Iron in PDB 4pv1: Cytochrome B6F Structure From M. Laminosus with the Quinone Analog Inhibitor Stigmatellin
Enzymatic activity of Cytochrome B6F Structure From M. Laminosus with the Quinone Analog Inhibitor Stigmatellin
All present enzymatic activity of Cytochrome B6F Structure From M. Laminosus with the Quinone Analog Inhibitor Stigmatellin:
1.10.9.1;
Protein crystallography data
The structure of Cytochrome B6F Structure From M. Laminosus with the Quinone Analog Inhibitor Stigmatellin, PDB code: 4pv1
was solved by
S.S.Hasan,
E.Yamashita,
W.A.Cramer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.34 /
3.00
|
Space group
|
P 61 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
159.085,
159.085,
361.322,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
21.6 /
24.7
|
Other elements in 4pv1:
The structure of Cytochrome B6F Structure From M. Laminosus with the Quinone Analog Inhibitor Stigmatellin also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Cytochrome B6F Structure From M. Laminosus with the Quinone Analog Inhibitor Stigmatellin
(pdb code 4pv1). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Cytochrome B6F Structure From M. Laminosus with the Quinone Analog Inhibitor Stigmatellin, PDB code: 4pv1:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 4pv1
Go back to
Iron Binding Sites List in 4pv1
Iron binding site 1 out
of 6 in the Cytochrome B6F Structure From M. Laminosus with the Quinone Analog Inhibitor Stigmatellin
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Cytochrome B6F Structure From M. Laminosus with the Quinone Analog Inhibitor Stigmatellin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe303
b:63.3
occ:1.00
|
FE
|
A:HEM303
|
0.0
|
63.3
|
1.0
|
NC
|
A:HEM303
|
2.0
|
71.7
|
1.0
|
NE2
|
A:HIS187
|
2.1
|
54.8
|
1.0
|
NA
|
A:HEM303
|
2.1
|
65.4
|
1.0
|
ND
|
A:HEM303
|
2.1
|
59.3
|
1.0
|
NB
|
A:HEM303
|
2.1
|
64.5
|
1.0
|
NE2
|
A:HIS86
|
2.1
|
45.6
|
1.0
|
CE1
|
A:HIS187
|
2.9
|
50.8
|
1.0
|
CE1
|
A:HIS86
|
2.9
|
56.3
|
1.0
|
C4C
|
A:HEM303
|
3.0
|
72.2
|
1.0
|
C1D
|
A:HEM303
|
3.1
|
70.5
|
1.0
|
C1C
|
A:HEM303
|
3.1
|
79.9
|
1.0
|
C4D
|
A:HEM303
|
3.1
|
65.4
|
1.0
|
C1A
|
A:HEM303
|
3.1
|
68.6
|
1.0
|
C4A
|
A:HEM303
|
3.1
