Iron in PDB 4ogq: Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex
Enzymatic activity of Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex
All present enzymatic activity of Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex:
1.10.9.1;
Protein crystallography data
The structure of Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex, PDB code: 4ogq
was solved by
S.S.Hasan,
W.A.Cramer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.57 /
2.50
|
Space group
|
P 61 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
159.228,
159.228,
365.879,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
20.1 /
23.2
|
Other elements in 4ogq:
The structure of Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex
(pdb code 4ogq). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex, PDB code: 4ogq:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 4ogq
Go back to
Iron Binding Sites List in 4ogq
Iron binding site 1 out
of 6 in the Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:48.2
occ:1.00
|
FE
|
A:HEM301
|
0.0
|
48.2
|
1.0
|
NB
|
A:HEM301
|
2.1
|
55.3
|
1.0
|
NC
|
A:HEM301
|
2.1
|
65.7
|
1.0
|
NA
|
A:HEM301
|
2.1
|
63.8
|
1.0
|
ND
|
A:HEM301
|
2.1
|
54.5
|
1.0
|
NE2
|
A:HIS187
|
2.3
|
39.4
|
1.0
|
NE2
|
A:HIS86
|
2.4
|
37.9
|
1.0
|
C4D
|
A:HEM301
|
3.1
|
52.0
|
1.0
|
C4B
|
A:HEM301
|
3.1
|
44.7
|
1.0
|
C1D
|
A:HEM301
|
3.1
|
52.0
|
1.0
|
C4C
|
A:HEM301
|
3.1
|
52.1
|
1.0
|
C1C
|
A:HEM301
|
3.1
|
52.9
|
1.0
|
C1A
|
A:HEM301
|
3.1
|
45.2
|
1.0
|
C1B
|
A:HEM301
|
3.1
|
60.3
|
1.0
|
C4A
|
A:HEM301
|
3.1
|
45.6
|
1.0
|
CD2
|
A:HIS86
|
3.2
|
37.4
|
1.0
|
CE1
|
A:HIS187
|
3.3
|
49.6
|
1.0
|
CD2
|
A:HIS187
|
3.3
|
42.2
|
1.0
|
CHA
|
A:HEM301
|
3.4
|
46.9
|
1.0
|
CHD
|
A:HEM301
|
3.4
|
52.6
|
1.0
|
CHC
|
A:HEM301
|
3.4
|
48.5
|
1.0
|
CE1
|
A:HIS86
|
3.5
|
45.5
|
1.0
|
CHB
|
A:HEM301
|
3.5
|
56.1
|
1.0
|
C3D
|
A:HEM301
|
4.3
|
59.2
|
1.0
|
C2D
|
A:HEM301
|
4.3
|
51.9
|
1.0
|
C3B
|
A:HEM301
|
4.3
|
49.4
|
1.0
|
C2B
|
A:HEM301
|
4.3
|
47.9
|
1.0
|
C3C
|
A:HEM301
|
4.3
|
69.4
|
1.0
|
C2C
|
A:HEM301
|
4.3
|
59.7
|
1.0
|
C3A
|
A:HEM301
|
4.3
|
50.0
|
1.0
|
C2A
|
A:HEM301
|
4.3
|
54.3
|
1.0
|
CG
|
A:HIS86
|
4.4
|
55.7
|
1.0
|
ND1
|
A:HIS187
|
4.4
|
52.0
|
1.0
|
CG
|
A:HIS187
|
4.4
|
46.6
|
1.0
|
ND1
|
A:HIS86
|
4.5
|
44.7
|
1.0
|
NE2
|
A:GLN47
|
4.6
|
44.4
|
1.0
|
|
Iron binding site 2 out
of 6 in 4ogq
