Iron in PDB 3o3m: (R)-2-Hydroxyisocaproyl-Coa Dehydratase

The structure of (R)-2-Hydroxyisocaproyl-Coa Dehydratase, PDB code: 3o3m 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)	19.70 / 1.82
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.764, 129.192, 179.166, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 22

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iron atom in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase (pdb code 3o3m). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 16 binding sites of Iron where determined in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase, PDB code: 3o3m:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 16 in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe409 b:21.3 occ:1.00 FE1 A:SF4409 0.0 21.3 1.0 S2 A:SF4409 2.2 32.9 1.0 S3 A:SF4409 2.3 23.2 1.0 S4 A:SF4409 2.3 26.5 1.0 SG A:CYS346 2.5 27.1 1.0 FE4 A:SF4409 2.9 19.4 1.0 FE2 A:SF4409 2.9 22.4 1.0 FE3 A:SF4409 2.9 27.0 0.7 HB2 A:CYS346 3.0 26.7 1.0 HA A:CYS346 3.1 28.8 1.0 CB A:CYS346 3.2 22.4 1.0 CA A:CYS346 3.7 24.1 1.0 S1 A:SF4409 3.8 31.1 1.0 O A:HOH2237 4.0 25.8 1.0 HB3 A:CYS346 4.1 26.7 1.0 HB3 A:CYS117 4.2 23.1 1.0 O B:HOH446 4.3 21.2 1.0 N A:CYS346 4.6 19.1 1.0 O A:HOH2471 4.7 39.1 0.7 C A:CYS346 4.8 24.0 1.0 SG A:CYS117 4.8 19.0 1.0 CB A:CYS117 4.8 19.4 1.0 HB2 A:CYS117 4.9 23.1 1.0 SG A:CYS84 4.9 19.0 1.0 H A:CYS346 5.0 22.8 1.0

Iron binding site 2 out of 16 in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe409 b:22.4 occ:1.00 FE2 A:SF4409 0.0 22.4 1.0 S1 A:SF4409 2.2 31.1 1.0 S3 A:SF4409 2.3 23.2 1.0 S4 A:SF4409 2.3 26.5 1.0 SG A:CYS84 2.3 19.0 1.0 FE1 A:SF4409 2.9 21.3 1.0 FE4 A:SF4409 2.9 19.4 1.0 FE3 A:SF4409 2.9 27.0 0.7 HB2 A:CYS84 3.2 27.7 1.0 CB A:CYS84 3.4 23.2 1.0 HE21 A:GLN375 3.7 39.2 1.0 HB3 A:CYS84 3.8 27.7 1.0 HD2 A:TYR86 3.8 31.0 1.0 S2 A:SF4409 3.8 32.9 1.0 HB2 A:TYR86 3.9 19.8 1.0 HB3 A:SER345 4.0 19.8 1.0 NE2 A:GLN375 4.2 32.8 1.0 HA A:CYS346 4.3 28.8 1.0 HE22 A:GLN375 4.4 39.2 1.0 CD2 A:TYR86 4.5 25.9 1.0 H A:TYR86 4.6 13.7 1.0 HB2 A:CYS346 4.7 26.7 1.0 CA A:CYS84 4.7 19.9 1.0 HA A:CYS84 4.7 23.7 1.0 O A:HOH2471 4.7 39.1 0.7 CB A:TYR86 4.8 16.6 1.0 HZ3 A:TRP123 4.8 19.5 1.0 HB2 A:GLN119 4.8 21.4 1.0 O A:SER345 4.9 25.7 1.0 CB A:SER345 4.9 16.6 1.0 SG A:CYS117 4.9 19.0 1.0 CG A:TYR86 5.0 21.5 1.0

