Iron in PDB 6eno: Double Cubane Cluster Oxidoreductase

The structure of Double Cubane Cluster Oxidoreductase, PDB code: 6eno was solved by J.H.Jeoung, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.46 / 1.64
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	80.591, 80.591, 217.428, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 21.3

The binding sites of Iron atom in the Double Cubane Cluster Oxidoreductase (pdb code 6eno). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Double Cubane Cluster Oxidoreductase, PDB code: 6eno:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Double Cubane Cluster Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Double Cubane Cluster Oxidoreductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:19.1 occ:1.00 FE1 A:BJ8501 0.0 19.1 1.0 S3 A:BJ8501 2.2 19.4 1.0 S4 A:BJ8501 2.2 20.2 1.0 S9 A:BJ8501 2.3 22.8 1.0 S2 A:BJ8501 2.3 18.3 1.0 FE2 A:BJ8501 2.7 20.8 1.0 FE4 A:BJ8501 2.7 19.5 1.0 FE3 A:BJ8501 2.7 20.5 1.0 HD13 A:LEU115 3.5 25.8 1.0 HZ2 A:LYS146 3.7 32.4 1.0 FE8 A:BJ8501 3.7 20.2 1.0 S1 A:BJ8501 3.8 20.3 1.0 HD2 A:LYS146 3.9 28.9 1.0 HD2 A:PRO283 4.0 28.2 1.0 HE3 A:LYS146 4.1 29.9 1.0 HD22 A:LEU115 4.3 27.0 1.0 CD1 A:LEU115 4.4 21.5 1.0 HG2 A:PRO283 4.4 24.3 1.0 HG22 A:THR282 4.5 26.1 1.0 NZ A:LYS146 4.5 27.0 1.0 S7 A:BJ8501 4.6 20.2 1.0 CE A:LYS146 4.6 24.9 1.0 HD11 A:LEU115 4.6 25.8 1.0 S6 A:BJ8501 4.7 20.1 1.0 CD A:PRO283 4.7 23.5 1.0 CD A:LYS146 4.7 24.1 1.0 HZ1 A:LYS146 4.7 32.4 1.0 HG3 A:PRO283 4.8 24.3 1.0 SG A:CYS143 4.8 18.9 1.0 HB A:THR282 4.8 29.7 1.0 HB3 A:LEU115 4.8 25.9 1.0 CG A:PRO283 4.8 20.2 1.0 HD12 A:LEU115 4.9 25.8 1.0 SG A:CYS113 4.9 22.8 1.0 HD12 A:LEU370 4.9 26.8 1.0 HG21 A:THR282 4.9 26.1 1.0 HD3 A:PRO283 4.9 28.2 1.0 SG A:CYS373 5.0 20.7 1.0