Go back to
Iron Binding Sites List in 4ogq
Iron binding site 2 out
of 6 in the Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe302
b:51.9
occ:1.00
|
FE
|
A:HEM302
|
0.0
|
51.9
|
1.0
|
NA
|
A:HEM302
|
2.0
|
43.7
|
1.0
|
NB
|
A:HEM302
|
2.0
|
73.8
|
1.0
|
NC
|
A:HEM302
|
2.1
|
60.4
|
1.0
|
ND
|
A:HEM302
|
2.1
|
71.2
|
1.0
|
NE2
|
A:HIS202
|
2.4
|
40.7
|
1.0
|
NE2
|
A:HIS100
|
2.5
|
53.1
|
1.0
|
CD2
|
A:HIS100
|
3.0
|
52.3
|
1.0
|
C4A
|
A:HEM302
|
3.0
|
59.3
|
1.0
|
C1C
|
A:HEM302
|
3.0
|
64.8
|
1.0
|
C1A
|
A:HEM302
|
3.0
|
53.6
|
1.0
|
C4B
|
A:HEM302
|
3.0
|
54.2
|
1.0
|
C1B
|
A:HEM302
|
3.1
|
54.7
|
1.0
|
C4C
|
A:HEM302
|
3.1
|
61.7
|
1.0
|
C4D
|
A:HEM302
|
3.1
|
51.7
|
1.0
|
C1D
|
A:HEM302
|
3.1
|
61.6
|
1.0
|
CD2
|
A:HIS202
|
3.3
|
44.7
|
1.0
|
CHC
|
A:HEM302
|
3.4
|
61.6
|
1.0
|
CHB
|
A:HEM302
|
3.4
|
58.4
|
1.0
|
CHA
|
A:HEM302
|
3.4
|
54.6
|
1.0
|
CE1
|
A:HIS202
|
3.4
|
65.5
|
1.0
|
CHD
|
A:HEM302
|
3.5
|
55.0
|
1.0
|
CE1
|
A:HIS100
|
3.7
|
75.7
|
1.0
|
C2C
|
A:HEM302
|
4.2
|
61.1
|
1.0
|
C3A
|
A:HEM302
|
4.2
|
56.6
|
1.0
|
C3C
|
A:HEM302
|
4.3
|
59.8
|
1.0
|
C2A
|
A:HEM302
|
4.3
|
53.8
|
1.0
|
C3B
|
A:HEM302
|
4.3
|
59.7
|
1.0
|
C2B
|
A:HEM302
|
4.3
|
57.4
|
1.0
|
C3D
|
A:HEM302
|
4.3
|
57.9
|
1.0
|
CG
|
A:HIS100
|
4.3
|
54.3
|
1.0
|
C2D
|
A:HEM302
|
4.3
|
56.5
|
1.0
|
CG
|
A:HIS202
|
4.5
|
61.9
|
1.0
|
ND1
|
A:HIS202
|
4.5
|
73.8
|
1.0
|
ND1
|
A:HIS100
|
4.6
|
76.7
|
1.0
|
|
Iron binding site 3 out
of 6 in 4ogq
Go back to
Iron Binding Sites List in 4ogq
Iron binding site 3 out
of 6 in the Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe303
b:59.3
occ:1.00
|
FE
|
A:HEM303
|
0.0
|
59.3
|
1.0
|
NB
|
A:HEM303
|
2.1
|
69.3
|
1.0
|
NC
|
A:HEM303
|
2.1
|
82.1
|
1.0
|
NA
|
A:HEM303
|
2.1
|
85.5
|
1.0
|
ND
|
A:HEM303
|
2.1
|
57.6
|
1.0
|
O
|
A:HOH401
|
2.5
|
59.7
|
1.0
|
C1C
|
A:HEM303
|
3.1
|
71.0
|
1.0
|
C4B
|
A:HEM303
|
3.1
|
71.1
|
1.0
|
C4A
|
A:HEM303
|
3.1
|
71.1
|
1.0
|
C1B
|
A:HEM303
|
3.1
|
63.8
|
1.0
|
C1A
|
A:HEM303
|
3.1
|
68.5
|
1.0
|
C4C
|
A:HEM303
|
3.1
|
54.9
|
1.0
|
C4D
|
A:HEM303
|
3.1
|
52.1
|
1.0
|
C1D
|
A:HEM303
|
3.1
|
49.2
|
1.0
|
CHC
|
A:HEM303
|
3.4
|
75.1
|
1.0
|
CHB
|
A:HEM303
|
3.5
|
60.1
|
1.0
|
CHD
|
A:HEM303
|
3.5
|
49.5
|
1.0
|
CHA
|
A:HEM303
|
3.5
|
52.9
|
1.0
|
CZ
|
B:PHE40
|
3.8
|
52.1
|
1.0
|
C6
|
B:UMQ203
|
3.8
|
0.9
|
0.5
|
CE2
|
B:PHE40
|
4.0
|
62.1