Iron binding site 3 out of 16 in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe409 b:27.0 occ:0.70 FE3 A:SF4409 0.0 27.0 0.7 O A:HOH2471 2.0 39.1 0.7 S2 A:SF4409 2.2 32.9 1.0 S1 A:SF4409 2.2 31.1 1.0 S4 A:SF4409 2.3 26.5 1.0 FE1 A:SF4409 2.9 21.3 1.0 FE2 A:SF4409 2.9 22.4 1.0 FE4 A:SF4409 2.9 19.4 1.0 HD2 A:TYR86 3.6 31.0 1.0 HD12 A:ILE116 3.7 21.1 1.0 S3 A:SF4409 3.9 23.2 1.0 HE2 A:TYR86 4.0 27.2 1.0 O A:HOH2263 4.1 32.4 0.5 OE1 A:GLU55 4.1 16.6 1.0 CD2 A:TYR86 4.3 25.9 1.0 HG2 A:GLU55 4.4 22.8 1.0 CE2 A:TYR86 4.5 22.8 1.0 HB A:ILE116 4.6 19.4 1.0 CD1 A:ILE116 4.7 17.7 1.0 CD A:GLU55 4.7 19.0 1.0 HD13 A:ILE265 4.9 41.3 0.5 O A:HOH2237 4.9 25.8 1.0 SG A:CYS117 5.0 19.0 1.0 SG A:CYS84 5.0 19.0 1.0

Iron binding site 4 out of 16 in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe409 b:19.4 occ:1.00 FE4 A:SF4409 0.0 19.4 1.0 S1 A:SF4409 2.2 31.1 1.0 S2 A:SF4409 2.2 32.9 1.0 SG A:CYS117 2.3 19.0 1.0 S3 A:SF4409 2.3 23.2 1.0 FE1 A:SF4409 2.9 21.3 1.0 FE2 A:SF4409 2.9 22.4 1.0 FE3 A:SF4409 2.9 27.0 0.7 HB3 A:CYS117 2.9 23.1 1.0 CB A:CYS117 3.2 19.4 1.0 HB2 A:CYS117 3.5 23.1 1.0 HG13 A:VAL120 3.6 15.8 1.0 HB2 A:GLN119 3.7 21.4 1.0 HD12 A:ILE116 3.9 21.1 1.0 S4 A:SF4409 3.9 26.5 1.0 HG13 A:ILE116 4.0 23.9 1.0 CG1 A:VAL120 4.5 13.2 1.0 CA A:CYS117 4.5 21.9 1.0 HB A:ILE116 4.5 19.4 1.0 CD1 A:ILE116 4.6 17.7 1.0 O B:HOH446 4.6 21.2 1.0 HD11 A:ILE116 4.7 21.1 1.0 HG11 A:VAL120 4.7 15.8 1.0 CG1 A:ILE116 4.7 20.0 1.0 H A:VAL120 4.7 14.5 1.0 HG12 A:VAL120 4.7 15.8 1.0 CB A:GLN119 4.7 17.9 1.0 O A:HOH2471 4.7 39.1 0.7 H A:GLN119 4.7 21.7 1.0 N A:CYS117 4.8 21.3 1.0 O A:ILE116 4.9 23.4 1.0 C A:ILE116 4.9 27.9 1.0 HB2 A:CYS84 5.0 27.7 1.0

