 3.1 21.5 1.0 H A:THR165 3.2 19.9 1.0 CB A:CYS164 3.2 17.7 1.0 HB2 A:CYS164 3.2 21.2 1.0 H B:ALA126 3.3 21.3 1.0 CA A:CYS164 3.5 18.0 1.0 H A:VAL166 3.6 21.4 1.0 HA B:CYS125 3.7 23.0 1.0 S1 A:SF4301 3.7 18.1 1.0 N A:THR165 3.7 16.7 1.0 HG23 A:VAL166 3.9 27.2 1.0 C A:CYS164 4.0 17.2 1.0 HB3 A:CYS164 4.1 21.2 1.0 N B:ALA126 4.1 17.8 1.0 HB3 B:ALA126 4.2 26.1 1.0 HB A:THR165 4.3 25.9 1.0 HG1 A:THR165 4.4 22.5 1.0 SG B:CYS125 4.5 18.4 1.0 N A:VAL166 4.5 17.9 1.0 CA B:CYS125 4.5 19.2 1.0 HB A:VAL166 4.5 24.6 1.0 H B:ALA127 4.6 17.2 1.0 HG23 B:VAL166 4.7 28.7 1.0 CG2 A:VAL166 4.7 22.7 1.0 H B:THR165 4.7 22.0 1.0 CA A:THR165 4.7 19.7 1.0 HB2 B:ALA126 4.8 26.1 1.0 HB B:THR165 4.8 24.2 1.0 HG21 A:VAL166 4.8 27.2 1.0 SG B:CYS164 4.8 19.7 1.0 HB2 A:ALA127 4.8 21.0 1.0 C B:CYS125 4.8 19.7 1.0 CB A:THR165 4.8 21.7 1.0 HG1 B:THR165 4.8 22.9 1.0 CB B:ALA126 4.9 21.8 1.0 SG A:CYS125 4.9 19.4 1.0 N A:CYS164 4.9 18.6 1.0 CB B:CYS125 4.9 20.4 1.0 HB2 B:CYS125 4.9 24.4 1.0 OG1 A:THR165 5.0 18.8 1.0

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


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 Adpnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:17.1 occ:1.00 FE2 A:SF4301 0.0 17.1 1.0 S1 A:SF4301 2.2 18.1 1.0 S4 A:SF4301 2.2 15.4 1.0 S3 A:SF4301 2.3 16.0 1.0 SG B:CYS164 2.3 19.7 1.0 FE4 A:SF4301 2.6 17.9 1.0 FE1 A:SF4301 2.6 15.9 1.0 FE3 A:SF4301 2.7 17.3 1.0 HA B:CYS164 3.1 25.5 1.0 H B:THR165 3.2 22.0 1.0 HB2 B:CYS164 3.2 21.1 1.0 CB B:CYS164 3.2 17.7 1.0 H A:ALA126 3.3 22.8 1.0 CA B:CYS164 3.6 21.3 1.0 H B:VAL166 3.6 24.7 1.0 N B:THR165 3.7 18.4 1.0 S2 A:SF4301 3.7 16.2 1.0 HA A:CYS125 3.7 26.4 1.0 HG23 B:VAL166 3.8 28.7 1.0 C B:CYS164 4.0 24.1 1.0 HB3 B:CYS164 4.1 21.1 1.0 N A:ALA126 4.1 19.1 1.0 HB3 A:ALA126 4.2 28.7 1.0 HB B:THR165 4.3 24.2 1.0 HG1 B:THR165 4.4 22.9 1.0 N B:VAL166 4.5 20.7 1.0 SG A:CYS125 4.5 19.4 1.0 HB B:VAL166 4.5 26.6 1.0 CA A:CYS125 4.6 22.1 1.0 HG23 A:VAL166 4.6 27.2 1.0 CG2 B:VAL166 4.6 24.0 1.0 H A:ALA127 4.7 19.1 1.0 H A:THR165 4.7 19.9 1.0 CA B:THR165 4.7 21.9 1.0 HB A:THR165 4.7 25.9 1.0 HB2 A:ALA126 4.8 28.7 1.0 HG21 B:VAL166 4.8 28.7 1.0 SG A:CYS164 4.8 20.4 1.0 HG1 A:THR165 4.8 22.5 1.0 CB A:ALA126 4.8 24.0 1.0 CB B:THR165 4.8 20.3 1.0 SG B:CYS125 4.8 18.4 1.0 C A:CYS125 4.9 21.9 1.0 HB2 B:ALA127 4.9 23.9 1.0 N B:CYS164 4.9 20.3 1.0 CB A:CYS125 4.9 24.2 1.0 HB2 A:CYS125 5.0 28.9 1.0 OG1 B:THR165 5.0 19.2 1.0

