Iron in PDB 4i7z: Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain
Enzymatic activity of Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain
All present enzymatic activity of Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain:
1.10.9.1;
Protein crystallography data
The structure of Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain, PDB code: 4i7z
was solved by
S.S.Hasan,
J.T.Stofleth,
E.Yamashita,
W.A.Cramer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.52 /
2.80
|
Space group
|
P 61 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
159.451,
159.451,
362.746,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
24.8 /
27.2
|
Other elements in 4i7z:
The structure of Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain
(pdb code 4i7z). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain, PDB code: 4i7z:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 4i7z
Go back to
Iron Binding Sites List in 4i7z
Iron binding site 1 out
of 4 in the Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain
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 Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:57.0
occ:1.00
|
FE
|
A:HEM301
|
0.0
|
57.0
|
1.0
|
NC
|
A:HEM301
|
2.0
|
54.0
|
1.0
|
NB
|
A:HEM301
|
2.0
|
51.5
|
1.0
|
ND
|
A:HEM301
|
2.1
|
51.8
|
1.0
|
NA
|
A:HEM301
|
2.1
|
49.3
|
1.0
|
NE2
|
A:HIS86
|
2.1
|
51.7
|
1.0
|
NE2
|
A:HIS187
|
2.2
|
54.1
|
1.0
|
CE1
|
A:HIS187
|
3.0
|
55.2
|
1.0
|
CE1
|
A:HIS86
|
3.0
|
51.8
|
1.0
|
C1D
|
A:HEM301
|
3.0
|
53.0
|
1.0
|
C4C
|
A:HEM301
|
3.0
|
57.5
|
1.0
|
C4B
|
A:HEM301
|
3.1
|
50.6
|
1.0
|
C4D
|
A:HEM301
|
3.1
|
51.3
|
1.0
|
C1C
|
A:HEM301
|
3.1
|
52.5
|
1.0
|
C1B
|
A:HEM301
|
3.1
|
49.4
|
1.0
|
HE1
|
A:HIS187
|
3.1
|
66.2
|
1.0
|
C1A
|
A:HEM301
|
3.1
|
46.6
|
1.0
|
C4A
|
A:HEM301
|
3.1
|
49.5
|
1.0
|
CD2
|
A:HIS86
|
3.1
|
53.9
|
1.0
|
HE1
|
A:HIS86
|
3.1
|
62.2
|
1.0
|
CD2
|
A:HIS187
|
3.3
|
55.4
|
1.0
|
HD2
|
A:HIS86
|
3.4
|
64.7
|
1.0
|
CHD
|
A:HEM301
|
3.4
|
57.8
|
1.0
|
CHC
|
A:HEM301
|
3.4
|
50.5
|
1.0
|
CHA
|
A:HEM301
|
3.5
|
46.2
|
1.0
|
CHB
|
A:HEM301
|
3.5
|
50.0
|
1.0
|
HD2
|
A:HIS187
|
3.5
|
66.4
|
1.0
|
HE21
|
A:GLN47
|
3.9
|
72.7
|
1.0
|
ND1
|
A:HIS86
|
4.1
|
53.0
|
1.0
|
HE22
|
A:GLN47
|
4.1
|
72.7
|
1.0
|
ND1
|
A:HIS187
|
4.2
|
57.1
|
1.0
|
CG
|
A:HIS86
|
4.2
|
54.2
|
1.0
|
C3C
|
A:HEM301
|
4.3
|
58.1
|
1.0
|
C2D