Iron binding site 2 out of 8 in the Double Cubane Cluster Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Double Cubane Cluster Oxidoreductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:20.8 occ:1.00 FE2 A:BJ8501 0.0 20.8 1.0 S4 A:BJ8501 2.2 20.2 1.0 S3 A:BJ8501 2.2 19.4 1.0 S1 A:BJ8501 2.3 20.3 1.0 SG A:CYS113 2.4 22.8 1.0 FE3 A:BJ8501 2.7 20.5 1.0 FE4 A:BJ8501 2.7 19.5 1.0 FE1 A:BJ8501 2.7 19.1 1.0 HB2 A:CYS113 3.1 30.1 1.0 CB A:CYS113 3.2 25.1 1.0 HB3 A:CYS113 3.3 30.1 1.0 HB3 A:LEU115 3.5 25.9 1.0 HB2 A:CYS373 3.5 32.2 1.0 HD12 A:LEU370 3.7 26.8 1.0 HD13 A:LEU115 3.8 25.8 1.0 HG13 A:ILE116 3.8 24.6 1.0 HD11 A:ILE116 3.9 26.5 1.0 S2 A:BJ8501 3.9 18.3 1.0 HD22 A:LEU115 4.2 27.0 1.0 HB2 A:LEU115 4.3 25.9 1.0 CB A:LEU115 4.3 21.6 1.0 CB A:CYS373 4.3 26.9 1.0 HB2 A:LEU370 4.4 34.2 1.0 CD1 A:ILE116 4.5 22.1 1.0 CG1 A:ILE116 4.5 20.5 1.0 HA A:CYS373 4.5 24.6 1.0 HD12 A:ILE116 4.5 26.5 1.0 SG A:CYS373 4.6 20.7 1.0 CD1 A:LEU370 4.6 22.3 1.0 CD1 A:LEU115 4.6 21.5 1.0 CA A:CYS113 4.6 22.1 1.0 H A:LEU115 4.7 23.0 1.0 S9 A:BJ8501 4.7 22.8 1.0 H A:ILE116 4.7 24.8 1.0 HD13 A:LEU370 4.8 26.8 1.0 HG12 A:ILE116 4.8 24.6 1.0 HG21 A:THR282 4.8 26.1 1.0 SG A:CYS143 4.8 18.9 1.0 HA A:CYS113 4.9 26.5 1.0 CG A:LEU115 4.9 22.6 1.0 HD12 A:LEU115 4.9 25.8 1.0 HD2 A:LYS146 5.0 28.9 1.0 CA A:CYS373 5.0 20.5 1.0 CD2 A:LEU115 5.0 22.5 1.0

Iron binding site 3 out of 8 in the Double Cubane Cluster Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Double Cubane Cluster Oxidoreductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:20.5 occ:1.00 FE3 A:BJ8501 0.0 20.5 1.0 S1 A:BJ8501 2.2 20.3 1.0 S4 A:BJ8501 2.3 20.2 1.0 S2 A:BJ8501 2.3 18.3 1.0 SG A:CYS373 2.3 20.7 1.0 FE2 A:BJ8501 2.7 20.8 1.0 FE4 A:BJ8501 2.7 19.5 1.0 FE1 A:BJ8501 2.7 19.1 1.0 HB2 A:CYS373 2.8 32.2 1.0 CB A:CYS373 3.1 26.9 1.0 HG22 A:THR282 3.5 26.1 1.0 HG21 A:THR282 3.5 26.1 1.0 HD2 A:TYR376 3.6 25.0 1.0 HA A:CYS373 3.7 24.6 1.0 S3 A:BJ8501 3.8 19.4 1.0 HB3 A:CYS373 3.9 32.2 1.0 HD2 A:PRO375 3.9 23.6 1.0 CG2 A:THR282 4.0 21.7 1.0 CA A:CYS373 4.0 20.5 1.0 HB3 A:CYS143 4.3 23.5 1.0 CD2 A:TYR376 4.4 20.8 1.0 HE2 A:TYR376 4.5 24.4 1.0 SG A:CYS113 4.6 22.8 1.0 HG23 A:THR282 4.6 26.1 1.0 HB2 A:CYS113 4.7 30.1 1.0 HB A:THR282 4.7 29.7 1.0 H A:TYR376 4.8 23.3 1.0 C A:CYS373 4.8 22.8 1.0 HB2 A:TYR376 4.8 25.1 1.0 SG A:CYS143 4.8 18.9 1.0 HG2 A:PRO375 4.9 20.2 1.0 S9 A:BJ8501 4.9 22.8 1.0 CE2 A:TYR376 4.9 20.3 1.0 CD A:PRO375 4.9 19.7 1.0 HB2 A:PRO375 4.9 21.1 1.0 CB A:CYS143 4.9 19.6 1.0 HB2 A:LEU370 4.9 34.2 1.0 HB2 A:CYS143 5.0 23.5 1.0

