Iron in PDB 7dgz: Activity Optimized Complex I (Closed Form)
Enzymatic activity of Activity Optimized Complex I (Closed Form)
All present enzymatic activity of Activity Optimized Complex I (Closed Form):
7.1.1.2;
Other elements in 7dgz:
The structure of Activity Optimized Complex I (Closed Form) also contains other interesting chemical elements:
Iron Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
28;
Binding sites:
The binding sites of Iron atom in the Activity Optimized Complex I (Closed Form)
(pdb code 7dgz). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 28 binding sites of Iron where determined in the
Activity Optimized Complex I (Closed Form), PDB code: 7dgz:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 28 in 7dgz
Go back to
Iron Binding Sites List in 7dgz
Iron binding site 1 out
of 28 in the Activity Optimized Complex I (Closed Form)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Activity Optimized Complex I (Closed Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
8:Fe502
b:49.7
occ:1.00
|
FE1
|
8:SF4502
|
0.0
|
49.7
|
1.0
|
S4
|
8:SF4502
|
2.3
|
49.7
|
1.0
|
S2
|
8:SF4502
|
2.3
|
49.7
|
1.0
|
S3
|
8:SF4502
|
2.3
|
49.7
|
1.0
|
FE3
|
8:SF4502
|
2.7
|
49.7
|
1.0
|
FE4
|
8:SF4502
|
2.7
|
49.7
|
1.0
|
FE2
|
8:SF4502
|
2.7
|
49.7
|
1.0
|
CB
|
8:CYS385
|
3.0
|
22.2
|
1.0
|
SG
|
8:CYS385
|
3.7
|
22.2
|
1.0
|
CB
|
8:THR423
|
3.8
|
20.5
|
1.0
|
S1
|
8:SF4502
|
3.9
|
49.7
|
1.0
|
CG2
|
8:THR423
|
4.0
|
20.5
|
1.0
|
CB
|
8:CYS382
|
4.2
|
21.8
|
1.0
|
CA
|
8:CYS385
|
4.4
|
22.2
|
1.0
|
N
|
8:ILE424
|
4.6
|
23.8
|
1.0
|
N
|
8:CYS382
|
4.6
|
21.8
|
1.0
|
CA
|
8:THR423
|
4.7
|
20.5
|
1.0
|
N
|
8:CYS385
|
4.7
|
22.2
|
1.0
|
OG1
|
8:THR423
|
4.8
|
20.5
|
1.0
|
O
|
8:CYS382
|
4.8
|
21.8
|
1.0
|
SG
|
8:CYS382
|
4.9
|
21.8
|
1.0
|
CA
|
8:CYS382
|
4.9
|
21.8
|
1.0
|
N
|
8:CYS425
|
5.0
|
27.7
|
1.0
|
|
Iron binding site 2 out
of 28 in 7dgz
Go back to
Iron Binding Sites List in 7dgz
Iron binding site 2 out
of 28 in the Activity Optimized Complex I (Closed Form)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Activity Optimized Complex I (Closed Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
8:Fe502
b:49.7
occ:1.00
|
FE2
|
8:SF4502
|
0.0
|
49.7
|
1.0
|
S3
|
8:SF4502
|
2.3
|
49.7
|
1.0
|
S4
|
8:SF4502
|
2.3
|
49.7
|
1.0
|
S1
|
8:SF4502
|
2.3
|
49.7
|
1.0
|
FE4
|
8:SF4502
|
2.7
|
49.7
|
1.0
|
FE1
|
8:SF4502
|
2.7
|
49.7
|
1.0
|
FE3
|
8:SF4502
|
2.7
|
49.7
|
1.0
|
OH
|
8:TYR204
|
2.8
|
35.1
|
