Iron in PDB 2e75: Crystal Structure of the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus
Enzymatic activity of Crystal Structure of the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus
All present enzymatic activity of Crystal Structure of the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus:
1.10.99.1;
Protein crystallography data
The structure of Crystal Structure of the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus, PDB code: 2e75
was solved by
W.A.Cramer,
E.Yamashita,
H.Zhang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.94 /
3.55
|
Space group
|
P 61 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
159.164,
159.164,
362.269,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
20.1 /
26.7
|
Other elements in 2e75:
The structure of Crystal Structure of the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus
(pdb code 2e75). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Crystal Structure of the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus, PDB code: 2e75:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 2e75
Go back to
Iron Binding Sites List in 2e75
Iron binding site 1 out
of 6 in the Crystal Structure of the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus
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 the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:13.4
occ:1.00
|
FE
|
A:HEM301
|
0.0
|
13.4
|
1.0
|
NB
|
A:HEM301
|
1.8
|
5.8
|
1.0
|
NA
|
A:HEM301
|
1.8
|
11.8
|
1.0
|
NE2
|
A:HIS86
|
1.9
|
8.5
|
1.0
|
NE2
|
A:HIS187
|
1.9
|
13.2
|
1.0
|
ND
|
A:HEM301
|
2.0
|
15.4
|
1.0
|
NC
|
A:HEM301
|
2.1
|
5.6
|
1.0
|
C4A
|
A:HEM301
|
2.7
|
2.8
|
1.0
|
CE1
|
A:HIS187
|
2.7
|
23.8
|
1.0
|
CE1
|
A:HIS86
|
2.7
|
18.1
|
1.0
|
C1B
|
A:HEM301
|
2.8
|
10.9
|
1.0
|
C4B
|
A:HEM301
|
2.9
|
28.6
|
1.0
|
C1D
|
A:HEM301
|
2.9
|
13.6
|
1.0
|
C4C
|
A:HEM301
|
3.0
|
6.9
|
1.0
|
CD2
|
A:HIS86
|
3.0
|
7.8
|
1.0
|
C1A
|
A:HEM301
|
3.0
|
23.9
|
1.0
|
CD2
|
A:HIS187
|
3.1
|
15.9
|
1.0
|
CHB
|
A:HEM301
|
3.1
|
17.0
|
1.0
|
C4D
|
A:HEM301
|
3.1
|
17.9
|
1.0
|
C1C
|
A:HEM301
|
3.2
|
28.2
|
1.0
|
CHD
|
A:HEM301
|
3.2
|
25.5
|
1.0
|
CHC
|
A:HEM301
|
3.4
|
33.9
|
1.0
|
CHA
|
A:HEM301
|
3.6
|
24.8
|
1.0
|
ND1
|
A:HIS187
|
3.9
|
22.0
|
1.0
|
ND1
|
A:HIS86
|
3.9
|
28.5
|
1.0
|
C3A
|
A:HEM301
|
4.0
|
2.1
|
1.0
|
C3B
|
A:HEM301
|
4.1
|
28.8
|
1.0
|
CG
|
A:HIS86
|
4.1
|
12.9
|
1.0
|
C2B
|
A:HEM301
|
4.1
|
28.2
|
1.0
|
CG
|
A:HIS187
|
4.1
|
11.2
|
1.0
|
C2A
|
A:HEM301
|
4.2
|
3.7
|
1.0
|
C2D
|
A:HEM301
|
4.2
|
12.4
|
1.0
|
C3C
|
A:HEM301
|
4.2
|
30.3
|
1.0
|
C3D
|
A:HEM301
|
4.3
|
10.3
|
1.0
|
C2C
|
A:HEM301
|
4.4
|
42.4
|
1.0
|
|
Iron binding site 2 out
