Iron in PDB 1q90: Structure of the Cytochrome B6F (Plastohydroquinone : Plastocyanin Oxidoreductase) From Chlamydomonas Reinhardtii
Enzymatic activity of Structure of the Cytochrome B6F (Plastohydroquinone : Plastocyanin Oxidoreductase) From Chlamydomonas Reinhardtii
All present enzymatic activity of Structure of the Cytochrome B6F (Plastohydroquinone : Plastocyanin Oxidoreductase) From Chlamydomonas Reinhardtii:
1.10.99.1;
Protein crystallography data
The structure of Structure of the Cytochrome B6F (Plastohydroquinone : Plastocyanin Oxidoreductase) From Chlamydomonas Reinhardtii, PDB code: 1q90
was solved by
D.Stroebel,
Y.Choquet,
J.-L.Popot,
D.Picot,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
34.42 /
3.10
|
Space group
|
I 2 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
102.454,
171.205,
351.009,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.2 /
26.1
|
Other elements in 1q90:
The structure of Structure of the Cytochrome B6F (Plastohydroquinone : Plastocyanin Oxidoreductase) From Chlamydomonas Reinhardtii also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Structure of the Cytochrome B6F (Plastohydroquinone : Plastocyanin Oxidoreductase) From Chlamydomonas Reinhardtii
(pdb code 1q90). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Structure of the Cytochrome B6F (Plastohydroquinone : Plastocyanin Oxidoreductase) From Chlamydomonas Reinhardtii, PDB code: 1q90:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 1q90
Go back to
Iron Binding Sites List in 1q90
Iron binding site 1 out
of 6 in the Structure of the Cytochrome B6F (Plastohydroquinone : Plastocyanin Oxidoreductase) From Chlamydomonas Reinhardtii
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Structure of the Cytochrome B6F (Plastohydroquinone : Plastocyanin Oxidoreductase) From Chlamydomonas Reinhardtii within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe900
b:66.9
occ:1.00
|
FE
|
A:HEM900
|
0.0
|
66.9
|
1.0
|
NB
|
A:HEM900
|
2.0
|
67.2
|
1.0
|
NA
|
A:HEM900
|
2.0
|
67.7
|
1.0
|
N
|
A:TYR1
|
2.0
|
64.6
|
1.0
|
ND
|
A:HEM900
|
2.0
|
70.0
|
1.0
|
NC
|
A:HEM900
|
2.0
|
68.0
|
1.0
|
NE2
|
A:HIS25
|
2.0
|
73.5
|
1.0
|
CD2
|
A:HIS25
|
3.0
|
74.0
|
1.0
|
C4B
|
A:HEM900
|
3.0
|
66.6
|
1.0
|
C1D
|
A:HEM900
|
3.0
|
70.5
|
1.0
|
CE1
|
A:HIS25
|
3.0
|
73.5
|
1.0
|
C4A
|
A:HEM900
|
3.0
|
67.7
|
1.0
|
C1C
|
A:HEM900
|
3.0
|
67.8
|
1.0
