Iron in PDB 8ab6: Complex III2 From Yarrowia Lipolytica, Combined Datasets, Consensus Refinement
Enzymatic activity of Complex III2 From Yarrowia Lipolytica, Combined Datasets, Consensus Refinement
All present enzymatic activity of Complex III2 From Yarrowia Lipolytica, Combined Datasets, Consensus Refinement:
7.1.1.8;
Iron Binding Sites:
The binding sites of Iron atom in the Complex III2 From Yarrowia Lipolytica, Combined Datasets, Consensus Refinement
(pdb code 8ab6). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Complex III2 From Yarrowia Lipolytica, Combined Datasets, Consensus Refinement, PDB code: 8ab6:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 8ab6
Go back to
Iron Binding Sites List in 8ab6
Iron binding site 1 out
of 6 in the Complex III2 From Yarrowia Lipolytica, Combined Datasets, Consensus Refinement
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Complex III2 From Yarrowia Lipolytica, Combined Datasets, Consensus Refinement within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe501
b:4.0
occ:1.00
|
FE
|
C:HEM501
|
0.0
|
4.0
|
1.0
|
|
ND
|
C:HEM501
|
1.9
|
4.2
|
1.0
|
|
NA
|
C:HEM501
|
2.0
|
4.1
|
1.0
|
|
NE2
|
C:HIS183
|
2.1
|
5.0
|
1.0
|
|
NC
|
C:HEM501
|
2.1
|
4.1
|
1.0
|
|
NE2
|
C:HIS82
|
2.1
|
4.3
|
1.0
|
|
NB
|
C:HEM501
|
2.1
|
4.1
|
1.0
|
|
C4D
|
C:HEM501
|
2.9
|
4.2
|
1.0
|
|
C1D
|
C:HEM501
|
2.9
|
4.2
|
1.0
|
|
C1A
|
C:HEM501
|
3.0
|
4.2
|
1.0
|
|
CE1
|
C:HIS183
|
3.0
|
5.0
|
1.0
|
|
C4A
|
C:HEM501
|
3.0
|
4.2
|
1.0
|
|
CE1
|
C:HIS82
|
3.1
|
4.2
|
1.0
|
|
C4C
|
C:HEM501
|
3.1
|
4.2
|
1.0
|
|
C4B
|
C:HEM501
|
3.1
|
4.1
|
1.0
|
|
C1B
|
C:HEM501
|
3.1
|
4.1
|
1.0
|
|
CD2
|
C:HIS183
|
3.1
|
5.0
|
1.0
|
|
C1C
|
C:HEM501
|
3.1
|
4.2
|
1.0
|
|
CD2
|
C:HIS82
|
3.1
|
4.3
|
1.0
|
|
CHA
|
C:HEM501
|
3.4
|
4.2
|
1.0
|
|
CHD
|
C:HEM501
|
3.4
|
4.2
|
1.0
|
|
CHB
|
C:HEM501
|
3.4
|
4.1
|
1.0
|
|
CHC
|
C:HEM501
|
3.5
|
4.1
|
1.0
|
|
ND1
|
C:HIS183
|
4.1
|
5.1
|
1.0
|
|
C2A
|
C:HEM501
|
4.2
|
4.4
|
1.0
|
|
ND1
|
C:HIS82
|
4.2
|
4.3
|
1.0
|
|
C3D
|
C:HEM501
|
4.2
|
4.4
|
1.0
|
|
C2D
|
C:HEM501
|
4.2
|
4.3
|
1.0
|
|
C3A
|
C:HEM501
|
4.2
|
4.3
|
1.0
|
|
CG
|
C:HIS183
|
4.2
|
5.2
|
1.0
|
|
CG
|
C:HIS82
|
4.2
|
4.5
|
1.0
|
|
C3C
|
C:HEM501
|
4.3
|
4.3
|
1.0
|
|
C2C
|