|
63.1
|
1.0
|
C1B
|
A:HEM303
|
3.1
|
71.7
|
1.0
|
C4B
|
A:HEM303
|
3.1
|
59.2
|
1.0
|
CD2
|
A:HIS187
|
3.2
|
71.5
|
1.0
|
CD2
|
A:HIS86
|
3.3
|
63.6
|
1.0
|
CHD
|
A:HEM303
|
3.4
|
70.2
|
1.0
|
CHA
|
A:HEM303
|
3.4
|
72.1
|
1.0
|
CHC
|
A:HEM303
|
3.5
|
77.1
|
1.0
|
CHB
|
A:HEM303
|
3.5
|
67.5
|
1.0
|
ND1
|
A:HIS187
|
4.1
|
53.4
|
1.0
|
ND1
|
A:HIS86
|
4.1
|
58.6
|
1.0
|
CG
|
A:HIS187
|
4.3
|
62.4
|
1.0
|
C3C
|
A:HEM303
|
4.3
|
82.6
|
1.0
|
C2D
|
A:HEM303
|
4.3
|
58.3
|
1.0
|
C2C
|
A:HEM303
|
4.3
|
73.2
|
1.0
|
C3D
|
A:HEM303
|
4.3
|
65.8
|
1.0
|
C2A
|
A:HEM303
|
4.3
|
52.1
|
1.0
|
C3A
|
A:HEM303
|
4.3
|
58.5
|
1.0
|
CG
|
A:HIS86
|
4.3
|
55.3
|
1.0
|
C2B
|
A:HEM303
|
4.3
|
66.5
|
1.0
|
C3B
|
A:HEM303
|
4.3
|
64.1
|
1.0
|
NE2
|
A:GLN47
|
4.5
|
79.1
|
1.0
|
|
Iron binding site 2 out
of 6 in 4pv1
Go back to
Iron Binding Sites List in 4pv1
Iron binding site 2 out
of 6 in the Cytochrome B6F Structure From M. Laminosus with the Quinone Analog Inhibitor Stigmatellin
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Cytochrome B6F Structure From M. Laminosus with the Quinone Analog Inhibitor Stigmatellin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe304
b:62.2
occ:1.00
|
FE
|
A:HEM304
|
0.0
|
62.2
|
1.0
|
NC
|
A:HEM304
|
2.1
|
67.1
|
1.0
|
ND
|
A:HEM304
|
2.1
|
61.3
|
1.0
|
NA
|
A:HEM304
|
2.1
|
46.9
|
1.0
|
NB
|
A:HEM304
|
2.1
|
61.0
|
1.0
|
NE2
|
A:HIS100
|
2.2
|
72.5
|
1.0
|
NE2
|
A:HIS202
|
2.2
|
76.5
|
1.0
|
CD2
|
A:HIS100
|
3.0
|
71.5
|
1.0
|
CE1
|
A:HIS202
|
3.0
|
73.8
|
1.0
|
C4C
|
A:HEM304
|
3.0
|
65.9
|
1.0
|
C1D
|
A:HEM304
|
3.0
|
68.4
|
1.0
|
C4D
|
A:HEM304
|
3.0
|
71.5
|
1.0
|
C1C
|
A:HEM304
|
3.1
|
68.8
|
1.0
|
C1A
|
A:HEM304
|
3.1
|
64.9
|
1.0
|
C4A
|
A:HEM304
|
3.1
|
63.5
|
1.0
|
C4B
|
A:HEM304
|
3.1
|
65.5
|
1.0
|
C1B
|
A:HEM304
|
3.1
|
66.1
|
1.0
|
CD2
|
A:HIS202
|
3.3
|
81.5
|
1.0
|
CE1
|
A:HIS100
|
3.3
|
77.2
|
1.0
|
CHD
|
A:HEM304
|
3.4
|
72.5
|
1.0
|
CHA
|
A:HEM304
|
3.4
|
68.5
|
1.0
|
CHC
|
A:HEM304
|
3.4
|
66.7
|
1.0
|
CHB
|
A:HEM304
|
3.5
|
57.8
|
1.0
|
ND1
|
A:HIS202
|
4.2
|
68.0
|
1.0
|
CG
|
A:HIS100
|
4.2
|
77.7
|
1.0
|
C3C
|
A:HEM304
|
4.2
|
59.4
|
1.0
|
C2C
|
A:HEM304
|
4.2
|
68.4
|
1.0
|
C3D
|
A:HEM304
|
4.3
|
61.3
|
1.0
|
C2D
|
A:HEM304