Iron binding site 4 out of 8 in the Double Cubane Cluster Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Double Cubane Cluster Oxidoreductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:19.5 occ:1.00 FE4 A:BJ8501 0.0 19.5 1.0 S1 A:BJ8501 2.2 20.3 1.0 S3 A:BJ8501 2.3 19.4 1.0 SG A:CYS143 2.3 18.9 1.0 S2 A:BJ8501 2.4 18.3 1.0 FE2 A:BJ8501 2.7 20.8 1.0 FE1 A:BJ8501 2.7 19.1 1.0 FE3 A:BJ8501 2.7 20.5 1.0 HB3 A:CYS143 3.0 23.5 1.0 HD2 A:LYS146 3.2 28.9 1.0 CB A:CYS143 3.2 19.6 1.0 HD11 A:ILE116 3.3 26.5 1.0 HB2 A:CYS143 3.5 23.5 1.0 S4 A:BJ8501 3.8 20.2 1.0 HG3 A:LYS146 3.9 28.1 1.0 O A:HOH859 4.0 22.4 1.0 CD A:LYS146 4.1 24.1 1.0 CD1 A:ILE116 4.3 22.1 1.0 H A:CYS143 4.3 24.8 1.0 HB2 A:CYS113 4.4 30.1 1.0 CG A:LYS146 4.5 23.4 1.0 HE3 A:LYS146 4.5 29.9 1.0 CA A:CYS143 4.6 21.2 1.0 H A:LYS146 4.6 21.4 1.0 HG13 A:ILE116 4.6 24.6 1.0 HD12 A:ILE116 4.6 26.5 1.0 HB3 A:CYS113 4.6 30.1 1.0 HZ2 A:LYS146 4.6 32.4 1.0 S9 A:BJ8501 4.6 22.8 1.0 HD3 A:LYS146 4.7 28.9 1.0 HB2 A:LYS146 4.7 20.8 1.0 SG A:CYS373 4.8 20.7 1.0 HG12 A:ILE116 4.8 24.6 1.0 HA A:CYS373 4.8 24.6 1.0 HB2 A:CYS373 4.8 32.2 1.0 CE A:LYS146 4.8 24.9 1.0 SG A:CYS113 4.8 22.8 1.0 HD13 A:ILE116 4.8 26.5 1.0 CG1 A:ILE116 4.8 20.5 1.0 CB A:CYS113 4.8 25.1 1.0 N A:CYS143 4.9 20.7 1.0 HD2 A:PRO375 4.9 23.6 1.0

Iron binding site 5 out of 8 in the Double Cubane Cluster Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Double Cubane Cluster Oxidoreductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:19.9 occ:1.00 FE5 A:BJ8501 0.0 19.9 1.0 S7 A:BJ8501 2.2 20.2 1.0 S6 A:BJ8501 2.3 20.1 1.0 S8 A:BJ8501 2.3 19.2 1.0 SG A:CYS340 2.3 20.9 1.0 FE7 A:BJ8501 2.7 20.5 1.0 FE8 A:BJ8501 2.7 20.2 1.0 FE6 A:BJ8501 2.7 19.1 1.0 HB2 A:CYS340 3.1 31.2 1.0 CB A:CYS340 3.4 26.0 1.0 HE2 A:TYR376 3.8 24.4 1.0 HB3 A:CYS340 3.9 31.2 1.0 S5 A:BJ8501 3.9 20.4 1.0 HG A:CYS342 3.9 26.6 0.8 OH A:TYR376 4.0 20.7 1.0 HG21 A:THR142 4.1 22.0 1.0 HG A:CYS342 4.2 19.2 0.2 HA A:CYS340 4.5 24.4 1.0 HB A:THR142 4.6 19.4 1.0 CA A:CYS340 4.6 20.4 1.0 HH A:TYR376 4.6 24.9 1.0 CE2 A:TYR376 4.6 20.3 1.0 SG A:CYS342 4.7 22.2 0.8 HH21 A:ARG312 4.7 28.6 1.0 SG A:CYS308 4.7 21.5 1.0 HG22 A:THR142 4.7 22.0 1.0 S2 A:BJ8501 4.7 18.3 1.0 H A:CYS342 4.7 22.0 0.8 H A:CYS342 4.7 22.0 0.2 HB3 A:CYS342 4.8 21.8 0.2 S9 A:BJ8501 4.8 22.8 1.0 CG2 A:THR142 4.8 18.3 1.0 CZ A:TYR376 4.8 24.9 1.0 SG A:CYS75 4.9 18.3 1.0 HB2 A:CYS342 4.9 21.2 0.8 SG A:CYS342 4.9 16.0 0.2 H A:ALA341 4.9 24.5 1.0