C:HEM501
|
4.3
|
4.3
|
1.0
|
|
C2B
|
C:HEM501
|
4.3
|
4.1
|
1.0
|
|
C3B
|
C:HEM501
|
4.3
|
4.2
|
1.0
|
|
CA
|
C:GLY131
|
4.7
|
8.6
|
1.0
|
|
NE2
|
C:GLN43
|
4.9
|
6.0
|
1.0
|
|
Iron binding site 2 out
of 6 in 8ab6
Go back to
Iron Binding Sites List in 8ab6
Iron binding site 2 out
of 6 in the Complex III2 From Yarrowia Lipolytica, Combined Datasets, Consensus Refinement
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Complex III2 From Yarrowia Lipolytica, Combined Datasets, Consensus Refinement within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe502
b:3.2
occ:1.00
|
FE
|
C:HEM502
|
0.0
|
3.2
|
1.0
|
|
ND
|
C:HEM502
|
1.9
|
3.4
|
1.0
|
|
NA
|
C:HEM502
|
2.0
|
3.4
|
1.0
|
|
NC
|
C:HEM502
|
2.1
|
3.2
|
1.0
|
|
NB
|
C:HEM502
|
2.1
|
3.3
|
1.0
|
|
NE2
|
C:HIS197
|
2.2
|
5.3
|
1.0
|
|
NE2
|
C:HIS96
|
2.2
|
4.4
|
1.0
|
|
C4D
|
C:HEM502
|
2.9
|
3.4
|
1.0
|
|
C1D
|
C:HEM502
|
2.9
|
3.4
|
1.0
|
|
C1A
|
C:HEM502
|
3.0
|
3.4
|
1.0
|
|
C4C
|
C:HEM502
|
3.0
|
3.2
|
1.0
|
|
C4A
|
C:HEM502
|
3.0
|
3.4
|
1.0
|
|
CE1
|
C:HIS197
|
3.1
|
5.4
|
1.0
|
|
C4B
|
C:HEM502
|
3.1
|
3.2
|
1.0
|
|
C1B
|
C:HEM502
|
3.1
|
3.3
|
1.0
|
|
C1C
|
C:HEM502
|
3.1
|
3.2
|
1.0
|
|
CD2
|
C:HIS96
|
3.2
|
4.5
|
1.0
|
|
CE1
|
C:HIS96
|
3.2
|
4.5
|
1.0
|
|
CD2
|
C:HIS197
|
3.2
|
5.5
|
1.0
|
|
CHA
|
C:HEM502
|
3.4
|
3.4
|
1.0
|
|
CHD
|
C:HEM502
|
3.4
|
3.3
|
1.0
|
|
CHB
|
C:HEM502
|
3.5
|
3.3
|
1.0
|
|
CHC
|
C:HEM502
|
3.5
|
3.2
|
1.0
|
|
C3D
|
C:HEM502
|
4.2
|
3.6
|
1.0
|
|
C2D
|
C:HEM502
|
4.2
|
3.5
|
1.0
|
|
C2A
|
C:HEM502
|
4.2
|
3.6
|
1.0
|
|
C3C
|
C:HEM502
|
4.2
|
3.3
|
1.0
|
|
ND1
|
C:HIS197
|
4.2
|
5.5
|
1.0
|
|
C3A
|
C:HEM502
|
4.2
|
3.5
|
1.0
|
|
C2C
|
C:HEM502
|
4.2
|
3.3
|
1.0
|
|
ND1
|
C:HIS96
|
4.3
|
4.6
|
1.0
|
|
CG
|
C:HIS96
|
4.3
|
4.8
|
1.0
|
|
CG
|
C:HIS197
|
4.3
|
5.7
|
1.0
|
|
C2B
|
C:HEM502
|
4.3
|
3.3
|
1.0
|
|
C3B
|
C:HEM502
|
4.3
|
3.3
|
1.0
|
|
Iron binding site 3 out
of 6 in 8ab6
Go back to
Iron Binding Sites List in 8ab6
Iron binding site 3 out
of 6 in the Complex III2 From Yarrowia Lipolytica, Combined Datasets, Consensus Refinement
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Complex III2 From Yarrowia Lipolytica, Combined Datasets, Consensus Refinement within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe401