|
1.0
|
C2C
|
A:HEM303
|
4.3
|
64.7
|
1.0
|
C3A
|
A:HEM303
|
4.3
|
83.6
|
1.0
|
C3B
|
A:HEM303
|
4.3
|
68.8
|
1.0
|
C2B
|
A:HEM303
|
4.3
|
66.2
|
1.0
|
C2A
|
A:HEM303
|
4.3
|
81.2
|
1.0
|
C3C
|
A:HEM303
|
4.3
|
65.4
|
1.0
|
C3D
|
A:HEM303
|
4.3
|
52.0
|
1.0
|
C2D
|
A:HEM303
|
4.3
|
56.0
|
1.0
|
CMA
|
A:HEM302
|
4.4
|
49.0
|
1.0
|
O
|
A:TYR34
|
4.4
|
61.3
|
1.0
|
CA
|
A:GLY38
|
4.5
|
47.5
|
1.0
|
O6
|
B:UMQ203
|
4.5
|
1.0
|
0.5
|
O2A
|
A:HEM302
|
4.5
|
65.7
|
1.0
|
O5
|
B:UMQ203
|
4.5
|
88.3
|
0.5
|
N
|
A:GLY38
|
4.6
|
48.3
|
1.0
|
CAA
|
A:HEM302
|
4.6
|
46.2
|
1.0
|
C5
|
B:UMQ203
|
4.7
|
94.5
|
0.5
|
CE1
|
B:PHE40
|
4.7
|
50.2
|
1.0
|
CBA
|
A:HEM302
|
4.9
|
58.3
|
1.0
|
|
Iron binding site 4 out
of 6 in 4ogq
Go back to
Iron Binding Sites List in 4ogq
Iron binding site 4 out
of 6 in the Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe301
b:62.9
occ:1.00
|
FE
|
C:HEM301
|
0.0
|
62.9
|
1.0
|
NA
|
C:HEM301
|
2.0
|
60.9
|
1.0
|
NC
|
C:HEM301
|
2.0
|
46.4
|
1.0
|
NB
|
C:HEM301
|
2.0
|
62.3
|
1.0
|
ND
|
C:HEM301
|
2.1
|
71.6
|
1.0
|
NE2
|
C:HIS26
|
2.5
|
73.8
|
1.0
|
N
|
C:TYR1
|
2.6
|
87.3
|
1.0
|
C4A
|
C:HEM301
|
3.0
|
71.3
|
1.0
|
C1A
|
C:HEM301
|
3.0
|
75.7
|
1.0
|
C1B
|
C:HEM301
|
3.1
|
59.9
|
1.0
|
C1C
|
C:HEM301
|
3.1
|
63.5
|
1.0
|
C4C
|
C:HEM301
|
3.1
|
59.2
|
1.0
|
C4B
|
C:HEM301
|
3.1
|
49.5
|
1.0
|
C4D
|
C:HEM301
|
3.1
|
74.1
|
1.0
|
C1D
|
C:HEM301
|
3.1
|
69.4
|
1.0
|
CA
|
C:TYR1
|
3.2
|
77.6
|
1.0
|
CD2
|
C:HIS26
|
3.4
|
72.6
|
1.0
|
CHB
|
C:HEM301
|
3.4
|
68.1
|
1.0
|
CHC
|
C:HEM301
|
3.4
|
50.8
|
1.0
|
CHA
|
C:HEM301
|
3.4
|
71.9
|
1.0
|
CHD
|
C:HEM301
|
3.4
|
65.4
|
1.0
|
CE1
|
C:HIS26
|
3.6
|
88.8
|
1.0
|
C
|
C:TYR1
|
3.8
|
81.6
|
1.0
|
O
|
C:TYR1
|
4.1
|
79.1
|
1.0
|
C3A
|
C:HEM301
|
4.2
|
67.9
|
1.0
|
C2A
|
C:HEM301
|
4.2
|
73.6
|
1.0
|
C2C
|
C:HEM301
|
4.3
|
60.1
|
1.0
|
C2B
|
C:HEM301
|
4.3
|
60.4
|
1.0
|
C3B
|
C:HEM301
|
4.3
|
58.0
|
1.0
|
C3C
|
C:HEM301
|
4.3
|
55.9
|
1.0
|
C3D
|
C:HEM301
|
4.3
|
80.8
|
1.0
|
C2D
|
C:HEM301
|
4.3
|
71.7
|
1.0
|
CB
|
C:TYR1
|
4.5
|
77.1
|
1.0
|
CG
|
C:HIS26
|
4.6
|
82.8
|
1.0
|
ND1
|
C:HIS26
|
4.6
|
0.6
|
1.0
|
N
|
C:PRO2
|
4.7
|
73.3
|
1.0
|
CG
|
C:TYR1
|
4.7
|
81.0
|
1.0
|
CE3
|
C:TRP4
|
4.9
|
82.1
|
1.0
|
ND2
|
C:ASN154
|
5.0
|
0.1
|
1.0
|
CD
|
C:PRO2
|
5.0
|
68.1
|
1.0
|
|
Iron binding site 5 out
of 6 in 4ogq
Go back to
Iron Binding Sites List in 4ogq
