Iron in PDB 1nu1: Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno)
Enzymatic activity of Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno)
All present enzymatic activity of Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno):
1.10.2.2;
Protein crystallography data
The structure of Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno), PDB code: 1nu1
was solved by
X.Gao,
X.Wen,
L.Esser,
B.Quinn,
L.Yu,
C.-A.Yu,
D.Xia,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
10.00 /
3.20
|
Space group
|
I 41 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
153.842,
153.842,
590.374,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.5 /
29.6
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno)
(pdb code 1nu1). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the
Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno), PDB code: 1nu1:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
Iron binding site 1 out
of 5 in 1nu1
Go back to
Iron Binding Sites List in 1nu1
Iron binding site 1 out
of 5 in the Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe381
b:31.4
occ:1.00
|
FE
|
C:HEM381
|
0.0
|
31.4
|
1.0
|
ND
|
C:HEM381
|
2.0
|
41.6
|
1.0
|
NB
|
C:HEM381
|
2.0
|
41.5
|
1.0
|
NC
|
C:HEM381
|
2.0
|
43.9
|
1.0
|
NE2
|
C:HIS182
|
2.0
|
15.9
|
1.0
|
NE2
|
C:HIS83
|
2.1
|
4.5
|
1.0
|
NA
|
C:HEM381
|
2.1
|
40.0
|
1.0
|
CE1
|
C:HIS83
|
2.8
|
15.6
|
1.0
|
CE1
|
C:HIS182
|
2.9
|
15.9
|
1.0
|
C4C
|
C:HEM381
|
3.0
|
48.8
|
1.0
|
C4D
|
C:HEM381
|
3.0
|
49.4
|
1.0
|
C1D
|
C:HEM381
|
3.1
|
44.9
|
1.0
|
CD2
|
C:HIS182
|
3.1
|
17.6
|
1.0
|
C4B
|
C:HEM381
|
3.1
|
49.1
|
1.0
|
C1A
|
C:HEM381
|
3.1
|
43.4
|
1.0
|
C1C
|
C:HEM381
|
3.1
|
41.5
|
1.0
|
C1B
|
C:HEM381
|
3.1
|
41.3
|
1.0
|
C4A
|
C:HEM381
|
3.1
|
40.6
|
1.0
|
CD2
|
C:HIS83
|
3.3
|
10.1
|
1.0
|
CHA
|
C:HEM381
|
3.6
|
48.8
|
1.0
|
CHD
|
C:HEM381
|
3.6
|
48.6
|
1.0
|
CHB
|
C:HEM381
|
3.6
|
36.2
|
1.0
|
CHC
|
C:HEM381
|
3.6
|
45.8
|
1.0
|
ND1
|
C:HIS83
|
4.0
|
23.0
|
1.0
|
ND1
|
C:HIS182
|
4.1
|
22.3
|
1.0
|
C3C
|
C:HEM381
|
4.1
|
48.1
|
1.0
|
C3D
|
C:HEM381
|
4.2
|
49.0
|
1.0
|
CG
|
C:HIS182
|
4.2
|
18.5
|
1.0
|
C2D
|