|
A:HEM301
|
4.3
|
49.1
|
1.0
|
C3B
|
A:HEM301
|
4.3
|
46.4
|
1.0
|
C2C
|
A:HEM301
|
4.3
|
54.6
|
1.0
|
C2B
|
A:HEM301
|
4.3
|
45.5
|
1.0
|
C3D
|
A:HEM301
|
4.3
|
52.7
|
1.0
|
CG
|
A:HIS187
|
4.3
|
57.3
|
1.0
|
C2A
|
A:HEM301
|
4.3
|
46.9
|
1.0
|
C3A
|
A:HEM301
|
4.3
|
47.5
|
1.0
|
NE2
|
A:GLN47
|
4.4
|
60.6
|
1.0
|
HA2
|
A:GLY51
|
4.4
|
69.2
|
1.0
|
HA3
|
A:GLY135
|
4.5
|
77.8
|
1.0
|
HA3
|
A:GLY51
|
4.7
|
69.2
|
1.0
|
HD2
|
A:PHE131
|
4.7
|
68.7
|
1.0
|
HD12
|
A:LEU138
|
4.7
|
71.2
|
1.0
|
HE3
|
A:MET54
|
4.8
|
89.2
|
1.0
|
HA2
|
A:GLY135
|
4.8
|
77.8
|
1.0
|
HD1
|
A:HIS86
|
4.9
|
63.6
|
1.0
|
HD1
|
A:HIS187
|
4.9
|
68.6
|
1.0
|
HE1
|
A:MET54
|
5.0
|
89.2
|
1.0
|
|
Iron binding site 2 out
of 4 in 4i7z
Go back to
Iron Binding Sites List in 4i7z
Iron binding site 2 out
of 4 in the Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain
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 Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe302
b:61.5
occ:1.00
|
FE
|
A:HEM302
|
0.0
|
61.5
|
1.0
|
NA
|
A:HEM302
|
2.0
|
63.3
|
1.0
|
NB
|
A:HEM302
|
2.1
|
60.8
|
1.0
|
NC
|
A:HEM302
|
2.1
|
69.5
|
1.0
|
NE2
|
A:HIS100
|
2.1
|
60.8
|
1.0
|
ND
|
A:HEM302
|
2.1
|
72.2
|
1.0
|
NE2
|
A:HIS202
|
2.2
|
52.8
|
1.0
|
CE1
|
A:HIS100
|
2.9
|
62.3
|
1.0
|
HE1
|
A:HIS100
|
3.0
|
74.8
|
1.0
|
C4C
|
A:HEM302
|
3.0
|
70.9
|
1.0
|
CE1
|
A:HIS202
|
3.0
|
54.7
|
1.0
|
C1A
|
A:HEM302
|
3.0
|
64.5
|
1.0
|
C4A
|
A:HEM302
|
3.0
|
61.4
|
1.0
|
C1D
|
A:HEM302
|
3.1
|
73.3
|
1.0
|
C1B
|
A:HEM302
|
3.1
|
60.4
|
1.0
|
C1C
|
A:HEM302
|
3.1
|
67.7
|
1.0
|
C4D
|
A:HEM302
|
3.1
|
71.7
|
1.0
|
C4B
|
A:HEM302
|
3.1
|
61.2
|
1.0
|
HE1
|
A:HIS202
|
3.1
|
65.7
|
1.0
|
CD2
|
A:HIS100
|
3.1
|
63.0
|
1.0
|
CD2
|
A:HIS202
|
3.2
|
57.0
|
1.0
|
CHD
|
A:HEM302
|
3.4
|
73.8
|
1.0
|
HD2
|
A:HIS100
|
3.4
|
75.6
|
1.0
|
CHA
|
A:HEM302
|
3.4
|
69.0
|
1.0
|
CHB
|
A:HEM302
|
3.4
|
60.2
|
1.0
|
CHC
|
A:HEM302
|
3.5
|
63.6
|
1.0
|
HD2
|
A:HIS202
|
3.5
|
68.3
|
1.0
|
ND1
|
A:HIS100
|
4.1
|
64.4
|
1.0
|
HD11
|
A:ILE206
|
4.1
|
82.2
|
1.0
|
ND1
|
A:HIS202
|
4.2
|
56.4
|
1.0
|
CG
|
A:HIS100
|
4.2
|
63.4
|
1.0
|
C3C
|
A:HEM302
|
4.2
|
71.2
|
1.0
|
C2C
|
A:HEM302
|
4.2
|
67.5
|
1.0
|
C2A
|
A:HEM302
|
4.2
|
60.4
|
1.0
|
C3A
|
A:HEM302
|
4.3
|
60.4
|
1.0
|
C2B
|
A:HEM302
|
4.3
|
57.2
|
1.0
|
C2D
|
A:HEM302
|
4.3
|
73.1
|
1.0
|
C3D
|
A:HEM302
|
4.3
|
72.2
|
1.0
|
HG21
|