Iron binding site 5 out
of 6 in the Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe205
b:0.2
occ:1.00
|
FE1
|
D:FES205
|
0.0
|
0.2
|
1.0
|
S2
|
D:FES205
|
2.2
|
97.6
|
1.0
|
S1
|
D:FES205
|
2.2
|
96.5
|
1.0
|
SG
|
D:CYS108
|
2.3
|
0.4
|
1.0
|
SG
|
D:CYS126
|
2.3
|
0.7
|
1.0
|
CB
|
D:CYS108
|
3.0
|
98.5
|
1.0
|
FE2
|
D:FES205
|
3.1
|
0.2
|
1.0
|
CB
|
D:CYS126
|
3.3
|
0.6
|
1.0
|
OG
|
D:SER131
|
4.1
|
0.4
|
1.0
|
CB
|
D:SER131
|
4.2
|
0.6
|
1.0
|
CB
|
D:HIS110
|
4.2
|
0.9
|
1.0
|
CB
|
D:CYS128
|
4.4
|
98.8
|
1.0
|
CB
|
D:CYS113
|
4.5
|
93.4
|
1.0
|
CA
|
D:CYS108
|
4.5
|
99.3
|
1.0
|
ND1
|
D:HIS110
|
4.5
|
0.9
|
1.0
|
N
|
D:CYS113
|
4.7
|
99.2
|
1.0
|
CA
|
D:CYS126
|
4.7
|
0.9
|
1.0
|
O
|
D:CYS113
|
4.8
|
0.5
|
1.0
|
N
|
D:HIS129
|
4.8
|
0.9
|
1.0
|
ND1
|
D:HIS129
|
4.9
|
0.1
|
1.0
|
CG
|
D:HIS110
|
4.9
|
0.8
|
1.0
|
N
|
D:LEU111
|
4.9
|
0.3
|
1.0
|
|
Iron binding site 6 out
of 6 in 4ogq
Go back to
Iron Binding Sites List in 4ogq
Iron binding site 6 out
of 6 in the Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe205
b:0.2
occ:1.00
|
FE2
|
D:FES205
|
0.0
|
0.2
|
1.0
|
ND1
|
D:HIS129
|
2.1
|
0.1
|
1.0
|
ND1
|
D:HIS110
|
2.1
|
0.9
|
1.0
|
S2
|
D:FES205
|
2.2
|
97.6
|
1.0
|
S1
|
D:FES205
|
2.2
|
96.5
|
1.0
|
CE1
|
D:HIS110
|
2.9
|
0.7
|
1.0
|
CG
|
D:HIS129
|
3.0
|
0.1
|
1.0
|
CE1
|
D:HIS129
|
3.1
|
0.4
|
1.0
|
FE1
|
D:FES205
|
3.1
|
0.2
|
1.0
|
CG
|
D:HIS110
|
3.2
|
0.8
|
1.0
|
CB
|
D:HIS129
|
3.3
|
0.7
|
1.0
|
CB
|
D:HIS110
|
3.6
|
0.9
|
1.0
|
N
|
D:HIS129
|
3.8
|
0.9
|
1.0
|
CB
|
D:CYS128
|
3.9
|
98.8
|
1.0
|
NE2
|
D:HIS110
|
4.1
|
0.1
|
1.0
|
CD2
|
D:HIS129
|
4.1
|
0.2
|
1.0
|
CA
|
D:HIS129
|
4.1
|
0.3
|
1.0
|
NE2
|
D:HIS129
|
4.1
|
0.9
|
1.0
|
CD2
|
D:HIS110
|
4.2
|
0.9
|
1.0
|
CB
|
D:LEU111
|
4.3
|
0.6
|
1.0
|
CG
|
D:PRO143
|
4.5
|
0.9
|
1.0
|
C
|
D:CYS128
|
4.5
|
0.3
|
1.0
|
N
|
D:LEU111
|
4.5
|
0.3
|
1.0
|
SG
|
D:CYS126
|
4.6
|
0.7
|
1.0
|
SG
|
D:CYS108
|
4.6
|
0.4
|
1.0
|
OG
|
D:SER131
|
4.7
|
0.4
|
1.0
|
CA
|
D:CYS128
|
4.8
|
0.0
|
1.0
|
CA
|
D:HIS110
|
4.9
|
0.1
|
1.0
|
C
|
D:HIS110
|
4.9
|
0.8
|
1.0
|
C
|
D:HIS129
|
4.9
|
0.2
|
1.0
|
|
Reference:
S.S.Hasan,
W.A.Cramer.
Internal Lipid Architecture of the Hetero-Oligomeric Cytochrome B6F Complex. Structure V. 22 1008 2014.
ISSN: ISSN 0969-2126
PubMed: 24931468
DOI: 10.1016/J.STR.2014.05.004
Page generated: Mon Aug 5 08:09:45 2024
|