b:13.0
occ:1.00
|
FE
|
D:HEC401
|
0.0
|
13.0
|
1.0
|
|
NE2
|
D:HIS128
|
2.0
|
10.8
|
1.0
|
|
NB
|
D:HEC401
|
2.1
|
13.5
|
1.0
|
|
NC
|
D:HEC401
|
2.1
|
13.6
|
1.0
|
|
ND
|
D:HEC401
|
2.1
|
13.5
|
1.0
|
|
NA
|
D:HEC401
|
2.1
|
13.2
|
1.0
|
|
SD
|
D:MET248
|
2.3
|
14.4
|
1.0
|
|
CE1
|
D:HIS128
|
3.0
|
10.8
|
1.0
|
|
CD2
|
D:HIS128
|
3.0
|
10.8
|
1.0
|
|
C1B
|
D:HEC401
|
3.0
|
13.5
|
1.0
|
|
C4B
|
D:HEC401
|
3.1
|
13.7
|
1.0
|
|
C4C
|
D:HEC401
|
3.1
|
13.9
|
1.0
|
|
C4A
|
D:HEC401
|
3.1
|
13.1
|
1.0
|
|
C4D
|
D:HEC401
|
3.1
|
13.5
|
1.0
|
|
C1D
|
D:HEC401
|
3.1
|
13.5
|
1.0
|
|
C1A
|
D:HEC401
|
3.1
|
13.1
|
1.0
|
|
C1C
|
D:HEC401
|
3.1
|
13.9
|
1.0
|
|
CHB
|
D:HEC401
|
3.4
|
13.1
|
1.0
|
|
CE
|
D:MET248
|
3.4
|
14.4
|
1.0
|
|
CHA
|
D:HEC401
|
3.4
|
13.2
|
1.0
|
|
CHD
|
D:HEC401
|
3.4
|
13.8
|
1.0
|
|
CHC
|
D:HEC401
|
3.5
|
13.8
|
1.0
|
|
CG
|
D:MET248
|
3.5
|
15.3
|
1.0
|
|
ND1
|
D:HIS128
|
4.1
|
10.9
|
1.0
|
|
CB
|
D:MET248
|
4.1
|
16.2
|
1.0
|
|
CG
|
D:HIS128
|
4.1
|
11.3
|
1.0
|
|
C3B
|
D:HEC401
|
4.3
|
14.4
|
1.0
|
|
C3C
|
D:HEC401
|
4.3
|
14.5
|
1.0
|
|
C2B
|
D:HEC401
|
4.4
|
14.1
|
1.0
|
|
C3D
|
D:HEC401
|
4.4
|
13.8
|
1.0
|
|
C2D
|
D:HEC401
|
4.4
|
13.9
|
1.0
|
|
C2A
|
D:HEC401
|
4.4
|
13.2
|
1.0
|
|
C3A
|
D:HEC401
|
4.4
|
13.2
|
1.0
|
|
C2C
|
D:HEC401
|
4.4
|
14.3
|
1.0
|
|
Iron binding site 4 out
of 6 in 8ab6
Go back to
Iron Binding Sites List in 8ab6
Iron binding site 4 out
of 6 in the Complex III2 From Yarrowia Lipolytica, Combined Datasets, Consensus Refinement
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Complex III2 From Yarrowia Lipolytica, Combined Datasets, Consensus Refinement within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Fe501
b:4.0
occ:1.00
|
FE
|
N:HEM501
|
0.0
|
4.0
|
1.0
|
|
ND
|
N:HEM501
|
1.9
|
4.2
|
1.0
|
|
NA
|
N:HEM501
|
2.0
|
4.2
|
1.0
|
|
NE2
|
N:HIS183
|
2.1
|
5.1
|
1.0
|
|
NC
|
N:HEM501
|
2.1
|
4.1
|
1.0
|
|
NE2
|
N:HIS82
|
2.1
|
4.3
|
1.0
|
|
NB
|
N:HEM501
|
2.1
|
4.1
|
1.0
|
|
C4D
|
N:HEM501
|
2.9
|
4.2
|
1.0
|
|
C1D
|
N:HEM501
|
2.9
|
4.2
|
1.0
|
|
C1A
|
N:HEM501
|
3.0
|
4.2
|
1.0
|
|
CE1
|
N:HIS183
|
3.0
|
5.0
|
1.0
|
|
C4A
|
N:HEM501
|
3.0
|
4.2
|
1.0
|
|
CE1
|
N:HIS82
|
3.1
|
4.2
|
1.0
|
|
C4C
|
N:HEM501
|
3.1
|
