Iron in PDB 3o3o: (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with (R)-2- Hydroxyisocaproate

The structure of (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with (R)-2- Hydroxyisocaproate, PDB code: 3o3o was solved by S.H.Knauer, W.Buckel, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.07 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.309, 85.584, 149.508, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 25.7

The binding sites of Iron atom in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with (R)-2- Hydroxyisocaproate (pdb code 3o3o). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with (R)-2- Hydroxyisocaproate, PDB code: 3o3o:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with (R)-2- Hydroxyisocaproate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with (R)-2- Hydroxyisocaproate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe409 b:20.7 occ:1.00 FE1 A:SF4409 0.0 20.7 1.0 S2 A:SF4409 2.3 24.6 1.0 S3 A:SF4409 2.3 17.9 1.0 S4 A:SF4409 2.3 25.7 1.0 SG A:CYS346 2.6 24.0 1.0 FE4 A:SF4409 2.7 16.2 1.0 FE3 A:SF4409 2.7 30.8 1.0 FE2 A:SF4409 2.8 18.7 1.0 CB A:CYS346 3.3 20.3 1.0 CA A:CYS346 3.8 20.9 1.0 S1 A:SF4409 3.9 18.3 1.0 O A:HOH691 4.5 20.3 1.0 O B:HOH642 4.6 21.6 1.0 N A:CYS346 4.7 21.2 1.0 SG A:CYS117 4.8 18.3 1.0 O1 A:2RH410 4.8 40.4 0.7 CB A:CYS117 4.9 22.6 1.0 O A:SER345 4.9 19.9 1.0 C A:CYS346 4.9 20.5 1.0

Iron binding site 2 out of 8 in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with (R)-2- Hydroxyisocaproate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with (R)-2- Hydroxyisocaproate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe409 b:18.7 occ:1.00 FE2 A:SF4409 0.0 18.7 1.0 S3 A:SF4409 2.3 17.9 1.0 S1 A:SF4409 2.3 18.3 1.0 S4 A:SF4409 2.3 25.7 1.0 SG A:CYS84 2.5 15.9 1.0 FE3 A:SF4409 2.7 30.8 1.0 FE4 A:SF4409 2.7 16.2 1.0 FE1 A:SF4409 2.8 20.7 1.0 CB A:CYS84 3.5 21.8 1.0 S2 A:SF4409 3.9 24.6 1.0 OE1 A:GLN375 4.6 18.7 1.0 CD2 A:TYR86 4.6 28.4 1.0 O A:SER345 4.8 19.9 1.0 CA A:CYS84 4.9 17.9 1.0 SG A:CYS117 4.9 18.3 1.0 CB A:TYR86 4.9 22.3 1.0 O1 A:2RH410 5.0 40.4 0.7

Iron binding site 3 out of 8 in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with (R)-2- Hydroxyisocaproate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with (R)-2- Hydroxyisocaproate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe409 b:30.8 occ:1.00 FE3 A:SF4409 0.0 30.8 1.0 S4 A:SF4409 2.3 25.7 1.0 S1 A:SF4409 2.3 18.3 1.0 S2 A:SF4409 2.3 24.6 1.0 O1 A:2RH410 2.5 40.4 0.7 FE2 A:SF4409 2.7 18.7 1.0 FE1 A:SF4409 2.7 20.7 1.0 FE4 A:SF4409 2.7 16.2 1.0 C3 A:2RH410 3.6 43.5 0.7 S3 A:SF4409 3.9 17.9 1.0 O2 A:2RH410 4.3 43.6 0.7 C2 A:2RH410 4.4 39.0 0.7 OE1 A:GLU55 4.4 14.8 1.0 CD2 A:TYR86 4.5 28.4 1.0 C1 A:2RH410 4.6 43.9 0.7 CE2 A:TYR86 4.8 30.6 1.0 CD1 A:ILE116 4.8 10.7 1.0 SG A:CYS117 4.8 18.3 1.0 SG A:CYS84 4.9 15.9 1.0

Iron binding site 4 out of 8 in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with (R)-2- Hydroxyisocaproate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with (R)-2- Hydroxyisocaproate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe409 b:16.2 occ:1.00 FE4 A:SF4409 0.0 16.2 1.0 S1 A:SF4409 2.3 18.3 1.0 S3 A:SF4409 2.3 17.9 1.0 S2 A:SF4409 2.3 24.6 1.0 SG A:CYS117 2.4 18.3 1.0 FE1 A:SF4409 2.7 20.7 1.0 FE3 A:SF4409 2.7 30.8 1.0 FE2 A:SF4409 2.7 18.7 1.0 CB A:CYS117 3.3 22.6 1.0 S4 A:SF4409 3.9 25.7 1.0 CA A:CYS117 4.6 17.6 1.0 CG1 A:VAL120 4.7 19.2 1.0 CD1 A:ILE116 4.7 10.7 1.0 O A:ILE116 4.7 20.5 1.0 CG1 A:ILE116 4.9 11.2 1.0 N A:CYS117 4.9 14.6 1.0 CB A:GLN119 4.9 12.2 1.0 O B:HOH642 4.9 21.6 1.0 C A:ILE116 4.9 16.3 1.0