C:HEM381
|
4.2
|
45.2
|
1.0
|
C2C
|
C:HEM381
|
4.2
|
36.4
|
1.0
|
C3B
|
C:HEM381
|
4.2
|
47.9
|
1.0
|
C2B
|
C:HEM381
|
4.2
|
47.3
|
1.0
|
CG
|
C:HIS83
|
4.3
|
15.7
|
1.0
|
C2A
|
C:HEM381
|
4.4
|
38.9
|
1.0
|
C3A
|
C:HEM381
|
4.4
|
39.1
|
1.0
|
CA
|
C:GLY48
|
4.9
|
25.3
|
1.0
|
CA
|
C:GLY130
|
5.0
|
29.6
|
1.0
|
|
Iron binding site 2 out
of 5 in 1nu1
Go back to
Iron Binding Sites List in 1nu1
Iron binding site 2 out
of 5 in the Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe382
b:24.9
occ:1.00
|
FE
|
C:HEM382
|
0.0
|
24.9
|
1.0
|
ND
|
C:HEM382
|
1.9
|
29.4
|
1.0
|
NB
|
C:HEM382
|
2.0
|
35.9
|
1.0
|
NC
|
C:HEM382
|
2.0
|
33.9
|
1.0
|
NA
|
C:HEM382
|
2.1
|
24.1
|
1.0
|
NE2
|
C:HIS196
|
2.2
|
12.3
|
1.0
|
NE2
|
C:HIS97
|
2.4
|
21.8
|
1.0
|
C4D
|
C:HEM382
|
3.0
|
33.9
|
1.0
|
C4C
|
C:HEM382
|
3.0
|
38.3
|
1.0
|
C4B
|
C:HEM382
|
3.0
|
35.7
|
1.0
|
C1A
|
C:HEM382
|
3.0
|
31.2
|
1.0
|
C1C
|
C:HEM382
|
3.0
|
31.8
|
1.0
|
C1B
|
C:HEM382
|
3.0
|
23.2
|
1.0
|
C1D
|
C:HEM382
|
3.0
|
32.5
|
1.0
|
C4A
|
C:HEM382
|
3.0
|
30.4
|
1.0
|
CE1
|
C:HIS196
|
3.1
|
17.5
|
1.0
|
CD2
|
C:HIS97
|
3.1
|
20.4
|
1.0
|
CD2
|
C:HIS196
|
3.3
|
15.9
|
1.0
|
CHA
|
C:HEM382
|
3.5
|
38.9
|
1.0
|
CE1
|
C:HIS97
|
3.5
|
23.0
|
1.0
|
CHC
|
C:HEM382
|
3.6
|
37.3
|
1.0
|
CHD
|
C:HEM382
|
3.6
|
42.6
|
1.0
|
CHB
|
C:HEM382
|
3.6
|
23.5
|
1.0
|
C3D
|
C:HEM382
|
4.1
|
30.1
|
1.0
|
C3C
|
C:HEM382
|
4.1
|
29.2
|
1.0
|
C2B
|
C:HEM382
|
4.1
|
26.7
|
1.0
|
C2C
|
C:HEM382
|
4.1
|
29.4
|
1.0
|
C3B
|
C:HEM382
|
4.1
|
31.0
|
1.0
|
C2D
|
C:HEM382
|
4.1
|
35.3
|
1.0
|
ND1
|
C:HIS196
|
4.2
|
11.6
|
1.0
|
C2A
|
C:HEM382
|
4.3
|
28.7
|
1.0
|
C3A
|
C:HEM382
|
4.3
|
29.6
|
1.0
|
CG
|
C:HIS97
|
4.3
|
30.9
|
1.0
|
CG
|
C:HIS196
|
4.4
|
21.9
|
1.0
|
ND1
|
C:HIS97
|
4.5
|
36.7
|
1.0
|
|
Iron binding site 3 out
of 5 in 1nu1
Go back to
Iron Binding Sites List in 1nu1
Iron binding site 3 out
of 5 in the Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe242
b:28.5
occ:1.00
|
FE
|
D:HEM242
|
0.0
|
28.5
|
1.0
|
ND
|
D:HEM242
|
2.0
|
29.1
|
1.0
|
NC
|
D:HEM242
|
2.0
|
32.6
|
1.0
|
NB
|
D:HEM242
|
2.0
|
31.3
|
1.0
|
NA
|
D:HEM242
|
2.1
|
34.2
|
1.0
|
NE2