Iron binding site 6 out of 8 in the Double Cubane Cluster Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Double Cubane Cluster Oxidoreductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:19.1 occ:1.00 FE6 A:BJ8501 0.0 19.1 1.0 S8 A:BJ8501 2.3 19.2 1.0 S5 A:BJ8501 2.3 20.4 1.0 S7 A:BJ8501 2.3 20.2 1.0 SG A:CYS75 2.4 18.3 1.0 FE7 A:BJ8501 2.7 20.5 1.0 FE5 A:BJ8501 2.7 19.9 1.0 FE8 A:BJ8501 2.8 20.2 1.0 HA A:CYS75 3.3 19.3 1.0 CB A:CYS75 3.4 15.6 1.0 HG21 A:THR142 3.4 22.0 1.0 HB2 A:CYS75 3.4 18.8 1.0 H A:VAL76 3.4 20.9 1.0 HG22 A:VAL76 3.6 25.4 1.0 CA A:CYS75 3.8 16.1 1.0 HD1 A:TYR77 3.8 26.9 1.0 S6 A:BJ8501 3.9 20.1 1.0 N A:VAL76 4.0 17.4 1.0 HZ2 A:LYS146 4.1 32.4 1.0 HZ3 A:LYS146 4.2 32.4 1.0 H A:TYR77 4.2 19.7 1.0 HB3 A:CYS75 4.2 18.8 1.0 CG2 A:THR142 4.3 18.3 1.0 OE2 A:GLU140 4.4 23.4 1.0 C A:CYS75 4.4 22.7 1.0 NZ A:LYS146 4.5 27.0 1.0 HZ1 A:LYS146 4.5 32.4 1.0 CG2 A:VAL76 4.6 21.1 1.0 HG1 A:THR142 4.6 20.8 1.0 HG22 A:THR142 4.6 22.0 1.0 HG3 A:GLU140 4.6 33.4 1.0 HG13 A:VAL76 4.7 22.1 1.0 S9 A:BJ8501 4.7 22.8 1.0 CD1 A:TYR77 4.7 22.4 1.0 HB2 A:TYR77 4.7 19.6 1.0 SG A:CYS308 4.7 21.5 1.0 HB2 A:CYS340 4.8 31.2 1.0 HG23 A:THR142 4.8 22.0 1.0 SG A:CYS340 4.8 20.9 1.0 O A:PHE74 4.9 23.4 1.0 HG23 A:VAL76 4.9 25.4 1.0 N A:TYR77 5.0 16.4 1.0