Iron binding site 5 out of 16 in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe386 b:18.7 occ:1.00 FE1 B:SF4386 0.0 18.7 1.0 S4 B:SF4386 2.2 21.5 1.0 S3 B:SF4386 2.2 17.9 1.0 S B:H2S387 2.3 26.4 1.0 S2 B:SF4386 2.3 19.6 1.0 FE3 B:SF4386 2.7 17.7 1.0 FE2 B:SF4386 2.8 16.9 1.0 FE4 B:SF4386 2.8 16.7 1.0 HD12 B:ILE237 3.7 20.9 1.0 S1 B:SF4386 3.9 17.2 1.0 HG21 B:ILE74 4.0 27.0 1.0 HD11 B:LEU102 4.1 13.6 1.0 HE3 B:MET75 4.2 34.5 1.0 HG21 B:ILE237 4.2 24.2 1.0 HD11 B:ILE237 4.2 20.9 1.0 HG13 B:ILE237 4.3 24.9 1.0 CD1 B:ILE237 4.4 17.5 1.0 HD11 B:LEU293 4.4 12.2 0.5 HG2 B:MET75 4.4 19.2 1.0 HG B:LEU102 4.5 18.0 1.0 HG23 B:ILE74 4.5 27.0 1.0 CG2 B:ILE74 4.5 22.6 1.0 HG22 B:ILE74 4.5 27.0 1.0 HD12 B:LEU102 4.6 13.6 1.0 HB2 B:PRO35 4.6 27.6 1.0 HG23 B:ILE237 4.6 24.2 1.0 SG B:CYS99 4.7 15.3 1.0 HG23 B:VAL36 4.7 34.7 1.0 SG B:CYS325 4.8 15.7 1.0 CD1 B:LEU102 4.8 11.4 1.0 HD21 B:LEU293 4.8 12.6 0.5 SG B:CYS72 4.8 18.2 1.0 CG1 B:ILE237 4.8 20.9 1.0 CG2 B:ILE237 4.9 20.3 1.0 HD11 B:LEU293 4.9 24.4 0.5 HD21 B:LEU293 4.9 24.9 0.5

Iron binding site 6 out of 16 in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe386 b:16.9 occ:1.00 FE2 B:SF4386 0.0 16.9 1.0 S4 B:SF4386 2.3 21.5 1.0 S3 B:SF4386 2.3 17.9 1.0 S1 B:SF4386 2.3 17.2 1.0 SG B:CYS325 2.3 15.7 1.0 FE4 B:SF4386 2.7 16.7 1.0 FE1 B:SF4386 2.8 18.7 1.0 FE3 B:SF4386 2.8 17.7 1.0 HD2 B:PRO327 2.9 18.8 1.0 HB2 B:CYS325 3.1 20.3 1.0 CB B:CYS325 3.2 17.0 1.0 HA B:CYS325 3.2 24.9 1.0 HG2 B:PRO327 3.6 21.1 1.0 CA B:CYS325 3.7 20.8 1.0 CD B:PRO327 3.8 15.8 1.0 HD11 B:ILE237 3.8 20.9 1.0 S2 B:SF4386 3.9 19.6 1.0 HG13 B:ILE237 4.0 24.9 1.0 HB3 B:CYS325 4.1 20.3 1.0 HD3 B:PRO327 4.1 18.8 1.0 CG B:PRO327 4.2 17.7 1.0 HD12 B:ILE237 4.3 20.9 1.0 HB2 B:PRO327 4.3 20.1 1.0 C B:CYS325 4.3 27.9 1.0 H B:ASP326 4.4 16.9 1.0 CD1 B:ILE237 4.4 17.5 1.0 H B:GLU328 4.5 18.8 1.0 HB3 B:CYS72 4.5 13.9 1.0 N B:ASP326 4.6 14.2 1.0 HG2 B:MET322 4.6 23.6 1.0 CG1 B:ILE237 4.7 20.9 1.0 HD21 B:LEU293 4.8 24.9 0.5 CB B:PRO327 4.8 16.9 1.0 HB2 B:CYS72 4.8 13.9 1.0 HD21 B:LEU293 4.8 12.6 0.5 N B:PRO327 4.9 16.0 1.0 HB3 B:MET322 4.9 29.1 1.0 SG B:CYS72 4.9 18.2 1.0 HD11 B:LEU293 4.9 24.4 0.5 S B:H2S387 4.9 26.4 1.0 HG2 B:GLU328 4.9 21.5 1.0 SG B:CYS99 5.0 15.3 1.0 N B:CYS325 5.0 19.5 1.0 CB B:CYS72 5.0 11.7 1.0 HG3 B:PRO327 5.0 21.1 1.0