of 6 in 2e75
Go back to
Iron Binding Sites List in 2e75
Iron binding site 2 out
of 6 in the Crystal Structure of the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus
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 the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe302
b:9.7
occ:1.00
|
FE
|
A:HEM302
|
0.0
|
9.7
|
1.0
|
NE2
|
A:HIS202
|
1.9
|
15.1
|
1.0
|
NB
|
A:HEM302
|
1.9
|
2.6
|
1.0
|
NC
|
A:HEM302
|
1.9
|
2.0
|
1.0
|
ND
|
A:HEM302
|
1.9
|
11.7
|
1.0
|
NA
|
A:HEM302
|
2.0
|
8.1
|
1.0
|
NE2
|
A:HIS100
|
2.1
|
7.3
|
1.0
|
CE1
|
A:HIS100
|
2.5
|
21.7
|
1.0
|
CE1
|
A:HIS202
|
2.7
|
22.8
|
1.0
|
C1D
|
A:HEM302
|
2.8
|
7.5
|
1.0
|
C4C
|
A:HEM302
|
2.8
|
2.0
|
1.0
|
C4B
|
A:HEM302
|
2.9
|
2.0
|
1.0
|
CD2
|
A:HIS202
|
3.0
|
27.0
|
1.0
|
C1A
|
A:HEM302
|
3.0
|
10.4
|
1.0
|
C1B
|
A:HEM302
|
3.0
|
13.4
|
1.0
|
C1C
|
A:HEM302
|
3.0
|
2.0
|
1.0
|
C4A
|
A:HEM302
|
3.1
|
7.2
|
1.0
|
C4D
|
A:HEM302
|
3.1
|
14.4
|
1.0
|
CHD
|
A:HEM302
|
3.1
|
2.0
|
1.0
|
CHC
|
A:HEM302
|
3.3
|
3.5
|
1.0
|
CD2
|
A:HIS100
|
3.3
|
27.0
|
1.0
|
CHA
|
A:HEM302
|
3.4
|
2.0
|
1.0
|
CHB
|
A:HEM302
|
3.5
|
3.1
|
1.0
|
ND1
|
A:HIS100
|
3.8
|
54.7
|
1.0
|
ND1
|
A:HIS202
|
3.9
|
32.4
|
1.0
|
CG
|
A:HIS202
|
4.0
|
36.1
|
1.0
|
C3C
|
A:HEM302
|
4.1
|
3.4
|
1.0
|
C2D
|
A:HEM302
|
4.1
|
10.5
|
1.0
|
C3B
|
A:HEM302
|
4.1
|
11.9
|
1.0
|
C2B
|
A:HEM302
|
4.2
|
15.4
|
1.0
|
C2A
|
A:HEM302
|
4.2
|
43.9
|
1.0
|
CG
|
A:HIS100
|
4.2
|
37.1
|
1.0
|
C3A
|
A:HEM302
|
4.2
|
36.7
|
1.0
|
C3D
|
A:HEM302
|
4.3
|
2.0
|
1.0
|
C2C
|
A:HEM302
|
4.3
|
2.0
|
1.0
|
|
Iron binding site 3 out
of 6 in 2e75
Go back to
Iron Binding Sites List in 2e75
Iron binding site 3 out
of 6 in the Crystal Structure of the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus
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 the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe303
b:36.1
occ:1.00
|
FE
|
A:HEM303
|
0.0
|
36.1
|
1.0
|
NA
|
A:HEM303
|
2.0
|
41.4
|
1.0
|
NC
|
A:HEM303
|
2.1
|
37.2
|
1.0
|
NB
|
A:HEM303
|
2.1
|
32.8
|
1.0
|
OH
|
A:QNO501
|
2.2
|
56.5
|
1.0
|
ND
|
A:HEM303
|
2.2
|
18.0
|
1.0
|
O
|
A:HOH1107
|
2.3
|
3.7
|
1.0
|
C4A
|
A:HEM303
|
2.9
|
29.4
|
1.0
|
C4C
|
A:HEM303
|
3.0
|
29.0
|
1.0
|
C1C
|
A:HEM303
|
3.0
|
47.9
|
1.0
|
C1D
|
A:HEM303
|
3.0
|
30.3
|
1.0
|
C1B
|
A:HEM303
|
3.1
|
47.8
|
1.0
|
C1A
|
A:HEM303
|
3.1
|
52.7
|
1.0
|
C4B
|
A:HEM303
|
3.1
|
34.5
|
1.0
|
CE2
|
B:PHE40
|
3.2
|
69.7
|
1.0
|
CZ
|
B:PHE40
|
3.2
|
59.7
|
1.0
|
C4D
|
A:HEM303
|
3.3
|
30.2
|
1.0
|
CHD
|
A:HEM303
|
3.3
|
37.6
|
1.0
|
CHB
|
A:HEM303
|
3.4
|
49.5
|
1.0
|
CHC
|
A:HEM303
|
3.5
|
54.3
|
1.0
|
N1
|
A:QNO501
|
3.5
|
63.8
|
1.0
|
C61
|
A:QNO501
|
3.5
|
45.8
|
1.0
|