|
D:HIS41
|
2.3
|
23.9
|
1.0
|
C4D
|
D:HEM242
|
3.0
|
30.2
|
1.0
|
C1D
|
D:HEM242
|
3.0
|
29.8
|
1.0
|
C4C
|
D:HEM242
|
3.0
|
32.3
|
1.0
|
C1B
|
D:HEM242
|
3.0
|
30.5
|
1.0
|
C1C
|
D:HEM242
|
3.0
|
37.0
|
1.0
|
CE1
|
D:HIS41
|
3.1
|
29.6
|
1.0
|
C4B
|
D:HEM242
|
3.1
|
33.0
|
1.0
|
C1A
|
D:HEM242
|
3.1
|
34.9
|
1.0
|
C4A
|
D:HEM242
|
3.1
|
35.0
|
1.0
|
SD
|
D:MET160
|
3.1
|
28.4
|
1.0
|
CD2
|
D:HIS41
|
3.4
|
28.4
|
1.0
|
CE
|
D:MET160
|
3.5
|
26.7
|
1.0
|
CG
|
D:MET160
|
3.5
|
30.3
|
1.0
|
CHA
|
D:HEM242
|
3.6
|
37.1
|
1.0
|
CHD
|
D:HEM242
|
3.6
|
30.2
|
1.0
|
CHB
|
D:HEM242
|
3.6
|
34.4
|
1.0
|
CHC
|
D:HEM242
|
3.6
|
39.0
|
1.0
|
C2D
|
D:HEM242
|
4.1
|
30.1
|
1.0
|
C3D
|
D:HEM242
|
4.1
|
30.6
|
1.0
|
C3C
|
D:HEM242
|
4.1
|
36.7
|
1.0
|
C2C
|
D:HEM242
|
4.1
|
35.8
|
1.0
|
C2B
|
D:HEM242
|
4.1
|
29.4
|
1.0
|
C3B
|
D:HEM242
|
4.2
|
29.7
|
1.0
|
ND1
|
D:HIS41
|
4.3
|
33.3
|
1.0
|
C2A
|
D:HEM242
|
4.4
|
35.1
|
1.0
|
C3A
|
D:HEM242
|
4.4
|
32.5
|
1.0
|
CB
|
D:PRO110
|
4.4
|
34.1
|
1.0
|
CG
|
D:HIS41
|
4.5
|
33.3
|
1.0
|
CB
|
D:MET160
|
4.5
|
33.9
|
1.0
|
CA
|
D:PRO110
|
4.7
|
34.5
|
1.0
|
|
Iron binding site 4 out
of 5 in 1nu1
Go back to
Iron Binding Sites List in 1nu1
Iron binding site 4 out
of 5 in the Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe200
b:43.1
occ:1.00
|
FE1
|
E:FES200
|
0.0
|
43.1
|
1.0
|
S1
|
E:FES200
|
2.2
|
36.5
|
1.0
|
S2
|
E:FES200
|
2.2
|
23.4
|
1.0
|
SG
|
E:CYS158
|
2.4
|
8.4
|
1.0
|
FE2
|
E:FES200
|
2.7
|
40.3
|
1.0
|
SG
|
E:CYS139
|
2.7
|
2.8
|
1.0
|
CB
|
E:CYS160
|
3.4
|
29.0
|
1.0
|
CB
|
E:CYS158
|
3.4
|
28.3
|
1.0
|
CB
|
E:CYS139
|
3.5
|
24.7
|
1.0
|
CB
|
E:CYS144
|
3.6
|
31.6
|
1.0
|
CB
|
E:HIS141
|
3.8
|
27.6
|
1.0
|
ND1
|
E:HIS161
|
4.0
|
23.8
|
1.0
|
OG
|
E:SER163
|
4.2
|
34.9
|
1.0
|
N
|
E:LEU142
|
4.3
|
29.4
|
1.0
|
ND1
|
E:HIS141
|
4.3
|
16.8
|
1.0
|
N
|
E:HIS161
|
4.4
|
28.3
|
1.0
|
SG
|
E:CYS160
|
4.5
|
28.3
|
1.0
|
N
|
E:CYS144
|
4.5
|
31.9
|
1.0
|
CA
|
E:CYS160
|
4.5
|
29.2
|
1.0
|
CG
|
E:HIS141
|
4.6
|
22.6
|
1.0
|
CA
|
E:CYS144
|
4.6
|
31.8
|
1.0
|
CE1
|
E:HIS161
|
4.7
|
28.1
|
1.0
|
CA
|
E:HIS141
|
4.7
|
27.7
|
1.0
|
N
|
E:CYS160
|
4.8
|