A:VAL104
|
4.3
|
68.9
|
1.0
|
C3B
|
A:HEM302
|
4.3
|
59.5
|
1.0
|
CG
|
A:HIS202
|
4.3
|
57.0
|
1.0
|
HG22
|
A:THR117
|
4.6
|
82.8
|
1.0
|
HD1
|
A:HIS100
|
4.8
|
77.3
|
1.0
|
HA3
|
A:GLY121
|
4.8
|
76.0
|
1.0
|
HD13
|
A:ILE206
|
4.8
|
82.2
|
1.0
|
CD1
|
A:ILE206
|
4.8
|
68.5
|
1.0
|
HA2
|
A:GLY121
|
4.9
|
76.0
|
1.0
|
HD1
|
A:HIS202
|
4.9
|
67.6
|
1.0
|
HA3
|
A:GLY37
|
4.9
|
76.8
|
1.0
|
HA2
|
A:GLY37
|
5.0
|
76.8
|
1.0
|
|
Iron binding site 3 out
of 4 in 4i7z
Go back to
Iron Binding Sites List in 4i7z
Iron binding site 3 out
of 4 in the Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain
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 Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe303
b:71.7
occ:1.00
|
FE
|
A:HEM303
|
0.0
|
71.7
|
1.0
|
NA
|
A:HEM303
|
2.1
|
78.9
|
1.0
|
NB
|
A:HEM303
|
2.1
|
73.4
|
1.0
|
NC
|
A:HEM303
|
2.1
|
64.2
|
1.0
|
ND
|
A:HEM303
|
2.1
|
69.9
|
1.0
|
O
|
A:HOH401
|
2.2
|
47.4
|
1.0
|
C1B
|
A:HEM303
|
3.0
|
77.8
|
1.0
|
C4A
|
A:HEM303
|
3.1
|
80.2
|
1.0
|
C4B
|
A:HEM303
|
3.1
|
73.7
|
1.0
|
C1A
|
A:HEM303
|
3.1
|
78.1
|
1.0
|
C1D
|
A:HEM303
|
3.1
|
68.3
|
1.0
|
C4C
|
A:HEM303
|
3.1
|
61.5
|
1.0
|
C4D
|
A:HEM303
|
3.1
|
72.9
|
1.0
|
C1C
|
A:HEM303
|
3.1
|
65.5
|
1.0
|
HE2
|
B:PHE40
|
3.3
|
92.0
|
1.0
|
CHB
|
A:HEM303
|
3.4
|
80.5
|
1.0
|
CHD
|
A:HEM303
|
3.4
|
64.2
|
1.0
|
CHA
|
A:HEM303
|
3.5
|
74.9
|
1.0
|
CHC
|
A:HEM303
|
3.5
|
69.6
|
1.0
|
HZ
|
B:PHE40
|
3.6
|
92.1
|
1.0
|
HA3
|
A:GLY38
|
3.8
|
74.5
|
1.0
|
CE2
|
B:PHE40
|
3.8
|
76.7
|
1.0
|
CZ
|
B:PHE40
|
3.9
|
76.7
|
1.0
|
C2B
|
A:HEM303
|
4.2
|
77.6
|
1.0
|
C3B
|
A:HEM303
|
4.2
|
75.9
|
1.0
|
C3A
|
A:HEM303
|
4.3
|
81.8
|
1.0
|
C2A
|
A:HEM303
|
4.3
|
81.8
|
1.0
|
H
|
A:GLY38
|
4.3
|
79.0
|
1.0
|
C2D
|
A:HEM303
|
4.3
|
70.7
|
1.0
|
C3C
|
A:HEM303
|
4.3
|
59.2
|
1.0
|
C3D
|
A:HEM303
|
4.3
|
74.0
|
1.0
|
C2C
|
A:HEM303
|
4.3
|
62.9
|
1.0
|
O
|
A:TYR34
|
4.3
|
66.9
|
1.0
|
CMA
|
A:HEM302
|
4.4
|
56.6
|
1.0
|
O2A
|
A:HEM302
|
4.4
|
68.4
|
1.0
|
CA
|
A:GLY38
|
4.5
|
62.1
|
1.0
|
HA
|
A:CYS35
|
4.5
|
72.6
|
1.0
|
HA2
|
A:GLY38
|
4.6
|
74.5
|
1.0
|
CAA
|
A:HEM302
|
4.7
|
56.7
|
1.0
|
N
|
A:GLY38
|
4.7
|
65.8
|
1.0
|
CD2
|
B:PHE40
|
4.9
|
76.5
|
1.0
|
CGA
|
A:HEM302
|
4.9
|
64.9
|
1.0
|
|
Iron binding site 4 out
of 4 in 4i7z
Go back to
Iron Binding Sites List in 4i7z
Iron binding site 4 out