4.2
|
1.0
|
|
C4B
|
N:HEM501
|
3.1
|
4.1
|
1.0
|
|
C1B
|
N:HEM501
|
3.1
|
4.1
|
1.0
|
|
CD2
|
N:HIS183
|
3.1
|
5.1
|
1.0
|
|
C1C
|
N:HEM501
|
3.1
|
4.2
|
1.0
|
|
CD2
|
N:HIS82
|
3.1
|
4.3
|
1.0
|
|
CHA
|
N:HEM501
|
3.4
|
4.2
|
1.0
|
|
CHD
|
N:HEM501
|
3.4
|
4.2
|
1.0
|
|
CHB
|
N:HEM501
|
3.4
|
4.1
|
1.0
|
|
CHC
|
N:HEM501
|
3.5
|
4.2
|
1.0
|
|
ND1
|
N:HIS183
|
4.1
|
5.2
|
1.0
|
|
ND1
|
N:HIS82
|
4.2
|
4.3
|
1.0
|
|
C2A
|
N:HEM501
|
4.2
|
4.4
|
1.0
|
|
C3D
|
N:HEM501
|
4.2
|
4.5
|
1.0
|
|
C2D
|
N:HEM501
|
4.2
|
4.3
|
1.0
|
|
CG
|
N:HIS183
|
4.2
|
5.3
|
1.0
|
|
C3A
|
N:HEM501
|
4.2
|
4.3
|
1.0
|
|
CG
|
N:HIS82
|
4.2
|
4.5
|
1.0
|
|
C3C
|
N:HEM501
|
4.3
|
4.3
|
1.0
|
|
C2C
|
N:HEM501
|
4.3
|
4.3
|
1.0
|
|
C2B
|
N:HEM501
|
4.3
|
4.2
|
1.0
|
|
C3B
|
N:HEM501
|
4.3
|
4.2
|
1.0
|
|
CA
|
N:GLY131
|
4.7
|
8.8
|
1.0
|
|
NE2
|
N:GLN43
|
4.9
|
6.0
|
1.0
|
|
Iron binding site 5 out
of 6 in 8ab6
Go back to
Iron Binding Sites List in 8ab6
Iron binding site 5 out
of 6 in the Complex III2 From Yarrowia Lipolytica, Combined Datasets, Consensus Refinement
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Complex III2 From Yarrowia Lipolytica, Combined Datasets, Consensus Refinement within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Fe502
b:3.2
occ:1.00
|
FE
|
N:HEM502
|
0.0
|
3.2
|
1.0
|
|
ND
|
N:HEM502
|
1.9
|
3.3
|
1.0
|
|
NA
|
N:HEM502
|
2.0
|
3.3
|
1.0
|
|
NC
|
N:HEM502
|
2.1
|
3.2
|
1.0
|
|
NE2
|
N:HIS96
|
2.1
|
4.4
|
1.0
|
|
NB
|
N:HEM502
|
2.1
|
3.2
|
1.0
|
|
NE2
|
N:HIS197
|
2.2
|
5.3
|
1.0
|
|
C4D
|
N:HEM502
|
2.9
|
3.4
|
1.0
|
|
C1D
|
N:HEM502
|
2.9
|
3.3
|
1.0
|
|
C1A
|
N:HEM502
|
3.0
|
3.4
|
1.0
|
|
CE1
|
N:HIS96
|
3.0
|
4.5
|
1.0
|
|
C4C
|
N:HEM502
|
3.0
|
3.2
|
1.0
|
|
C4A
|
N:HEM502
|
3.0
|
3.3
|
1.0
|
|
CE1
|
N:HIS197
|
3.1
|
5.4
|
1.0
|
|
C4B
|
N:HEM502
|
3.1
|
3.2
|
1.0
|
|
C1B
|
N:HEM502
|
3.1
|
3.2
|
1.0
|
|
C1C
|
N:HEM502
|
3.1
|
3.2
|
1.0
|
|
CD2
|
N:HIS96
|
3.1
|
4.5
|
1.0
|
|
CD2
|
N:HIS197
|
3.2
|
5.5
|
1.0
|
|
CHA
|
N:HEM502
|
3.4
|
3.4
|
1.0
|
|
CHD
|
N:HEM502
|
3.4
|
3.2
|
1.0
|
|
CHB
|
N:HEM502
|
3.4
|
3.3
|
1.0
|
|
CHC
|
N:HEM502
|
3.5
|
3.2
|
1.0
|
|
ND1
|
N:HIS96
|
4.1
|
4.6
|
1.0
|
|
C3D
|
N:HEM502
|
4.2
|
3.5
|
1.0
|
|
C2D
|
N:HEM502
|
4.2
|
3.4
|
1.0
|
|
C2A
|
N:HEM502