|
4.3
|
66.7
|
1.0
|
C2A
|
A:HEM304
|
4.3
|
74.3
|
1.0
|
C3A
|
A:HEM304
|
4.3
|
74.2
|
1.0
|
CG
|
A:HIS202
|
4.3
|
68.2
|
1.0
|
C3B
|
A:HEM304
|
4.3
|
50.2
|
1.0
|
C2B
|
A:HEM304
|
4.3
|
62.9
|
1.0
|
ND1
|
A:HIS100
|
4.3
|
88.6
|
1.0
|
|
Iron binding site 3 out
of 6 in 4pv1
Go back to
Iron Binding Sites List in 4pv1
Iron binding site 3 out
of 6 in the Cytochrome B6F Structure From M. Laminosus with the Quinone Analog Inhibitor Stigmatellin
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Cytochrome B6F Structure From M. Laminosus with the Quinone Analog Inhibitor Stigmatellin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe305
b:88.2
occ:1.00
|
FE
|
A:HEM305
|
0.0
|
88.2
|
1.0
|
NC
|
A:HEM305
|
2.0
|
0.1
|
1.0
|
NA
|
A:HEM305
|
2.1
|
0.8
|
1.0
|
NB
|
A:HEM305
|
2.1
|
0.3
|
1.0
|
ND
|
A:HEM305
|
2.1
|
95.2
|
1.0
|
O
|
A:HOH401
|
2.1
|
91.7
|
1.0
|
O8
|
A:SMA308
|
2.2
|
77.5
|
1.0
|
C1A
|
A:HEM305
|
3.1
|
0.6
|
1.0
|
C4C
|
A:HEM305
|
3.1
|
0.8
|
1.0
|
C4A
|
A:HEM305
|
3.1
|
0.0
|
1.0
|
C1C
|
A:HEM305
|
3.1
|
98.8
|
1.0
|
C1D
|
A:HEM305
|
3.1
|
83.5
|
1.0
|
C1B
|
A:HEM305
|
3.1
|
0.1
|
1.0
|
C4B
|
A:HEM305
|
3.1
|
0.5
|
1.0
|
C4D
|
A:HEM305
|
3.1
|
92.9
|
1.0
|
CHD
|
A:HEM305
|
3.4
|
96.3
|
1.0
|
CHA
|
A:HEM305
|
3.4
|
0.5
|
1.0
|
CHB
|
A:HEM305
|
3.4
|
0.3
|
1.0
|
CHC
|
A:HEM305
|
3.5
|
0.6
|
1.0
|
C8
|
A:SMA308
|
3.6
|
89.0
|
0.4
|
CZ
|
B:PHE40
|
3.8
|
0.3
|
1.0
|
CE2
|
B:PHE40
|
3.9
|
0.6
|
1.0
|
O7
|
A:SMA308
|
4.0
|
0.2
|
0.5
|
C2A
|
A:HEM305
|
4.3
|
93.3
|
1.0
|
C3A
|
A:HEM305
|
4.3
|
0.5
|
1.0
|
C3C
|
A:HEM305
|
4.3
|
98.8
|
1.0
|
C2C
|
A:HEM305
|
4.3
|
85.1
|
1.0
|
C2B
|
A:HEM305
|
4.3
|
0.5
|
1.0
|
C3B
|
A:HEM305
|
4.3
|
0.4
|
1.0
|
C2D
|
A:HEM305
|
4.3
|
72.4
|
1.0
|
C3D
|
A:HEM305
|
4.3
|
83.8
|
1.0
|
O1
|
A:SMA308
|
4.3
|
91.2
|
0.7
|
C7
|
A:SMA308
|
4.4
|
97.5
|
1.0
|
C8A
|
A:SMA308
|
4.4
|
91.2
|
0.4
|
O
|
A:TYR34
|
4.4
|
96.0
|
1.0
|
CMA
|
A:HEM304
|
4.5
|
71.9
|
1.0
|
O2A
|
A:HEM304
|
4.6
|
91.8
|
1.0
|
CAA
|
A:HEM304
|
4.8
|
74.2
|
1.0
|
C7M
|
A:SMA308
|
4.8
|
0.7
|
1.0
|
CE1
|
B:PHE40
|
4.9
|
0.8
|
1.0
|
|
Iron binding site 4 out
of 6 in 4pv1
Go back to
Iron Binding Sites List in 4pv1
Iron binding site 4 out