|
C4C
|
A:HEM900
|
3.0
|
67.9
|
1.0
|
C4D
|
A:HEM900
|
3.0
|
71.3
|
1.0
|
C1A
|
A:HEM900
|
3.1
|
68.7
|
1.0
|
C1B
|
A:HEM900
|
3.1
|
67.0
|
1.0
|
CA
|
A:TYR1
|
3.1
|
64.8
|
1.0
|
CHD
|
A:HEM900
|
3.4
|
69.7
|
1.0
|
CHB
|
A:HEM900
|
3.4
|
67.7
|
1.0
|
CHC
|
A:HEM900
|
3.4
|
67.4
|
1.0
|
CHA
|
A:HEM900
|
3.4
|
69.5
|
1.0
|
C
|
A:TYR1
|
3.9
|
64.5
|
1.0
|
O
|
A:TYR1
|
4.1
|
64.9
|
1.0
|
ND1
|
A:HIS25
|
4.1
|
73.5
|
1.0
|
CG
|
A:HIS25
|
4.1
|
73.2
|
1.0
|
C3B
|
A:HEM900
|
4.3
|
65.8
|
1.0
|
C2C
|
A:HEM900
|
4.3
|
67.2
|
1.0
|
C3C
|
A:HEM900
|
4.3
|
67.1
|
1.0
|
C2D
|
A:HEM900
|
4.3
|
71.8
|
1.0
|
C2B
|
A:HEM900
|
4.3
|
66.4
|
1.0
|
C2A
|
A:HEM900
|
4.3
|
69.6
|
1.0
|
C3A
|
A:HEM900
|
4.3
|
68.6
|
1.0
|
C3D
|
A:HEM900
|
4.3
|
72.7
|
1.0
|
CB
|
A:TYR1
|
4.4
|
73.8
|
1.0
|
CD2
|
A:PHE4
|
4.4
|
90.8
|
1.0
|
CG
|
A:TYR1
|
4.6
|
75.1
|
1.0
|
N
|
A:PRO2
|
4.8
|
53.6
|
1.0
|
CD1
|
A:TYR1
|
5.0
|
76.4
|
1.0
|
ND2
|
A:ASN153
|
5.0
|
72.4
|
1.0
|
|
Iron binding site 2 out
of 6 in 1q90
Go back to
Iron Binding Sites List in 1q90
Iron binding site 2 out
of 6 in the Structure of the Cytochrome B6F (Plastohydroquinone : Plastocyanin Oxidoreductase) From Chlamydomonas Reinhardtii
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Structure of the Cytochrome B6F (Plastohydroquinone : Plastocyanin Oxidoreductase) From Chlamydomonas Reinhardtii within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe903
b:53.1
occ:1.00
|
FE
|
B:HEM903
|
0.0
|
53.1
|
1.0
|
NB
|
B:HEM903
|
2.0
|
53.1
|
1.0
|
NA
|
B:HEM903
|
2.0
|
53.1
|
1.0
|
ND
|
B:HEM903
|
2.0
|
53.1
|
1.0
|
NC
|
B:HEM903
|
2.0
|
53.1
|
1.0
|
O
|
B:HOH963
|
2.4
|
35.7
|
1.0
|
C4A
|
B:HEM903
|
3.0
|
53.1
|
1.0
|
C4B
|
B:HEM903
|
3.0
|
53.1
|
1.0
|
C1D
|
B:HEM903
|
3.0
|
53.1
|
1.0
|
C4C
|
B:HEM903
|
3.1
|
53.1
|
1.0
|
C1A
|
B:HEM903
|
3.1
|
53.1
|
1.0
|
C1C
|
B:HEM903
|
3.1
|
53.1
|
1.0
|
C4D
|
B:HEM903
|
3.1
|
53.1
|
1.0
|
C1B
|
B:HEM903
|
3.1
|
53.1
|
1.0
|
CHD
|
B:HEM903
|
3.4
|
53.1
|
1.0
|
CHB
|
B:HEM903
|
3.4
|
53.1
|
1.0
|
CHC
|
B:HEM903
|
3.4
|
53.1
|
1.0
|
CHA
|
B:HEM903
|
3.5
|
53.1
|
1.0
|
CZ
|
D:PHE40
|
3.5
|
70.8
|
1.0
|
CE2
|
D:PHE40
|
4.2
|
70.4
|
1.0
|
C2B
|
B:HEM903
|
4.3
|
53.1
|
1.0
|
C2A
|
B:HEM903
|
4.3
|
53.1
|
1.0
|
CE1
|
D:PHE40
|
4.3
|
70.5
|
1.0
|
C3A
|
B:HEM903
|
4.3
|
53.1
|
1.0
|
C2D
|
B:HEM903
|
4.3
|
53.1
|
1.0
|
C3C
|
B:HEM903
|
4.3
|
53.1
|
1.0
|
C2C
|
B:HEM903
|
4.3
|