1.0
|
CZ
|
8:TYR204
|
3.8
|
35.1
|
1.0
|
S2
|
8:SF4502
|
3.9
|
49.7
|
1.0
|
CB
|
8:LEU427
|
3.9
|
25.6
|
1.0
|
N
|
8:CYS379
|
4.1
|
23.9
|
1.0
|
SG
|
8:CYS385
|
4.1
|
22.2
|
1.0
|
CD2
|
8:LEU427
|
4.1
|
25.6
|
1.0
|
CB
|
8:CYS379
|
4.2
|
23.9
|
1.0
|
CE1
|
8:TYR204
|
4.3
|
35.1
|
1.0
|
CG
|
8:LEU427
|
4.6
|
25.6
|
1.0
|
CB
|
8:CYS425
|
4.6
|
27.7
|
1.0
|
CB
|
8:CYS385
|
4.6
|
22.2
|
1.0
|
CE2
|
8:TYR204
|
4.6
|
35.1
|
1.0
|
CA
|
8:CYS379
|
4.8
|
23.9
|
1.0
|
CA
|
8:LEU427
|
4.8
|
25.6
|
1.0
|
CA
|
8:SER378
|
4.9
|
22.9
|
1.0
|
CB
|
8:SER378
|
4.9
|
22.9
|
1.0
|
N
|
8:GLY428
|
4.9
|
27.3
|
1.0
|
C
|
8:LEU427
|
5.0
|
25.6
|
1.0
|
N
|
8:LEU427
|
5.0
|
25.6
|
1.0
|
|
Iron binding site 3 out
of 28 in 7dgz
Go back to
Iron Binding Sites List in 7dgz
Iron binding site 3 out
of 28 in the Activity Optimized Complex I (Closed Form)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Activity Optimized Complex I (Closed Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
8:Fe502
b:49.7
occ:1.00
|
FE3
|
8:SF4502
|
0.0
|
49.7
|
1.0
|
S2
|
8:SF4502
|
2.3
|
49.7
|
1.0
|
S1
|
8:SF4502
|
2.3
|
49.7
|
1.0
|
S4
|
8:SF4502
|
2.3
|
49.7
|
1.0
|
FE4
|
8:SF4502
|
2.7
|
49.7
|
1.0
|
FE1
|
8:SF4502
|
2.7
|
49.7
|
1.0
|
FE2
|
8:SF4502
|
2.7
|
49.7
|
1.0
|
CB
|
8:CYS379
|
3.2
|
23.9
|
1.0
|
SG
|
8:CYS379
|
3.8
|
23.9
|
1.0
|
S3
|
8:SF4502
|
3.9
|
49.7
|
1.0
|
N
|
8:GLY380
|
4.3
|
16.9
|
1.0
|
N
|
8:GLN381
|
4.3
|
24.8
|
1.0
|
CB
|
8:GLN381
|
4.3
|
24.8
|
1.0
|
CA
|
8:CYS379
|
4.3
|
23.9
|
1.0
|
N
|
8:CYS379
|
4.5
|
23.9
|
1.0
|
CD
|
8:PRO223
|
4.5
|
30.8
|
1.0
|
CG
|
8:PRO223
|
4.5
|
30.8
|
1.0
|
OE1
|
8:GLN381
|
4.5
|
24.8
|
1.0
|
N
|
8:CYS382
|
4.5
|
21.8
|
1.0
|
OH
|
8:TYR204
|
4.7
|
35.1
|
1.0
|
CA
|
8:GLN381
|
4.8
|
24.8
|
1.0
|
C
|
8:CYS379
|
4.8
|
23.9
|
1.0
|
|
Iron binding site 4 out
of 28 in 7dgz
Go back to
Iron Binding Sites List in 7dgz
Iron binding site 4 out
of 28 in the Activity Optimized Complex I (Closed Form)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Activity Optimized Complex I (Closed Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
8:Fe502
b:49.7
occ:1.00
|
FE4
|
8:SF4502
|
0.0
|
49.7
|
1.0
|
S1
|
8:SF4502
|
2.3
|
49.7
|
1.0
|
S2
|
8:SF4502
|
2.3
|
49.7
|
1.0
|
S3
|
8:SF4502
|
2.3
|
49.7
|
1.0
|
FE3
|
8:SF4502
|
2.7
|
49.7
|
1.0
|
FE2
|
8:SF4502
|
2.7
|
49.7
|
1.0
|
FE1
|
8:SF4502
|
2.7
|
49.7
|
1.0
|
N
|
8:CYS425
|
2.8
|
27.7
|
1.0
|
CB
|
8:CYS425
|
3.1
|
27.7
|
1.0
|
CA
|
8:CYS425
|
3.5
|
27.7
|
1.0