of 6 in the Cytochrome B6F Structure From M. Laminosus with the Quinone Analog Inhibitor Stigmatellin
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Cytochrome B6F Structure From M. Laminosus with the Quinone Analog Inhibitor Stigmatellin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe301
b:85.8
occ:1.00
|
FE
|
C:HEM301
|
0.0
|
85.8
|
1.0
|
N
|
C:TYR1
|
2.0
|
79.7
|
1.0
|
NC
|
C:HEM301
|
2.0
|
65.3
|
1.0
|
NA
|
C:HEM301
|
2.0
|
71.5
|
1.0
|
ND
|
C:HEM301
|
2.1
|
96.9
|
1.0
|
NB
|
C:HEM301
|
2.1
|
89.9
|
1.0
|
NE2
|
C:HIS26
|
2.1
|
94.1
|
1.0
|
C4C
|
C:HEM301
|
3.0
|
75.3
|
1.0
|
C4A
|
C:HEM301
|
3.0
|
76.9
|
1.0
|
C1D
|
C:HEM301
|
3.1
|
95.7
|
1.0
|
C1A
|
C:HEM301
|
3.1
|
85.3
|
1.0
|
C1B
|
C:HEM301
|
3.1
|
90.5
|
1.0
|
C1C
|
C:HEM301
|
3.1
|
69.1
|
1.0
|
C4D
|
C:HEM301
|
3.1
|
99.9
|
1.0
|
CD2
|
C:HIS26
|
3.1
|
95.4
|
1.0
|
CE1
|
C:HIS26
|
3.1
|
89.2
|
1.0
|
C4B
|
C:HEM301
|
3.1
|
80.2
|
1.0
|
CHD
|
C:HEM301
|
3.4
|
89.9
|
1.0
|
CHB
|
C:HEM301
|
3.4
|
83.9
|
1.0
|
CA
|
C:TYR1
|
3.4
|
99.6
|
1.0
|
CHA
|
C:HEM301
|
3.4
|
89.2
|
1.0
|
CHC
|
C:HEM301
|
3.5
|
60.8
|
1.0
|
C
|
C:TYR1
|
4.0
|
98.4
|
1.0
|
O
|
C:TYR1
|
4.1
|
0.2
|
1.0
|
ND1
|
C:HIS26
|
4.2
|
86.8
|
1.0
|
CG
|
C:HIS26
|
4.3
|
94.6
|
1.0
|
C3A
|
C:HEM301
|
4.3
|
84.3
|
1.0
|
C3C
|
C:HEM301
|
4.3
|
74.0
|
1.0
|
C2A
|
C:HEM301
|
4.3
|
87.1
|
1.0
|
C2C
|
C:HEM301
|
4.3
|
76.4
|
1.0
|
C2B
|
C:HEM301
|
4.3
|
91.9
|
1.0
|
C2D
|
C:HEM301
|
4.3
|
92.2
|
1.0
|
C3D
|
C:HEM301
|
4.3
|
0.8
|
1.0
|
C3B
|
C:HEM301
|
4.3
|
87.2
|
1.0
|
CB
|
C:TYR1
|
4.3
|
0.5
|
1.0
|
CG
|
C:TYR1
|
4.8
|
0.2
|
1.0
|
CE3
|
C:TRP4
|
4.8
|
0.1
|
1.0
|
N
|
C:PRO2
|
4.9
|
94.1
|
1.0
|
CD1
|
C:TYR1
|
4.9
|
95.1
|
1.0
|
ND2
|
C:ASN154
|
4.9
|
90.0
|
1.0
|
|
Iron binding site 5 out
of 6 in 4pv1
Go back to
Iron Binding Sites List in 4pv1
Iron binding site 5 out
of 6 in the Cytochrome B6F Structure From M. Laminosus with the Quinone Analog Inhibitor Stigmatellin
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Cytochrome B6F Structure From M. Laminosus with the Quinone Analog Inhibitor Stigmatellin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe201
b:0.3
occ:1.00
|
FE1
|
D:FES201
|
0.0
|
0.3
|
1.0
|
S1
|
D:FES201
|
2.2
|
0.2
|
1.0
|
S2
|
D:FES201
|
2.2
|
0.8
|
1.0