of 4 in the Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain
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 Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe301
b:79.8
occ:1.00
|
FE
|
C:HEM301
|
0.0
|
79.8
|
1.0
|
H1
|
C:TYR1
|
1.5
|
98.4
|
1.0
|
NC
|
C:HEM301
|
2.0
|
78.5
|
1.0
|
ND
|
C:HEM301
|
2.0
|
83.5
|
1.0
|
NA
|
C:HEM301
|
2.1
|
81.8
|
1.0
|
NB
|
C:HEM301
|
2.1
|
77.4
|
1.0
|
N
|
C:TYR1
|
2.2
|
82.0
|
1.0
|
NE2
|
C:HIS26
|
2.2
|
86.6
|
1.0
|
H2
|
C:TYR1
|
2.3
|
98.4
|
1.0
|
H3
|
C:TYR1
|
2.9
|
98.4
|
1.0
|
C4C
|
C:HEM301
|
2.9
|
81.0
|
1.0
|
HA
|
C:TYR1
|
3.0
|
96.5
|
1.0
|
C1D
|
C:HEM301
|
3.0
|
83.4
|
1.0
|
C1C
|
C:HEM301
|
3.0
|
78.1
|
1.0
|
C1A
|
C:HEM301
|
3.1
|
84.0
|
1.0
|
C4D
|
C:HEM301
|
3.1
|
85.9
|
1.0
|
C4A
|
C:HEM301
|
3.1
|
81.4
|
1.0
|
CA
|
C:TYR1
|
3.1
|
80.5
|
1.0
|
C1B
|
C:HEM301
|
3.1
|
78.0
|
1.0
|
C4B
|
C:HEM301
|
3.1
|
76.2
|
1.0
|
CE1
|
C:HIS26
|
3.2
|
88.3
|
1.0
|
CD2
|
C:HIS26
|
3.2
|
84.9
|
1.0
|
CHD
|
C:HEM301
|
3.3
|
80.9
|
1.0
|
HE1
|
C:HIS26
|
3.3
|
0.9
|
1.0
|
HD2
|
C:HIS26
|
3.4
|
0.9
|
1.0
|
CHA
|
C:HEM301
|
3.4
|
85.8
|
1.0
|
CHC
|
C:HEM301
|
3.5
|
76.1
|
1.0
|
CHB
|
C:HEM301
|
3.5
|
79.2
|
1.0
|
C
|
C:TYR1
|
3.8
|
79.3
|
1.0
|
O
|
C:TYR1
|
4.0
|
79.4
|
1.0
|
HE3
|
C:TRP4
|
4.1
|
0.2
|
1.0
|
C3C
|
C:HEM301
|
4.1
|
83.0
|
1.0
|
C2C
|
C:HEM301
|
4.2
|
80.2
|
1.0
|
C2D
|
C:HEM301
|
4.3
|
86.3
|
1.0
|
C3D
|
C:HEM301
|
4.3
|
88.2
|
1.0
|
C2A
|
C:HEM301
|
4.3
|
84.1
|
1.0
|
C3A
|
C:HEM301
|
4.3
|
82.7
|
1.0
|
ND1
|
C:HIS26
|
4.3
|
87.9
|
1.0
|
C2B
|
C:HEM301
|
4.4
|
77.8
|
1.0
|
C3B
|
C:HEM301
|
4.4
|
77.6
|
1.0
|
CG
|
C:HIS26
|
4.4
|
86.2
|
1.0
|
CB
|
C:TYR1
|
4.5
|
81.7
|
1.0
|
HD3
|
C:PRO2
|
4.5
|
96.4
|
1.0
|
HG
|
C:CYS22
|
4.6
|
0.7
|
1.0
|
HA3
|
C:GLY158
|
4.6
|
0.6
|
1.0
|
N
|
C:PRO2
|
4.7
|
79.1
|
1.0
|
CG
|
C:TYR1
|
4.7
|
82.5
|
1.0
|
H
|
C:GLY158
|
4.8
|
0.1
|
1.0
|
CE3
|
C:TRP4
|
4.9
|
84.3
|
1.0
|
HB2
|
C:TYR1
|
4.9
|
98.1
|
1.0
|
HZ3
|
C:TRP4
|
4.9
|
0.8
|
1.0
|
OD1
|
C:ASN154
|
4.9
|
91.5
|
1.0
|
HB2
|
C:TRP4
|
4.9
|
0.2
|
1.0
|
|
Reference:
S.S.Hasan,
J.T.Stofleth,
E.Yamashita,
W.A.Cramer.
Lipid-Induced Conformational Changes Within the Cytochrome B6F Complex of Oxygenic Photosynthesis. Biochemistry V. 52 2649 2013.
ISSN: ISSN 0006-2960
PubMed: 23514009
DOI: 10.1021/BI301638H
Page generated: Mon Aug 5 03:53:36 2024
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