|
SG
|
8:CYS425
|
3.6
|
27.7
|
1.0
|
S4
|
8:SF4502
|
3.9
|
49.7
|
1.0
|
N
|
8:ILE424
|
3.9
|
23.8
|
1.0
|
C
|
8:ILE424
|
3.9
|
23.8
|
1.0
|
CB
|
8:ILE424
|
3.9
|
23.8
|
1.0
|
CA
|
8:ILE424
|
4.1
|
23.8
|
1.0
|
OH
|
8:TYR204
|
4.1
|
35.1
|
1.0
|
C
|
8:CYS425
|
4.1
|
27.7
|
1.0
|
O
|
8:CYS425
|
4.3
|
27.7
|
1.0
|
CB
|
8:THR423
|
4.5
|
20.5
|
1.0
|
CG
|
8:PRO223
|
4.8
|
30.8
|
1.0
|
CG1
|
8:ILE424
|
4.8
|
23.8
|
1.0
|
C
|
8:THR423
|
4.9
|
20.5
|
1.0
|
CG2
|
8:ILE424
|
4.9
|
23.8
|
1.0
|
OG1
|
8:THR423
|
5.0
|
20.5
|
1.0
|
|
Iron binding site 5 out
of 28 in 7dgz
Go back to
Iron Binding Sites List in 7dgz
Iron binding site 5 out
of 28 in the Activity Optimized Complex I (Closed Form)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Activity Optimized Complex I (Closed Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
9:Fe301
b:93.3
occ:1.00
|
FE1
|
9:FES301
|
0.0
|
93.3
|
1.0
|
S1
|
9:FES301
|
2.2
|
93.3
|
1.0
|
S2
|
9:FES301
|
2.2
|
93.3
|
1.0
|
OG1
|
9:THR137
|
2.8
|
73.1
|
1.0
|
FE2
|
9:FES301
|
3.1
|
93.3
|
1.0
|
SG
|
9:CYS140
|
3.1
|
69.7
|
1.0
|
O
|
9:CYS135
|
3.2
|
73.1
|
1.0
|
CB
|
9:CYS135
|
3.2
|
73.1
|
1.0
|
C
|
9:CYS135
|
3.7
|
73.1
|
1.0
|
CA
|
9:CYS135
|
4.0
|
73.1
|
1.0
|
CB
|
9:THR137
|
4.0
|
73.1
|
1.0
|
SG
|
9:CYS180
|
4.2
|
75.6
|
1.0
|
N
|
9:CYS176
|
4.4
|
76.2
|
1.0
|
CB
|
9:CYS140
|
4.4
|
69.7
|
1.0
|
N
|
9:THR136
|
4.5
|
59.3
|
1.0
|
N
|
9:THR137
|
4.5
|
73.1
|
1.0
|
C
|
9:THR136
|
4.6
|
59.3
|
1.0
|
SG
|
9:CYS135
|
4.6
|
73.1
|
1.0
|
N
|
9:LEU177
|
4.8
|
70.8
|
1.0
|
O
|
9:THR136
|
4.9
|
59.3
|
1.0
|
CA
|
9:GLU175
|
4.9
|
55.3
|
1.0
|
O
|
9:VAL174
|
4.9
|
54.7
|
1.0
|
CA
|
9:THR137
|
4.9
|
73.1
|
1.0
|
CG2
|
9:THR137
|
4.9
|
73.1
|
1.0
|
C
|
9:GLU175
|
4.9
|
55.3
|
1.0
|
CA
|
9:THR136
|
5.0
|
59.3
|
1.0
|
|
Iron binding site 6 out
of 28 in 7dgz
Go back to
Iron Binding Sites List in 7dgz
Iron binding site 6 out
of 28 in the Activity Optimized Complex I (Closed Form)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Activity Optimized Complex I (Closed Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
9:Fe301
b:93.3
occ:1.00
|
FE2
|
9:FES301
|
0.0
|
93.3
|
1.0
|
S1
|
9:FES301
|
2.2
|
93.3
|
1.0
|
S2
|
9:FES301
|
2.2
|
93.3
|
1.0
|
FE1
|
9:FES301
|
3.1
|
93.3
|
1.0
|
SG
|
9:CYS180
|
3.1
|
75.6
|
1.0
|
O
|
9:GLY178
|
3.4
|
76.5
|
1.0
|
O
|
9:LEU177
|
3.5
|
70.8
|
1.0
|
O
|
9:ALA179
|
3.5
|
77.7
|
1.0
|
C
|
9:ALA179
|
3.6
|
77.7
|
1.0
|
N
|
9:CYS180
|
3.6
|
75.6
|
1.0
|
C
|
9:GLY178
|