Iron binding site 7 out of 16 in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe386 b:17.7 occ:1.00 FE3 B:SF4386 0.0 17.7 1.0 S4 B:SF4386 2.3 21.5 1.0 S2 B:SF4386 2.3 19.6 1.0 S1 B:SF4386 2.3 17.2 1.0 SG B:CYS72 2.3 18.2 1.0 FE1 B:SF4386 2.7 18.7 1.0 FE2 B:SF4386 2.8 16.9 1.0 FE4 B:SF4386 2.8 16.7 1.0 HB3 B:CYS72 3.1 13.9 1.0 CB B:CYS72 3.2 11.7 1.0 HB2 B:CYS72 3.3 13.9 1.0 HG2 B:MET75 3.4 19.2 1.0 HG22 B:ILE74 3.7 27.0 1.0 S3 B:SF4386 3.8 17.9 1.0 HB B:THR101 3.9 27.0 1.0 HG3 B:MET75 3.9 19.2 1.0 HG21 B:THR101 4.0 18.6 1.0 HG23 B:ILE74 4.0 27.0 1.0 HA B:CYS325 4.0 24.9 1.0 CG B:MET75 4.1 16.1 1.0 HG21 B:ILE74 4.2 27.0 1.0 CG2 B:ILE74 4.2 22.6 1.0 HB2 B:CYS325 4.2 20.3 1.0 HG2 B:MET322 4.4 23.6 1.0 HB2 B:MET75 4.5 30.2 1.0 HG1 B:THR101 4.5 21.5 1.0 O B:HOH399 4.5 21.8 1.0 H B:MET75 4.6 22.4 1.0 CB B:THR101 4.6 22.6 1.0 H B:CYS72 4.6 21.3 1.0 CG2 B:THR101 4.6 15.6 1.0 S B:H2S387 4.7 26.4 1.0 CA B:CYS72 4.7 23.0 1.0 HG22 B:THR101 4.7 18.6 1.0 SG B:CYS99 4.7 15.3 1.0 SG B:CYS325 4.8 15.7 1.0 CB B:CYS325 4.8 17.0 1.0 HE3 B:MET75 4.8 34.5 1.0 CA B:CYS325 4.8 20.8 1.0 CB B:MET75 4.9 25.3 1.0 HG B:LEU102 4.9 18.0 1.0 OG1 B:THR101 5.0 18.0 1.0

Iron binding site 8 out of 16 in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe386 b:16.7 occ:1.00 FE4 B:SF4386 0.0 16.7 1.0 S3 B:SF4386 2.3 17.9 1.0 SG B:CYS99 2.3 15.3 1.0 S1 B:SF4386 2.3 17.2 1.0 S2 B:SF4386 2.3 19.6 1.0 FE2 B:SF4386 2.7 16.9 1.0 FE1 B:SF4386 2.8 18.7 1.0 FE3 B:SF4386 2.8 17.7 1.0 CB B:CYS99 3.5 11.8 1.0 HB3 B:CYS99 3.5 14.0 1.0 HB B:THR101 3.5 27.0 1.0 HG2 B:PRO327 3.6 21.1 1.0 HB2 B:CYS99 3.6 14.0 1.0 S4 B:SF4386 3.9 21.5 1.0 HG B:LEU102 3.9 18.0 1.0 HD12 B:LEU102 4.0 13.6 1.0 O B:HOH390 4.0 15.5 1.0 HD2 B:PRO327 4.0 18.8 1.0 HD11 B:LEU293 4.2 24.4 0.5 HD21 B:LEU293 4.2 24.9 0.5 H B:LEU102 4.2 23.8 1.0 CG B:PRO327 4.4 17.7 1.0 HD3 B:PRO327 4.4 18.8 1.0 HD11 B:LEU102 4.5 13.6 1.0 CD B:PRO327 4.5 15.8 1.0 CB B:THR101 4.5 22.6 1.0 H B:THR101 4.5 17.2 1.0 CD1 B:LEU102 4.5 11.4 1.0 CG B:LEU102 4.7 15.1 1.0 S B:H2S387 4.8 26.4 1.0 HG3 B:PRO327 4.8 21.1 1.0 HG1 B:THR101 4.8 21.5 1.0 CA B:CYS99 4.8 17.1 1.0 SG B:CYS72 4.9 18.2 1.0 N B:LEU102 4.9 19.9 1.0 SG B:CYS325 4.9 15.7 1.0 HD11 B:LEU293 5.0 12.2 0.5 OG1 B:THR101 5.0 18.0 1.0 HA B:CYS325 5.0 24.9 1.0 HB2 B:LEU102 5.0 16.8 1.0 HG3 B:MET75 5.0 19.2 1.0