CHA
|
A:HEM303
|
3.6
|
50.9
|
1.0
|
C6
|
A:QNO501
|
4.0
|
53.9
|
1.0
|
C3A
|
A:HEM303
|
4.1
|
39.0
|
1.0
|
C3C
|
A:HEM303
|
4.1
|
23.1
|
1.0
|
C2C
|
A:HEM303
|
4.2
|
21.3
|
1.0
|
C2A
|
A:HEM303
|
4.3
|
48.9
|
1.0
|
C2D
|
A:HEM303
|
4.3
|
29.3
|
1.0
|
C2B
|
A:HEM303
|
4.3
|
37.9
|
1.0
|
C3B
|
A:HEM303
|
4.3
|
23.8
|
1.0
|
C3D
|
A:HEM303
|
4.4
|
28.2
|
1.0
|
CD2
|
B:PHE40
|
4.6
|
76.0
|
1.0
|
CE1
|
B:PHE40
|
4.6
|
63.9
|
1.0
|
C2
|
A:QNO501
|
4.6
|
63.4
|
1.0
|
C62
|
A:QNO501
|
4.6
|
61.7
|
1.0
|
O
|
A:TYR34
|
4.8
|
39.0
|
1.0
|
O2A
|
A:HEM302
|
5.0
|
47.9
|
1.0
|
|
Iron binding site 4 out
of 6 in 2e75
Go back to
Iron Binding Sites List in 2e75
Iron binding site 4 out
of 6 in the Crystal Structure of the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus
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 the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe301
b:35.0
occ:1.00
|
FE
|
C:HEM301
|
0.0
|
35.0
|
1.0
|
NA
|
C:HEM301
|
1.8
|
20.6
|
1.0
|
NC
|
C:HEM301
|
1.9
|
24.0
|
1.0
|
ND
|
C:HEM301
|
2.0
|
33.7
|
1.0
|
N
|
C:TYR1
|
2.0
|
27.9
|
1.0
|
NE2
|
C:HIS26
|
2.1
|
38.4
|
1.0
|
NB
|
C:HEM301
|
2.1
|
29.7
|
1.0
|
CD2
|
C:HIS26
|
2.8
|
36.5
|
1.0
|
C1A
|
C:HEM301
|
2.8
|
28.8
|
1.0
|
CA
|
C:TYR1
|
2.9
|
38.7
|
1.0
|
C4A
|
C:HEM301
|
2.9
|
24.4
|
1.0
|
C4D
|
C:HEM301
|
2.9
|
44.0
|
1.0
|
C4C
|
C:HEM301
|
2.9
|
7.1
|
1.0
|
C1C
|
C:HEM301
|
3.0
|
37.0
|
1.0
|
C1B
|
C:HEM301
|
3.0
|
33.0
|
1.0
|
C1D
|
C:HEM301
|
3.1
|
50.8
|
1.0
|
CHA
|
C:HEM301
|
3.1
|
33.6
|
1.0
|
C4B
|
C:HEM301
|
3.2
|
24.4
|
1.0
|
CE1
|
C:HIS26
|
3.3
|
52.0
|
1.0
|
CHB
|
C:HEM301
|
3.3
|
32.4
|
1.0
|
CHD
|
C:HEM301
|
3.5
|
27.9
|
1.0
|
CHC
|
C:HEM301
|
3.5
|
8.2
|
1.0
|
C
|
C:TYR1
|
3.6
|
38.3
|
1.0
|
O
|
C:TYR1
|
4.0
|
43.3
|
1.0
|
CG
|
C:HIS26
|
4.0
|
51.8
|
1.0
|
C2A
|
C:HEM301
|
4.1
|
33.7
|
1.0
|
C3A
|
C:HEM301
|
4.1
|
40.5
|
1.0
|
C3C
|
C:HEM301
|
4.1
|
23.4
|
1.0
|
C2C
|
C:HEM301
|
4.2
|
28.1
|
1.0
|
ND1
|
C:HIS26
|
4.2
|
53.8
|
1.0
|
C3D
|
C:HEM301
|
4.2
|
36.6
|
1.0
|
CB
|
C:TYR1
|
4.2
|
48.7
|
1.0
|
C2D
|
C:HEM301
|
4.3
|
49.4
|
1.0
|
C2B
|
C:HEM301
|
4.3
|
46.8
|
1.0
|
C3B
|
C:HEM301
|
4.4
|
39.1
|
1.0
|
N
|
C:PRO2
|
4.4
|
37.5
|
1.0
|
CE3
|
C:TRP4
|
4.7
|
61.1
|
1.0
|
CG
|
C:TYR1
|
4.7
|
51.3
|
1.0
|
CD
|
C:PRO2
|
4.7
|
39.5
|
1.0
|
OD1
|
C:ASN154
|
4.9
|
34.2
|
1.0
|
CZ3
|
C:TRP4
|
4.9
|
57.4
|
1.0
|
|
Iron binding site 5 out
of 6 in 2e75
Go back to
Iron Binding Sites List in 2e75
Iron binding site 5 out
of 6 in the Crystal Structure of the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus
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 the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe200
b:0.1