29.8
|
1.0
|
CA
|
E:CYS158
|
4.8
|
28.4
|
1.0
|
N
|
E:HIS141
|
4.8
|
27.3
|
1.0
|
CB
|
E:SER163
|
4.8
|
27.8
|
1.0
|
SG
|
E:CYS144
|
4.8
|
24.7
|
1.0
|
C
|
E:CYS160
|
4.9
|
28.6
|
1.0
|
OH
|
E:TYR165
|
4.9
|
37.2
|
1.0
|
CA
|
E:CYS139
|
5.0
|
25.6
|
1.0
|
|
Iron binding site 5 out
of 5 in 1nu1
Go back to
Iron Binding Sites List in 1nu1
Iron binding site 5 out
of 5 in the Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe200
b:40.3
occ:1.00
|
FE2
|
E:FES200
|
0.0
|
40.3
|
1.0
|
ND1
|
E:HIS161
|
2.1
|
23.8
|
1.0
|
S2
|
E:FES200
|
2.2
|
23.4
|
1.0
|
ND1
|
E:HIS141
|
2.2
|
16.8
|
1.0
|
S1
|
E:FES200
|
2.2
|
36.5
|
1.0
|
FE1
|
E:FES200
|
2.7
|
43.1
|
1.0
|
CG
|
E:HIS161
|
2.9
|
27.9
|
1.0
|
CB
|
E:HIS161
|
3.0
|
28.3
|
1.0
|
CG
|
E:HIS141
|
3.1
|
22.6
|
1.0
|
CE1
|
E:HIS161
|
3.1
|
28.1
|
1.0
|
CE1
|
E:HIS141
|
3.2
|
16.0
|
1.0
|
CB
|
E:HIS141
|
3.3
|
27.6
|
1.0
|
N
|
E:HIS161
|
3.4
|
28.3
|
1.0
|
CA
|
E:HIS161
|
3.7
|
28.2
|
1.0
|
CB
|
E:CYS160
|
3.9
|
29.0
|
1.0
|
CG
|
E:PRO175
|
4.0
|
26.0
|
1.0
|
CD2
|
E:HIS161
|
4.0
|
29.3
|
1.0
|
C
|
E:CYS160
|
4.1
|
28.6
|
1.0
|
NE2
|
E:HIS161
|
4.1
|
31.4
|
1.0
|
OG
|
E:SER163
|
4.1
|
34.9
|
1.0
|
CD2
|
E:HIS141
|
4.2
|
19.3
|
1.0
|
NE2
|
E:HIS141
|
4.2
|
14.6
|
1.0
|
N
|
E:LEU142
|
4.3
|
29.4
|
1.0
|
C
|
E:HIS161
|
4.4
|
27.8
|
1.0
|
CA
|
E:CYS160
|
4.6
|
29.2
|
1.0
|
SG
|
E:CYS139
|
4.7
|
2.8
|
1.0
|
CA
|
E:HIS141
|
4.7
|
27.7
|
1.0
|
CG
|
E:LEU142
|
4.8
|
26.9
|
1.0
|
SG
|
E:CYS158
|
4.8
|
8.4
|
1.0
|
O
|
E:HIS161
|
4.8
|
28.0
|
1.0
|
CB
|
E:LEU142
|
4.8
|
30.3
|
1.0
|
CB
|
E:PRO175
|
4.8
|
27.0
|
1.0
|
O
|
E:CYS160
|
4.9
|
28.4
|
1.0
|
C
|
E:HIS141
|
4.9
|
28.4
|
1.0
|
CD1
|
E:LEU142
|
5.0
|
25.0
|
1.0
|
|
Reference:
X.Gao,
X.Wen,
L.Esser,
B.Quinn,
L.Yu,
C.-A.Yu,
D.Xia.
Structural Basis For the Quinone Reduction in the Bc(1) Complex: A Comparative Analysis of Crystal Structures of Mitochondrial Cytochrome Bc(1) with Bound Substrate and Inhibitors at the Q(I) Site Biochemistry V. 42 9067 2003.
ISSN: ISSN 0006-2960
PubMed: 12885240
DOI: 10.1021/BI0341814
Page generated: Sat Aug 3 12:01:42 2024
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