|
4.2
|
3.5
|
1.0
|
|
C3C
|
N:HEM502
|
4.2
|
3.2
|
1.0
|
|
ND1
|
N:HIS197
|
4.2
|
5.5
|
1.0
|
|
C3A
|
N:HEM502
|
4.2
|
3.4
|
1.0
|
|
CG
|
N:HIS96
|
4.2
|
4.7
|
1.0
|
|
C2C
|
N:HEM502
|
4.2
|
3.2
|
1.0
|
|
C2B
|
N:HEM502
|
4.3
|
3.2
|
1.0
|
|
C3B
|
N:HEM502
|
4.3
|
3.2
|
1.0
|
|
CG
|
N:HIS197
|
4.3
|
5.7
|
1.0
|
|
Iron binding site 6 out
of 6 in 8ab6
Go back to
Iron Binding Sites List in 8ab6
Iron binding site 6 out
of 6 in the Complex III2 From Yarrowia Lipolytica, Combined Datasets, Consensus Refinement
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Complex III2 From Yarrowia Lipolytica, Combined Datasets, Consensus Refinement within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
O:Fe401
b:13.0
occ:1.00
|
FE
|
O:HEC401
|
0.0
|
13.0
|
1.0
|
|
NE2
|
O:HIS128
|
2.0
|
10.8
|
1.0
|
|
NB
|
O:HEC401
|
2.1
|
13.5
|
1.0
|
|
NC
|
O:HEC401
|
2.1
|
13.6
|
1.0
|
|
ND
|
O:HEC401
|
2.1
|
13.5
|
1.0
|
|
NA
|
O:HEC401
|
2.1
|
13.2
|
1.0
|
|
SD
|
O:MET248
|
2.3
|
14.4
|
1.0
|
|
CE1
|
O:HIS128
|
3.0
|
10.8
|
1.0
|
|
CD2
|
O:HIS128
|
3.0
|
10.8
|
1.0
|
|
C1B
|
O:HEC401
|
3.0
|
13.5
|
1.0
|
|
C4B
|
O:HEC401
|
3.0
|
13.7
|
1.0
|
|
C4C
|
O:HEC401
|
3.1
|
13.9
|
1.0
|
|
C4A
|
O:HEC401
|
3.1
|
13.1
|
1.0
|
|
C4D
|
O:HEC401
|
3.1
|
13.4
|
1.0
|
|
C1D
|
O:HEC401
|
3.1
|
13.5
|
1.0
|
|
C1A
|
O:HEC401
|
3.1
|
13.1
|
1.0
|
|
C1C
|
O:HEC401
|
3.1
|
13.9
|
1.0
|
|
CHB
|
O:HEC401
|
3.4
|
13.1
|
1.0
|
|
CE
|
O:MET248
|
3.4
|
14.4
|
1.0
|
|
CHA
|
O:HEC401
|
3.4
|
13.2
|
1.0
|
|
CHD
|
O:HEC401
|
3.4
|
13.8
|
1.0
|
|
CHC
|
O:HEC401
|
3.5
|
13.8
|
1.0
|
|
CG
|
O:MET248
|
3.5
|
15.3
|
1.0
|
|
ND1
|
O:HIS128
|
4.1
|
10.9
|
1.0
|
|
CB
|
O:MET248
|
4.1
|
16.2
|
1.0
|
|
CG
|
O:HIS128
|
4.1
|
11.4
|
1.0
|
|
C3B
|
O:HEC401
|
4.3
|
14.4
|
1.0
|
|
C3C
|
O:HEC401
|
4.3
|
14.5
|
1.0
|
|
C2B
|
O:HEC401
|
4.4
|
14.1
|
1.0
|
|
C3D
|
O:HEC401
|
4.4
|
13.8
|
1.0
|
|
C2D
|
O:HEC401
|
4.4
|
13.8
|
1.0
|
|
C2A
|
O:HEC401
|
4.4
|
13.2
|
1.0
|
|
C3A
|
O:HEC401
|
4.4
|
13.2
|
1.0
|
|
C2C
|
O:HEC401
|
4.4
|
14.3
|
1.0
|
|
Reference:
J.P.Wieferig,
W.Kuhlbrandt.
Analysis of the Conformational Heterogeneity of the Rieske Iron-Sulfur Protein in Complex III2 By Cryo-Em Iucrj 2023.
ISSN: ESSN 2052-2525
Page generated: Wed Apr 5 07:54:47 2023
|