occ:1.00
|
FE1
|
D:FES200
|
0.0
|
0.1
|
1.0
|
SG
|
D:CYS108
|
1.3
|
86.5
|
1.0
|
S1
|
D:FES200
|
2.2
|
95.9
|
1.0
|
S2
|
D:FES200
|
2.2
|
89.5
|
1.0
|
SG
|
D:CYS126
|
2.4
|
85.1
|
1.0
|
OG
|
D:SER131
|
3.0
|
76.7
|
1.0
|
CB
|
D:CYS108
|
3.1
|
82.8
|
1.0
|
FE2
|
D:FES200
|
3.2
|
90.2
|
1.0
|
CB
|
D:CYS126
|
3.3
|
75.0
|
1.0
|
CB
|
D:HIS110
|
3.7
|
60.8
|
1.0
|
OH
|
D:TYR133
|
4.2
|
70.2
|
1.0
|
N
|
D:THR109
|
4.3
|
84.3
|
1.0
|
N
|
D:HIS110
|
4.3
|
72.2
|
1.0
|
CB
|
D:ALA144
|
4.3
|
98.9
|
1.0
|
CA
|
D:CYS108
|
4.3
|
85.2
|
1.0
|
CB
|
D:SER131
|
4.3
|
84.9
|
1.0
|
N
|
D:LEU111
|
4.4
|
78.2
|
1.0
|
ND1
|
D:HIS110
|
4.5
|
76.2
|
1.0
|
C
|
D:CYS108
|
4.5
|
85.8
|
1.0
|
CG
|
D:HIS110
|
4.6
|
71.4
|
1.0
|
CA
|
D:HIS110
|
4.6
|
67.3
|
1.0
|
CA
|
D:CYS126
|
4.8
|
82.3
|
1.0
|
C
|
D:HIS110
|
4.9
|
78.4
|
1.0
|
N
|
D:SER131
|
5.0
|
93.2
|
1.0
|
CB
|
D:HIS129
|
5.0
|
96.2
|
1.0
|
|
Iron binding site 6 out
of 6 in 2e75
Go back to
Iron Binding Sites List in 2e75
Iron binding site 6 out
of 6 in the Crystal Structure of the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Crystal Structure of the Cytochrome B6F Complex with 2-Nonyl-4- Hydroxyquinoline N-Oxide (Nqno) From M.Laminosus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe200
b:90.2
occ:1.00
|
FE2
|
D:FES200
|
0.0
|
90.2
|
1.0
|
S2
|
D:FES200
|
2.2
|
89.5
|
1.0
|
ND1
|
D:HIS129
|
2.2
|
62.8
|
1.0
|
S1
|
D:FES200
|
2.2
|
95.9
|
1.0
|
CB
|
D:HIS129
|
2.7
|
96.2
|
1.0
|
ND1
|
D:HIS110
|
2.8
|
76.2
|
1.0
|
CG
|
D:HIS129
|
2.8
|
85.5
|
1.0
|
FE1
|
D:FES200
|
3.2
|
0.1
|
1.0
|
CE1
|
D:HIS129
|
3.4
|
95.6
|
1.0
|
CE1
|
D:HIS110
|
3.6
|
0.2
|
1.0
|
CG
|
D:HIS110
|
3.8
|
71.4
|
1.0
|
CA
|
D:HIS129
|
3.9
|
99.2
|
1.0
|
N
|
D:HIS129
|
4.0
|
0.0
|
1.0
|
CB
|
D:HIS110
|
4.0
|
60.8
|
1.0
|
CD2
|
D:HIS129
|
4.0
|
94.7
|
1.0
|
N
|
D:LEU111
|
4.1
|
78.2
|
1.0
|
SG
|
D:CYS126
|
4.1
|
85.1
|
1.0
|
SG
|
D:CYS108
|
4.1
|
86.5
|
1.0
|
CB
|
D:CYS128
|
4.2
|
98.4
|
1.0
|
NE2
|
D:HIS129
|
4.3
|
75.2
|
1.0
|
CB
|
D:LEU111
|
4.3
|
63.4
|
1.0
|
C
|
D:CYS128
|
4.6
|
0.3
|
1.0
|
CG
|
D:PRO143
|
4.6
|
0.5
|
1.0
|
C
|
D:HIS129
|
4.7
|
99.1
|
1.0
|
NE2
|
D:HIS110
|
4.7
|
0.9
|
1.0
|
CA
|
D:LEU111
|
4.7
|
71.2
|
1.0
|
CD2
|
D:HIS110
|
4.9
|
1.0
|
1.0
|
CG
|
D:LEU111
|
4.9
|
78.5
|
1.0
|
SG
|
D:CYS113
|
4.9
|
0.6
|
1.0
|
CA
|
D:CYS128
|
5.0
|
99.2
|
1.0
|
|
Reference:
E.Yamashita,
H.Zhang,
W.A.Cramer.
Structure of the Cytochrome B(6)F Complex: Quinone Analogue Inhibitors As Ligands of Heme C(N) J.Mol.Biol. V. 370 39 2007.
ISSN: ISSN 0022-2836
PubMed: 17498743
DOI: 10.1016/J.JMB.2007.04.011
Page generated: Sat Aug 3 20:59:37 2024
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