Iron binding site 5 out of 8 in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with (R)-2- Hydroxyisocaproate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with (R)-2- Hydroxyisocaproate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe386 b:14.3 occ:1.00 FE1 B:SF4386 0.0 14.3 1.0 S4 B:SF4386 2.2 13.8 1.0 S2 B:SF4386 2.3 12.6 1.0 S3 B:SF4386 2.3 16.2 1.0 S B:H2S387 2.3 26.0 1.0 FE3 B:SF4386 2.5 12.6 1.0 FE4 B:SF4386 2.6 13.1 1.0 FE2 B:SF4386 2.8 13.9 1.0 S1 B:SF4386 3.9 12.9 1.0 CG2 B:ILE74 4.6 15.5 1.0 SG B:CYS99 4.7 15.4 1.0 CD1 B:ILE237 4.7 18.0 1.0 SG B:CYS72 4.8 11.9 1.0 CD1 B:LEU102 4.9 18.5 1.0 SG B:CYS325 4.9 15.3 1.0

Iron binding site 6 out of 8 in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with (R)-2- Hydroxyisocaproate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with (R)-2- Hydroxyisocaproate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe386 b:13.9 occ:1.00 FE2 B:SF4386 0.0 13.9 1.0 S3 B:SF4386 2.2 16.2 1.0 S4 B:SF4386 2.2 13.8 1.0 S1 B:SF4386 2.3 12.9 1.0 SG B:CYS325 2.5 15.3 1.0 FE4 B:SF4386 2.6 13.1 1.0 FE3 B:SF4386 2.6 12.6 1.0 FE1 B:SF4386 2.8 14.3 1.0 CB B:CYS325 3.3 10.7 1.0 CA B:CYS325 3.7 12.2 1.0 CD B:PRO327 3.9 12.2 1.0 S2 B:SF4386 3.9 12.6 1.0 CG B:PRO327 4.4 13.4 1.0 C B:CYS325 4.4 17.0 1.0 N B:ASP326 4.5 10.5 1.0 SG B:CYS72 4.7 11.9 1.0 CD1 B:ILE237 4.8 18.0 1.0 S B:H2S387 4.9 26.0 1.0 CB B:CYS72 4.9 11.8 1.0 CG1 B:ILE237 5.0 16.1 1.0 N B:CYS325 5.0 14.3 1.0 N B:PRO327 5.0 8.9 1.0

Iron binding site 7 out of 8 in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with (R)-2- Hydroxyisocaproate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with (R)-2- Hydroxyisocaproate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe386 b:12.6 occ:1.00 FE3 B:SF4386 0.0 12.6 1.0 S4 B:SF4386 2.2 13.8 1.0 S2 B:SF4386 2.3 12.6 1.0 S1 B:SF4386 2.3 12.9 1.0 SG B:CYS72 2.4 11.9 1.0 FE1 B:SF4386 2.5 14.3 1.0 FE4 B:SF4386 2.6 13.1 1.0 FE2 B:SF4386 2.6 13.9 1.0 CB B:CYS72 3.5 11.8 1.0 S3 B:SF4386 3.7 16.2 1.0 CG2 B:ILE74 4.2 15.5 1.0 CG B:MET75 4.4 16.5 1.0 S B:H2S387 4.5 26.0 1.0 O B:HOH448 4.7 15.8 1.0 SG B:CYS99 4.7 15.4 1.0 CB B:THR101 4.8 11.9 1.0 SG B:CYS325 4.8 15.3 1.0 CG2 B:THR101 4.9 14.1 1.0 CB B:CYS325 4.9 10.7 1.0 CA B:CYS72 4.9 8.9 1.0 CA B:CYS325 5.0 12.2 1.0

Iron binding site 8 out of 8 in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with (R)-2- Hydroxyisocaproate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of (R)-2-Hydroxyisocaproyl-Coa Dehydratase in Complex with (R)-2- Hydroxyisocaproate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe386 b:13.1 occ:1.00 FE4 B:SF4386 0.0 13.1 1.0 S3 B:SF4386 2.2 16.2 1.0 S1 B:SF4386 2.3 12.9 1.0 S2 B:SF4386 2.3 12.6 1.0 SG B:CYS99 2.5 15.4 1.0 FE3 B:SF4386 2.6 12.6 1.0 FE2 B:SF4386 2.6 13.9 1.0 FE1 B:SF4386 2.6 14.3 1.0 S4 B:SF4386 3.7 13.8 1.0 CB B:CYS99 3.7 17.9 1.0 O B:HOH398 4.3 16.2 1.0 CD B:PRO327 4.6 12.2 1.0 CG B:PRO327 4.6 13.4 1.0 CD1 B:LEU102 4.7 18.5 1.0 CB B:THR101 4.7 11.9 1.0 S B:H2S387 4.7 26.0 1.0 SG B:CYS72 4.8 11.9 1.0 SG B:CYS325 4.9 15.3 1.0 CG B:LEU102 5.0 18.5 1.0

S.H.Knauer, W.Buckel, H.Dobbek. Structural Basis For Reductive Radical Formation and Electron Recycling in (R)-2-Hydroxyisocaproyl-Coa Dehydratase. J.Am.Chem.Soc. V. 133 4342 2011.
ISSN: ISSN 0002-7863
PubMed: 21366233
DOI: 10.1021/JA1076537