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Iron in PDB 6eno: Double Cubane Cluster Oxidoreductase

Protein crystallography data

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

Iron Binding Sites:

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 6eno

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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 6eno

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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 6eno

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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 6eno

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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 6eno

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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 6eno

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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 6eno

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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 6eno

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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

Reference:

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
Page generated: Tue Aug 6 17:27:30 2024

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