Iron binding site 9 out of 16 in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of (R)-2-Hydroxyisocaproyl-Coa Dehydratase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe409 b:23.3 occ:1.00 FE1 C:SF4409 0.0 23.3 1.0 S2 C:SF4409 2.2 29.7 1.0 S3 C:SF4409 2.3 30.0 1.0 S4 C:SF4409 2.3 28.6 1.0 SG C:CYS346 2.5 23.4 1.0 FE4 C:SF4409 2.9 18.7 1.0 HB2 C:CYS346 2.9 22.1 1.0 FE3 C:SF4409 2.9 25.9 0.7 FE2 C:SF4409 2.9 20.8 1.0 HA C:CYS346 3.1 19.6 1.0 CB C:CYS346 3.1 18.5 1.0 CA C:CYS346 3.7 16.4 1.0 S1 C:SF4409 3.9 30.3 1.0 HB3 C:CYS346 4.0 22.1 1.0 HB3 C:CYS117 4.1 20.0 1.0 O C:HOH638 4.2 14.9 0.5 O D:HOH405 4.3 17.8 1.0 N C:CYS346 4.6 16.2 1.0 O C:HOH2472 4.7 33.8 0.7 C C:CYS346 4.7 22.2 1.0 CB C:CYS117 4.8 16.7 1.0 SG C:CYS117 4.8 17.7 1.0 HB2 C:CYS117 4.9 20.0 1.0 O C:HOH2279 4.9 40.4 1.0 H C:CYS346 4.9 19.3 1.0 HB3 C:LEU348 5.0 22.7 0.5 SG C:CYS84 5.0 19.7 1.0

Iron binding site 10 out of 16 in the (R)-2-Hydroxyisocaproyl-Coa Dehydratase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of (R)-2-Hydroxyisocaproyl-Coa Dehydratase within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe409 b:20.8 occ:1.00 FE2 C:SF4409 0.0 20.8 1.0 S1 C:SF4409 2.2 30.3 1.0 S3 C:SF4409 2.3 30.0 1.0 S4 C:SF4409 2.3 28.6 1.0 SG C:CYS84 2.3 19.7 1.0 FE3 C:SF4409 2.9 25.9 0.7 FE4 C:SF4409 2.9 18.7 1.0 FE1 C:SF4409 2.9 23.3 1.0 HB2 C:CYS84 3.2 24.0 1.0 CB C:CYS84 3.4 20.1 1.0 HE21 C:GLN375 3.7 33.5 1.0 HD2 C:TYR86 3.8 25.0 1.0 HB3 C:CYS84 3.8 24.0 1.0 HB2 C:TYR86 3.8 16.5 1.0 S2 C:SF4409 3.8 29.7 1.0 HB3 C:SER345 4.2 20.2 0.5 NE2 C:GLN375 4.2 28.0 1.0 HA C:CYS346 4.3 19.6 1.0 HE22 C:GLN375 4.4 33.5 1.0 CD2 C:TYR86 4.4 20.9 1.0 HB2 C:CYS346 4.5 22.1 1.0 HB2 C:SER345 4.6 24.0 0.5 HG C:SER345 4.6 37.7 0.5 H C:TYR86 4.6 12.5 1.0 O C:HOH2472 4.6 33.8 0.7 HA C:CYS84 4.7 22.2 1.0 CA C:CYS84 4.7 18.6 1.0 OG C:SER345 4.7 31.6 0.5 CB C:TYR86 4.7 13.9 1.0 HB2 C:GLN119 4.9 23.6 1.0 O C:SER345 4.9 21.8 1.0 CG C:TYR86 4.9 15.1 1.0 SG C:CYS117 4.9 17.7 1.0 HZ3 C:TRP123 5.0 18.7 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