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


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 Adpnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:17.3 occ:1.00 FE3 A:SF4301 0.0 17.3 1.0 S4 A:SF4301 2.2 15.4 1.0 S1 A:SF4301 2.2 18.1 1.0 S2 A:SF4301 2.2 16.2 1.0 SG B:CYS125 2.3 18.4 1.0 FE1 A:SF4301 2.6 15.9 1.0 FE2 A:SF4301 2.7 17.1 1.0 FE4 A:SF4301 2.8 17.9 1.0 CB B:CYS125 3.3 20.4 1.0 HB2 B:CYS125 3.3 24.4 1.0 HA B:CYS125 3.3 23.0 1.0 H B:ALA127 3.5 17.2 1.0 H B:ALA126 3.6 21.3 1.0 O A:HOH729 3.7 34.5 0.5 CA B:CYS125 3.8 19.2 1.0 HA B:CYS164 3.8 25.5 1.0 S3 A:SF4301 3.9 16.0 1.0 N B:ALA126 4.0 17.8 1.0 HB3 B:ALA127 4.0 23.9 1.0 HB2 B:ALA127 4.1 23.9 1.0 H B:THR165 4.1 22.0 1.0 HB3 B:CYS125 4.2 24.4 1.0 C B:CYS125 4.2 19.7 1.0 O B:HOH559 4.2 48.5 1.0 N B:ALA127 4.3 14.4 1.0 SG A:CYS164 4.4 20.4 1.0 HG1 B:THR165 4.5 22.9 1.0 CB B:ALA127 4.5 20.0 1.0 HB2 A:CYS164 4.6 21.2 1.0 HB2 B:CYS164 4.7 21.1 1.0 CA B:CYS164 4.7 21.3 1.0 O A:HOH728 4.8 47.1 1.0 SG B:CYS164 4.8 19.7 1.0 O B:HOH441 4.9 28.7 1.0 HB3 B:ALA126 4.9 26.1 1.0 N B:THR165 4.9 18.4 1.0 SG A:CYS125 4.9 19.4 1.0 CB B:CYS164 5.0 17.7 1.0 O A:HOH729 5.0 35.0 0.5 HA A:CYS164 5.0 21.5 1.0

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


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 Adpnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:17.9 occ:1.00 FE4 A:SF4301 0.0 17.9 1.0 S2 A:SF4301 2.2 16.2 1.0 S1 A:SF4301 2.2 18.1 1.0 S3 A:SF4301 2.2 16.0 1.0 SG A:CYS125 2.3 19.4 1.0 FE2 A:SF4301 2.6 17.1 1.0 FE1 A:SF4301 2.7 15.9 1.0 FE3 A:SF4301 2.8 17.3 1.0 CB A:CYS125 3.4 24.2 1.0 HB2 A:CYS125 3.4 28.9 1.0 HA A:CYS125 3.4 26.4 1.0 H A:ALA127 3.5 19.1 1.0 H A:ALA126 3.6 22.8 1.0 CA A:CYS125 3.8 22.1 1.0 O A:HOH728 3.8 47.1 1.0 HA A:CYS164 3.8 21.5 1.0 S4 A:SF4301 3.9 15.4 1.0 HB2 A:ALA127 4.0 21.0 1.0 N A:ALA126 4.0 19.1 1.0 HB3 A:ALA127 4.1 21.0 1.0 H A:THR165 4.1 19.9 1.0 O A:HOH662 4.2 23.3 0.6 HB3 A:CYS125 4.2 28.9 1.0 C A:CYS125 4.2 21.9 1.0 N A:ALA127 4.3 16.0 1.0 SG B:CYS164 4.4 19.7 1.0 O A:HOH729 4.4 34.5 0.5 HG1 A:THR165 4.4 22.5 1.0 CB A:ALA127 4.5 17.6 1.0 HB2 B:CYS164 4.5 21.1 1.0 CA A:CYS164 4.8 18.0 1.0 HB2 A:CYS164 4.8 21.2 1.0 HB3 A:ALA126 4.9 28.7 1.0 SG A:CYS164 4.9 20.4 1.0 SG B:CYS125 4.9 18.4 1.0 N A:THR165 4.9 16.7 1.0 O A:HOH483 4.9 31.0 1.0 HA B:CYS125 5.0 23.0 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