|
SG
|
D:CYS126
|
2.3
|
0.5
|
1.0
|
SG
|
D:CYS108
|
2.3
|
0.9
|
1.0
|
CB
|
D:CYS108
|
2.7
|
0.6
|
1.0
|
FE2
|
D:FES201
|
3.1
|
0.7
|
1.0
|
CB
|
D:CYS126
|
3.4
|
0.5
|
1.0
|
OG
|
D:SER131
|
4.0
|
0.6
|
1.0
|
CB
|
D:HIS110
|
4.2
|
0.5
|
1.0
|
ND1
|
D:HIS129
|
4.2
|
0.8
|
1.0
|
CA
|
D:CYS108
|
4.2
|
0.7
|
1.0
|
CB
|
D:CYS113
|
4.3
|
0.8
|
1.0
|
O
|
D:CYS113
|
4.4
|
0.8
|
1.0
|
CG2
|
D:VAL115
|
4.6
|
0.6
|
1.0
|
CA
|
D:CYS126
|
4.8
|
0.7
|
1.0
|
N
|
D:CYS113
|
4.8
|
0.9
|
1.0
|
C
|
D:CYS108
|
4.9
|
0.4
|
1.0
|
N
|
D:LEU111
|
4.9
|
0.5
|
1.0
|
N
|
D:HIS110
|
4.9
|
0.3
|
1.0
|
CE1
|
D:HIS129
|
5.0
|
0.2
|
1.0
|
CA
|
D:CYS113
|
5.0
|
0.0
|
1.0
|
|
Iron binding site 6 out
of 6 in 4pv1
Go back to
Iron Binding Sites List in 4pv1
Iron binding site 6 out
of 6 in the Cytochrome B6F Structure From M. Laminosus with the Quinone Analog Inhibitor Stigmatellin
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Cytochrome B6F Structure From M. Laminosus with the Quinone Analog Inhibitor Stigmatellin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe201
b:0.7
occ:1.00
|
FE2
|
D:FES201
|
0.0
|
0.7
|
1.0
|
ND1
|
D:HIS129
|
2.1
|
0.8
|
1.0
|
S2
|
D:FES201
|
2.2
|
0.8
|
1.0
|
S1
|
D:FES201
|
2.2
|
0.2
|
1.0
|
ND1
|
D:HIS110
|
2.3
|
0.4
|
1.0
|
CE1
|
D:HIS129
|
2.5
|
0.2
|
1.0
|
CG
|
D:HIS110
|
2.7
|
0.3
|
1.0
|
CB
|
D:HIS110
|
2.8
|
0.5
|
1.0
|
CG
|
D:HIS129
|
3.0
|
0.8
|
1.0
|
FE1
|
D:FES201
|
3.1
|
0.3
|
1.0
|
NE2
|
D:HIS129
|
3.3
|
0.6
|
1.0
|
CE1
|
D:HIS110
|
3.3
|
0.5
|
1.0
|
CD2
|
D:HIS129
|
3.6
|
0.7
|
1.0
|
CB
|
D:HIS129
|
3.8
|
0.1
|
1.0
|
CD2
|
D:HIS110
|
3.9
|
0.8
|
1.0
|
N
|
D:LEU111
|
4.0
|
0.5
|
1.0
|
NE2
|
D:HIS110
|
4.1
|
0.6
|
1.0
|
CA
|
D:HIS110
|
4.2
|
0.9
|
1.0
|
SG
|
D:CYS126
|
4.4
|
0.5
|
1.0
|
CG
|
D:LEU111
|
4.4
|
0.4
|
1.0
|
C
|
D:HIS110
|
4.4
|
0.6
|
1.0
|
CB
|
D:LEU111
|
4.5
|
0.8
|
1.0
|
SG
|
D:CYS108
|
4.6
|
0.9
|
1.0
|
CD1
|
D:LEU111
|
4.8
|
96.4
|
1.0
|
OG
|
D:SER131
|
4.8
|
0.6
|
1.0
|
N
|
D:HIS110
|
4.9
|
0.3
|
1.0
|
CA
|
D:LEU111
|
4.9
|
0.6
|
1.0
|
|
Reference:
S.S.Hasan,
E.Yamashita,
W.A.Cramer.
The Integral Chlorophyll Modulates Intra-Protein Quinone-Traffic Within the Cytochrome B6F Complex To Be Published.
Page generated: Mon Aug 5 08:31:42 2024
|