53.1
|
1.0
|
C3B
|
B:HEM903
|
4.3
|
53.1
|
1.0
|
C3D
|
B:HEM903
|
4.3
|
53.1
|
1.0
|
O
|
B:TYR34
|
4.6
|
54.5
|
1.0
|
CMA
|
B:HEM901
|
4.7
|
34.3
|
1.0
|
O2A
|
B:HEM901
|
4.8
|
46.5
|
1.0
|
CA
|
B:GLY38
|
4.9
|
35.4
|
1.0
|
CBA
|
B:HEM901
|
4.9
|
39.1
|
1.0
|
N
|
B:GLY38
|
5.0
|
36.0
|
1.0
|
|
Iron binding site 3 out
of 6 in 1q90
Go back to
Iron Binding Sites List in 1q90
Iron binding site 3 out
of 6 in the Structure of the Cytochrome B6F (Plastohydroquinone : Plastocyanin Oxidoreductase) From Chlamydomonas Reinhardtii
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Structure of the Cytochrome B6F (Plastohydroquinone : Plastocyanin Oxidoreductase) From Chlamydomonas Reinhardtii within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe901
b:35.4
occ:1.00
|
FE
|
B:HEM901
|
0.0
|
35.4
|
1.0
|
NA
|
B:HEM901
|
2.0
|
38.3
|
1.0
|
NE2
|
B:HIS100
|
2.0
|
45.6
|
1.0
|
ND
|
B:HEM901
|
2.0
|
36.6
|
1.0
|
NE2
|
B:HIS202
|
2.0
|
58.1
|
1.0
|
NB
|
B:HEM901
|
2.1
|
37.4
|
1.0
|
NC
|
B:HEM901
|
2.1
|
36.2
|
1.0
|
CD2
|
B:HIS100
|
3.0
|
46.0
|
1.0
|
CE1
|
B:HIS202
|
3.0
|
58.1
|
1.0
|
C1A
|
B:HEM901
|
3.0
|
39.1
|
1.0
|
C4D
|
B:HEM901
|
3.0
|
37.7
|
1.0
|
C4A
|
B:HEM901
|
3.0
|
39.3
|
1.0
|
CE1
|
B:HIS100
|
3.0
|
46.8
|
1.0
|
C1D
|
B:HEM901
|
3.0
|
36.7
|
1.0
|
CD2
|
B:HIS202
|
3.1
|
57.6
|
1.0
|
C1B
|
B:HEM901
|
3.1
|
39.0
|
1.0
|
C4C
|
B:HEM901
|
3.1
|
34.6
|
1.0
|
C4B
|
B:HEM901
|
3.1
|
37.5
|
1.0
|
C1C
|
B:HEM901
|
3.1
|
35.4
|
1.0
|
CHA
|
B:HEM901
|
3.3
|
37.4
|
1.0
|
CHD
|
B:HEM901
|
3.4
|
35.9
|
1.0
|
CHB
|
B:HEM901
|
3.4
|
39.4
|
1.0
|
CHC
|
B:HEM901
|
3.5
|
36.1
|
1.0
|
ND1
|
B:HIS202
|
4.1
|
57.2
|
1.0
|
ND1
|
B:HIS100
|
4.1
|
47.4
|
1.0
|
CG
|
B:HIS100
|
4.1
|
46.4
|
1.0
|
CG
|
B:HIS202
|
4.2
|
56.4
|
1.0
|
C2A
|
B:HEM901
|
4.2
|
37.4
|
1.0
|
C3A
|
B:HEM901
|
4.3
|
37.6
|
1.0
|
C3D
|
B:HEM901
|
4.3
|
38.4
|
1.0
|
C2D
|
B:HEM901
|
4.3
|
37.2
|
1.0
|
C3B
|
B:HEM901
|
4.3
|
40.0
|
1.0
|
C2B
|
B:HEM901
|
4.3
|
39.9
|
1.0
|
C3C
|
B:HEM901
|
4.4
|
33.1
|
1.0
|
C2C
|
B:HEM901
|
4.4
|
33.6
|
1.0
|
|
Iron binding site 4 out
of 6 in 1q90
Go back to
Iron Binding Sites List in 1q90
Iron binding site 4 out
of 6 in the Structure of the Cytochrome B6F (Plastohydroquinone : Plastocyanin Oxidoreductase) From Chlamydomonas Reinhardtii