Iron binding site 7 out of 8 in the Double Cubane Cluster Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Double Cubane Cluster Oxidoreductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:20.5 occ:1.00 FE7 A:BJ8501 0.0 20.5 1.0 S5 A:BJ8501 2.3 20.4 1.0 SG A:CYS308 2.3 21.5 1.0 S8 A:BJ8501 2.3 19.2 1.0 S6 A:BJ8501 2.3 20.1 1.0 FE5 A:BJ8501 2.7 19.9 1.0 FE6 A:BJ8501 2.7 19.1 1.0 FE8 A:BJ8501 2.7 20.2 1.0 HB2 A:CYS308 3.0 22.2 1.0 CB A:CYS308 3.2 18.5 1.0 HG22 A:VAL76 3.3 25.4 1.0 HB3 A:CYS308 3.4 22.2 1.0 HH21 A:ARG312 3.5 28.6 1.0 HE A:ARG312 3.7 25.9 1.0 S7 A:BJ8501 3.8 20.2 1.0 HG13 A:VAL76 4.0 22.1 1.0 HB2 A:CYS340 4.0 31.2 1.0 H A:VAL76 4.1 20.9 1.0 HG21 A:VAL76 4.1 25.4 1.0 CG2 A:VAL76 4.2 21.1 1.0 HG3 A:PRO283 4.3 24.3 1.0 NH2 A:ARG312 4.3 23.8 1.0 HG11 A:VAL338 4.3 23.7 1.0 HD3 A:PRO283 4.5 28.2 1.0 NE A:ARG312 4.5 21.6 1.0 SG A:CYS340 4.6 20.9 1.0 CA A:CYS308 4.6 20.7 1.0 H A:CYS308 4.6 24.9 1.0 HG11 A:VAL76 4.6 22.1 1.0 CG1 A:VAL76 4.7 18.4 1.0 S9 A:BJ8501 4.7 22.8 1.0 HA A:CYS75 4.8 19.3 1.0 CB A:CYS340 4.8 26.0 1.0 SG A:CYS75 4.8 18.3 1.0 HG23 A:VAL76 4.8 25.4 1.0 OH A:TYR376 4.8 20.7 1.0 HA A:CYS308 4.9 24.9 1.0 N A:VAL76 4.9 17.4 1.0 CZ A:ARG312 4.9 25.6 1.0 HH22 A:ARG312 4.9 28.6 1.0 N A:CYS308 5.0 20.7 1.0 CB A:VAL76 5.0 19.6 1.0 HG12 A:VAL338 5.0 23.7 1.0

Iron binding site 8 out of 8 in the Double Cubane Cluster Oxidoreductase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Double Cubane Cluster Oxidoreductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:20.2 occ:1.00 FE8 A:BJ8501 0.0 20.2 1.0 S9 A:BJ8501 2.2 22.8 1.0 S6 A:BJ8501 2.3 20.1 1.0 S7 A:BJ8501 2.3 20.2 1.0 S5 A:BJ8501 2.4 20.4 1.0 FE5 A:BJ8501 2.7 19.9 1.0 FE7 A:BJ8501 2.7 20.5 1.0 FE6 A:BJ8501 2.8 19.1 1.0 HZ2 A:LYS146 3.2 32.4 1.0 HG3 A:PRO283 3.6 24.3 1.0 FE1 A:BJ8501 3.7 19.1 1.0 NZ A:LYS146 3.9 27.0 1.0 HZ1 A:LYS146 3.9 32.4 1.0 S8 A:BJ8501 4.0 19.2 1.0 HD3 A:PRO283 4.1 28.2 1.0 S2 A:BJ8501 4.2 18.3 1.0 HZ3 A:LYS146 4.2 32.4 1.0 CG A:PRO283 4.3 20.2 1.0 HB2 A:CYS308 4.4 22.2 1.0 HA A:CYS75 4.5 19.3 1.0 HD2 A:PRO283 4.5 28.2 1.0 CD A:PRO283 4.5 23.5 1.0 HG2 A:PRO283 4.6 24.3 1.0 HE2 A:TYR376 4.8 24.4 1.0 HH21 A:ARG312 4.8 28.6 1.0 SG A:CYS308 4.8 21.5 1.0 HG21 A:THR142 4.9 22.0 1.0 O A:PHE74 4.9 23.4 1.0 SG A:CYS75 4.9 18.3 1.0 SG A:CYS340 4.9 20.9 1.0 HB2 A:CYS75 4.9 18.8 1.0 HG1 A:THR142 5.0 20.8 1.0

J.H.Jeoung, H.Dobbek. Atp-Dependent Substrate Reduction at An [FE8S9] Double-Cubane Cluster. Proc. Natl. Acad. Sci. V. 115 2994 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29507223
DOI: 10.1073/PNAS.1720489115