3.8
|
76.5
|
1.0
|
C
|
9:LEU177
|
3.8
|
70.8
|
1.0
|
N
|
9:LEU177
|
3.8
|
70.8
|
1.0
|
N
|
9:GLY178
|
4.1
|
76.5
|
1.0
|
N
|
9:ALA179
|
4.2
|
77.7
|
1.0
|
CA
|
9:CYS180
|
4.2
|
75.6
|
1.0
|
CB
|
9:CYS180
|
4.2
|
75.6
|
1.0
|
N
|
8:GLY123
|
4.3
|
72.6
|
1.0
|
CA
|
9:LEU177
|
4.5
|
70.8
|
1.0
|
CA
|
9:ALA179
|
4.5
|
77.7
|
1.0
|
CA
|
9:GLY178
|
4.5
|
76.5
|
1.0
|
CA
|
9:CYS176
|
4.6
|
76.2
|
1.0
|
CA
|
8:GLY123
|
4.6
|
72.6
|
1.0
|
C
|
9:CYS176
|
4.7
|
76.2
|
1.0
|
SG
|
9:CYS140
|
4.7
|
69.7
|
1.0
|
N
|
9:CYS176
|
4.8
|
76.2
|
1.0
|
OG1
|
9:THR137
|
4.8
|
73.1
|
1.0
|
|
Iron binding site 7 out
of 28 in 7dgz
Go back to
Iron Binding Sites List in 7dgz
Iron binding site 7 out
of 28 in the Activity Optimized Complex I (Closed Form)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Activity Optimized Complex I (Closed Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe801
b:49.7
occ:1.00
|
FE1
|
A:SF4801
|
0.0
|
49.7
|
1.0
|
S4
|
A:SF4801
|
2.3
|
49.7
|
1.0
|
S3
|
A:SF4801
|
2.3
|
49.7
|
1.0
|
S2
|
A:SF4801
|
2.3
|
49.7
|
1.0
|
FE3
|
A:SF4801
|
2.7
|
49.7
|
1.0
|
FE2
|
A:SF4801
|
2.7
|
49.7
|
1.0
|
FE4
|
A:SF4801
|
2.7
|
49.7
|
1.0
|
SG
|
A:CYS137
|
3.1
|
22.1
|
1.0
|
CB
|
A:LEU139
|
3.7
|
19.1
|
1.0
|
CD1
|
A:LEU139
|
3.8
|
19.1
|
1.0
|
S1
|
A:SF4801
|
3.9
|
49.7
|
1.0
|
CB
|
A:CYS137
|
4.0
|
22.1
|
1.0
|
CG
|
A:LEU139
|
4.1
|
19.1
|
1.0
|
NE2
|
A:HIS124
|
4.2
|
22.1
|
1.0
|
CE1
|
A:HIS124
|
4.5
|
22.1
|
1.0
|
CG1
|
A:VAL228
|
4.6
|
22.2
|
1.0
|
N
|
A:LEU139
|
4.6
|
19.1
|
1.0
|
CA
|
A:LEU139
|
4.6
|
19.1
|
1.0
|
CB
|
A:VAL228
|
4.7
|
22.2
|
1.0
|
C
|
A:LEU139
|
5.0
|
19.1
|
1.0
|
|
Iron binding site 8 out
of 28 in 7dgz
Go back to
Iron Binding Sites List in 7dgz
Iron binding site 8 out
of 28 in the Activity Optimized Complex I (Closed Form)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Activity Optimized Complex I (Closed Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe801
b:49.7
occ:1.00
|
FE2
|
A:SF4801
|
0.0
|
49.7
|
1.0
|
S3
|
A:SF4801
|
2.2
|
49.7
|
1.0
|
S4
|
A:SF4801
|
2.3
|
49.7
|
1.0
|
S1
|
A:SF4801
|
2.3
|
49.7
|
1.0
|
FE4
|
A:SF4801
|
2.7
|
49.7
|
1.0
|
FE1
|
A:SF4801
|
2.7
|
49.7
|
1.0
|
FE3
|
A:SF4801
|
2.7
|
49.7
|
1.0
|
SG
|
A:CYS128
|
3.0
|
20.2
|
1.0
|
O
|
A:ASP127
|
3.9
|
22.8
|
1.0
|
S2
|
A:SF4801
|
3.9
|
49.7
|
1.0
|
C
|
A:ASP127
|
4.3
|
22.8
|
1.0
|
CE
|
B:MET375
|
4.3
|
16.4
|
1.0
|
CB
|
A:CYS128
|
4.3
|
20.2
|
1.0
|
N
|
A:CYS128
|
4.4
|
20.2
|
1.0
|
NE2
|
A:HIS124
|
4.6
|
22.1
|