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Structure of the Cytochrome B6F (Plastohydroquinone : Plastocyanin Oxidoreductase) From Chlamydomonas Reinhardtii within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe902
b:40.4
occ:1.00
|
FE
|
B:HEM902
|
0.0
|
40.4
|
1.0
|
NE2
|
B:HIS187
|
2.0
|
49.8
|
1.0
|
NE2
|
B:HIS86
|
2.0
|
50.7
|
1.0
|
ND
|
B:HEM902
|
2.0
|
41.3
|
1.0
|
NA
|
B:HEM902
|
2.0
|
43.1
|
1.0
|
NB
|
B:HEM902
|
2.1
|
43.2
|
1.0
|
NC
|
B:HEM902
|
2.1
|
42.6
|
1.0
|
CE1
|
B:HIS187
|
2.8
|
50.9
|
1.0
|
CE1
|
B:HIS86
|
3.0
|
50.0
|
1.0
|
CD2
|
B:HIS86
|
3.0
|
50.7
|
1.0
|
C1D
|
B:HEM902
|
3.0
|
41.6
|
1.0
|
C4C
|
B:HEM902
|
3.0
|
42.7
|
1.0
|
C4D
|
B:HEM902
|
3.1
|
42.0
|
1.0
|
C4A
|
B:HEM902
|
3.1
|
44.0
|
1.0
|
C4B
|
B:HEM902
|
3.1
|
44.5
|
1.0
|
C1C
|
B:HEM902
|
3.1
|
43.5
|
1.0
|
C1A
|
B:HEM902
|
3.1
|
43.1
|
1.0
|
C1B
|
B:HEM902
|
3.1
|
43.0
|
1.0
|
CD2
|
B:HIS187
|
3.1
|
49.1
|
1.0
|
CHD
|
B:HEM902
|
3.4
|
42.9
|
1.0
|
CHA
|
B:HEM902
|
3.4
|
43.0
|
1.0
|
CHC
|
B:HEM902
|
3.4
|
44.0
|
1.0
|
CHB
|
B:HEM902
|
3.4
|
43.5
|
1.0
|
ND1
|
B:HIS187
|
4.0
|
50.6
|
1.0
|
ND1
|
B:HIS86
|
4.1
|
50.9
|
1.0
|
CG
|
B:HIS86
|
4.1
|
51.8
|
1.0
|
CG
|
B:HIS187
|
4.2
|
48.9
|
1.0
|
C2D
|
B:HEM902
|
4.3
|
39.9
|
1.0
|
C3D
|
B:HEM902
|
4.3
|
42.4
|
1.0
|
C3C
|
B:HEM902
|
4.3
|
43.7
|
1.0
|
C3B
|
B:HEM902
|
4.3
|
44.5
|
1.0
|
C2C
|
B:HEM902
|
4.3
|
44.0
|
1.0
|
C3A
|
B:HEM902
|
4.3
|
44.2
|
1.0
|
C2A
|
B:HEM902
|
4.3
|
43.8
|
1.0
|
C2B
|
B:HEM902
|
4.3
|
43.8
|
1.0
|
OE1
|
B:GLN47
|
4.7
|
41.6
|
1.0
|
|
Iron binding site 5 out
of 6 in 1q90
Go back to
Iron Binding Sites List in 1q90
Iron binding site 5 out
of 6 in the Structure of the Cytochrome B6F (Plastohydroquinone : Plastocyanin Oxidoreductase) From Chlamydomonas Reinhardtii
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Structure of the Cytochrome B6F (Plastohydroquinone : Plastocyanin Oxidoreductase) From Chlamydomonas Reinhardtii within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe210
b:65.0
occ:1.00
|
FE1
|
C:FES210
|
0.0
|
65.0
|
1.0
|
ND1
|
C:HIS155
|
2.0
|
74.8
|
1.0
|
ND1
|
C:HIS136
|
2.0
|
83.9
|
1.0
|
S2
|
C:FES210
|
2.2
|
62.1
|
1.0
|
S1
|
C:FES210
|
2.2
|
63.4
|
1.0
|
FE2
|
C:FES210
|
2.7
|
62.0
|
1.0
|
CE1
|
C:HIS136
|
2.8
|
83.8
|
1.0
|
CE1
|
C:HIS155
|
2.9
|
75.1
|
1.0
|
CG
|
C:HIS155
|
3.0
|
76.4
|
1.0
|
CG
|
C:HIS136
|
3.0
|
84.1
|
1.0
|
CB
|
C:HIS155
|
3.4
|
77.6
|
1.0
|
CB
|
C:HIS136
|
3.5
|
84.3
|
1.0
|
N
|
C:HIS155
|
3.6
|
99.8
|
1.0
|
CB
|
C:CYS154