1.0
|
OE1
|
A:GLN140
|
4.7
|
22.4
|
1.0
|
CA
|
A:CYS128
|
4.8
|
20.2
|
1.0
|
|
Iron binding site 9 out
of 28 in 7dgz
Go back to
Iron Binding Sites List in 7dgz
Iron binding site 9 out
of 28 in the Activity Optimized Complex I (Closed Form)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of Activity Optimized Complex I (Closed Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe801
b:49.7
occ:1.00
|
FE3
|
A:SF4801
|
0.0
|
49.7
|
1.0
|
S2
|
A:SF4801
|
2.3
|
49.7
|
1.0
|
S1
|
A:SF4801
|
2.3
|
49.7
|
1.0
|
S4
|
A:SF4801
|
2.3
|
49.7
|
1.0
|
FE1
|
A:SF4801
|
2.7
|
49.7
|
1.0
|
FE4
|
A:SF4801
|
2.7
|
49.7
|
1.0
|
FE2
|
A:SF4801
|
2.7
|
49.7
|
1.0
|
SG
|
A:CYS131
|
3.5
|
20.7
|
1.0
|
S3
|
A:SF4801
|
3.8
|
49.7
|
1.0
|
SG
|
A:CYS128
|
4.1
|
20.2
|
1.0
|
CB
|
A:CYS137
|
4.1
|
22.1
|
1.0
|
SG
|
A:CYS137
|
4.1
|
22.1
|
1.0
|
CB
|
A:CYS131
|
4.2
|
20.7
|
1.0
|
O
|
A:GLN133
|
4.5
|
23.0
|
1.0
|
N
|
A:GLY229
|
4.7
|
49.7
|
1.0
|
C
|
A:GLN133
|
4.7
|
23.0
|
1.0
|
OE1
|
A:GLN140
|
5.0
|
22.4
|
1.0
|
CA
|
A:GLY229
|
5.0
|
49.7
|
1.0
|
|
Iron binding site 10 out
of 28 in 7dgz
Go back to
Iron Binding Sites List in 7dgz
Iron binding site 10 out
of 28 in the Activity Optimized Complex I (Closed Form)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 10 of Activity Optimized Complex I (Closed Form) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe801
b:49.7
occ:1.00
|
FE4
|
A:SF4801
|
0.0
|
49.7
|
1.0
|
S1
|
A:SF4801
|
2.3
|
49.7
|
1.0
|
S2
|
A:SF4801
|
2.3
|
49.7
|
1.0
|
S3
|
A:SF4801
|
2.3
|
49.7
|
1.0
|
FE2
|
A:SF4801
|
2.7
|
49.7
|
1.0
|
FE3
|
A:SF4801
|
2.7
|
49.7
|
1.0
|
FE1
|
A:SF4801
|
2.7
|
49.7
|
1.0
|
NE2
|
A:HIS124
|
2.8
|
22.1
|
1.0
|
CD
|
A:ARG175
|
3.7
|
17.4
|
1.0
|
CE1
|
A:HIS124
|
3.7
|
22.1
|
1.0
|
CD2
|
A:HIS124
|
3.8
|
22.1
|
1.0
|
S4
|
A:SF4801
|
3.8
|
49.7
|
1.0
|
CG
|
A:ARG175
|
4.4
|
17.4
|
1.0
|
SG
|
A:CYS131
|
4.5
|
20.7
|
1.0
|
CB
|
A:ARG175
|
4.8
|
17.4
|
1.0
|
CB
|
A:ASP127
|
4.9
|
22.8
|
1.0
|
NE
|
A:ARG175
|
4.9
|
17.4
|
1.0
|
ND1
|
A:HIS124
|
4.9
|
22.1
|
1.0
|
CB
|
A:CYS131
|
4.9
|
20.7
|
1.0
|
CG
|
A:HIS124
|
4.9
|
22.1
|
1.0
|
O
|
A:PRO125
|
5.0
|
21.1
|
1.0
|
|
Reference:
T.J.Jeon,
S.G.Lee,
S.H.Yoo,
M.Kim,
D.Song,
J.Ryu,
H.Park,
D.S.Kim,
J.Hyun,
H.M.Kim,
S.E.Ryu.
A Dynamic Substrate Pool Revealed By Cryo-Em of A Lipid-Preserved Respiratory Supercomplex. Antioxid.Redox Signal. 2022.
ISSN: ESSN 1557-7716
PubMed: 34913730
DOI: 10.1089/ARS.2021.0114
Page generated: Thu Aug 8 03:56:09 2024
|