|
3.7
|
73.1
|
1.0
|
NE2
|
C:HIS136
|
3.9
|
83.5
|
1.0
|
N
|
C:LEU137
|
4.0
|
89.4
|
1.0
|
NE2
|
C:HIS155
|
4.0
|
75.5
|
1.0
|
CD2
|
C:HIS136
|
4.1
|
84.1
|
1.0
|
CB
|
C:LEU137
|
4.1
|
70.0
|
1.0
|
CD2
|
C:HIS155
|
4.1
|
76.1
|
1.0
|
CA
|
C:HIS155
|
4.1
|
99.6
|
1.0
|
SG
|
C:CYS152
|
4.2
|
80.3
|
1.0
|
C
|
C:CYS154
|
4.3
|
94.5
|
1.0
|
SG
|
C:CYS134
|
4.5
|
69.2
|
1.0
|
CA
|
C:CYS154
|
4.5
|
94.5
|
1.0
|
CA
|
C:LEU137
|
4.6
|
89.2
|
1.0
|
OG
|
C:SER157
|
4.6
|
83.5
|
1.0
|
CA
|
C:HIS136
|
4.8
|
81.1
|
1.0
|
CD2
|
C:LEU137
|
4.8
|
69.0
|
1.0
|
C
|
C:HIS136
|
4.8
|
80.7
|
1.0
|
C
|
C:HIS155
|
4.9
|
0.0
|
1.0
|
|
Iron binding site 6 out
of 6 in 1q90
Go back to
Iron Binding Sites List in 1q90
Iron binding site 6 out
of 6 in the Structure of the Cytochrome B6F (Plastohydroquinone : Plastocyanin Oxidoreductase) From Chlamydomonas Reinhardtii
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Structure of the Cytochrome B6F (Plastohydroquinone : Plastocyanin Oxidoreductase) From Chlamydomonas Reinhardtii within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe210
b:62.0
occ:1.00
|
FE2
|
C:FES210
|
0.0
|
62.0
|
1.0
|
SG
|
C:CYS152
|
2.1
|
80.3
|
1.0
|
SG
|
C:CYS134
|
2.1
|
69.2
|
1.0
|
S1
|
C:FES210
|
2.2
|
63.4
|
1.0
|
S2
|
C:FES210
|
2.3
|
62.1
|
1.0
|
FE1
|
C:FES210
|
2.7
|
65.0
|
1.0
|
CB
|
C:CYS134
|
3.1
|
68.4
|
1.0
|
CB
|
C:CYS152
|
3.2
|
77.7
|
1.0
|
CB
|
C:HIS136
|
3.7
|
84.3
|
1.0
|
OG
|
C:SER157
|
3.7
|
83.5
|
1.0
|
ND1
|
C:HIS136
|
3.9
|
83.9
|
1.0
|
CB
|
C:SER157
|
4.1
|
83.3
|
1.0
|
CG
|
C:HIS136
|
4.3
|
84.1
|
1.0
|
CB
|
C:CYS154
|
4.3
|
73.1
|
1.0
|
CB
|
C:CYS139
|
4.3
|
82.3
|
1.0
|
ND1
|
C:HIS155
|
4.5
|
74.8
|
1.0
|
N
|
C:LEU137
|
4.6
|
89.4
|
1.0
|
CA
|
C:CYS134
|
4.6
|
78.5
|
1.0
|
N
|
C:HIS155
|
4.6
|
99.8
|
1.0
|
CA
|
C:CYS152
|
4.7
|
84.0
|
1.0
|
CG2
|
C:VAL141
|
4.7
|
79.4
|
1.0
|
N
|
C:CYS139
|
4.7
|
85.3
|
1.0
|
CA
|
C:HIS136
|
4.8
|
81.1
|
1.0
|
N
|
C:HIS136
|
4.8
|
81.6
|
1.0
|
O
|
C:CYS139
|
4.8
|
85.9
|
1.0
|
SG
|
C:CYS139
|
4.9
|
84.0
|
1.0
|
N
|
C:SER157
|
5.0
|
0.1
|
1.0
|
C
|
C:CYS134
|
5.0
|
78.3
|
1.0
|
N
|
C:CYS154
|
5.0
|
94.4
|
1.0
|
OH
|
C:TYR159
|
5.0
|
0.8
|
1.0
|
|
Reference:
D.Stroebel,
Y.Choquet,
J.-L.Popot,
D.Picot.
An Atypical Haem in the Cytochrome B6F Complex Nature V. 426 413 2003.
ISSN: ISSN 0028-0836
PubMed: 14647374
DOI: 10.1038/NATURE02155
Page generated: Sat Aug 3 13:24:08 2024
|