Iron in PDB 9es9: Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site
Enzymatic activity of Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site
All present enzymatic activity of Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site:
7.1.1.6;
Other elements in 9es9:
The structure of Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site also contains other interesting chemical elements:
Iron Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Iron atom in the Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site
(pdb code 9es9). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the
Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site, PDB code: 9es9:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 12 in 9es9
Go back to
Iron Binding Sites List in 9es9
Iron binding site 1 out
of 12 in the Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe301
b:82.4
occ:1.00
|
FE
|
A:HEM301
|
0.0
|
82.4
|
1.0
|
|
ND
|
A:HEM301
|
2.0
|
70.5
|
1.0
|
|
NB
|
A:HEM301
|
2.0
|
70.9
|
1.0
|
|
NA
|
A:HEM301
|
2.0
|
68.5
|
1.0
|
|
NC
|
A:HEM301
|
2.0
|
71.8
|
1.0
|
|
NE2
|
A:HIS187
|
2.3
|
58.9
|
1.0
|
|
NE2
|
A:HIS86
|
2.4
|
51.0
|
1.0
|
|
C1D
|
A:HEM301
|
3.0
|
69.7
|
1.0
|
|
C1B
|
A:HEM301
|
3.1
|
67.8
|
1.0
|
|
C4A
|
A:HEM301
|
3.1
|
62.5
|
1.0
|
|
C4C
|
A:HEM301
|
3.1
|
64.3
|
1.0
|
|
C4B
|
A:HEM301
|
3.1
|
62.7
|
1.0
|
|
C4D
|
A:HEM301
|
3.1
|
64.9
|
1.0
|
|
C1A
|
A:HEM301
|
3.1
|
57.9
|
1.0
|
|
C1C
|
A:HEM301
|
3.1
|
65.4
|
1.0
|
|
CE1
|
A:HIS187
|
3.1
|
56.5
|
1.0
|
|
CE1
|
A:HIS86
|
3.3
|
54.4
|
1.0
|
|
CD2
|
A:HIS86
|
3.4
|
58.9
|
1.0
|
|
CHD
|
A:HEM301
|
3.4
|
68.4
|
1.0
|
|
CHB
|
A:HEM301
|
3.4
|
63.3
|
1.0
|
|
CHC
|
A:HEM301
|
3.4
|
57.9
|
1.0
|
|
CHA
|
A:HEM301
|
3.4
|
56.9
|
1.0
|
|
CD2
|
A:HIS187
|
3.5
|
68.3
|
1.0
|
|
C2D
|
A:HEM301
|
4.3
|
68.7
|
1.0
|
|
C2B
|
A:HEM301
|
4.3
|
66.9
|
1.0
|
|
C3D
|
A:HEM301
|
4.3
|
70.0
|
1.0
|
|
C3B
|
A:HEM301
|
4.3
|
64.7
|
1.0
|
|
C3A
|
A:HEM301
|
4.3
|
65.3
|
1.0
|
|
C3C
|
A:HEM301
|
4.3
|
63.8
|
1.0
|
|
C2A
|
A:HEM301
|
4.3
|
68.0
|
1.0
|
|
C2C
|
A:HEM301
|
4.3
|
61.3
|
1.0
|
|
ND1
|
A:HIS187
|
4.3
|
66.1
|
1.0
|
|
ND1
|
A:HIS86
|
4.4
|
62.1
|
1.0
|
|
CG
|
A:HIS187
|
4.5
|
66.5
|
1.0
|
|
CG
|
A:HIS86
|
4.5
|
62.1
|
1.0
|
|
NE2
|
A:GLN47
|
4.9
|
67.6
|
1.0
|
|
Iron binding site 2 out
of 12 in 9es9
Go back to
Iron Binding Sites List in 9es9
Iron binding site 2 out
of 12 in the Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe302
b:84.0
occ:1.00
|
FE
|
A:HEM302
|
0.0
|
84.0
|
1.0
|
|
ND
|
A:HEM302
|
2.0
|
75.1
|
1.0
|
|
NB
|
A:HEM302
|
2.0
|
67.6
|
1.0
|
|
NC
|
A:HEM302
|
2.0
|
74.4
|
1.0
|
|
NA
|
A:HEM302
|
2.0
|
62.1
|
1.0
|
|
NE2
|
A:HIS100
|
2.4
|
51.7
|
1.0
|
|
NE2
|
A:HIS202
|
2.4
|
50.9
|
1.0
|
|
C1D
|
A:HEM302
|
3.0
|
63.4
|
1.0
|
|
C4C
|
A:HEM302
|
3.0
|
63.5
|
1.0
|
|
C1B
|
A:HEM302
|
3.0
|
61.4
|
1.0
|
|
C4A
|
A:HEM302
|
3.0
|
66.5
|
1.0
|
|
C1C
|
A:HEM302
|
3.1
|
65.1
|
1.0
|
|
C4D
|
A:HEM302
|
3.1
|
67.8
|
1.0
|
|
C4B
|
A:HEM302
|
3.1
|
63.0
|
1.0
|
|
C1A
|
A:HEM302
|
3.1
|
57.2
|
1.0
|
|
CD2
|
A:HIS100
|
3.2
|
52.0
|
1.0
|
|
CE1
|
A:HIS202
|
3.3
|
64.3
|
1.0
|
|
CHD
|
A:HEM302
|
3.4
|
58.6
|
1.0
|
|
CHB
|
A:HEM302
|
3.4
|
63.8
|
1.0
|
|
CHC
|
A:HEM302
|
3.4
|
67.4
|
1.0
|
|
CD2
|
A:HIS202
|
3.4
|
59.7
|
1.0
|
|
CHA
|
A:HEM302
|
3.4
|
55.5
|
1.0
|
|
CE1
|
A:HIS100
|
3.5
|
54.3
|
1.0
|
|
C3C
|
A:HEM302
|
4.2
|
62.4
|
1.0
|
|
C2D
|
A:HEM302
|
4.2
|
63.0
|
1.0
|
|
C2C
|
A:HEM302
|
4.2
|
64.3
|
1.0
|
|
C3D
|
A:HEM302
|
4.3
|
63.4
|
1.0
|
|
C2B
|
A:HEM302
|
4.3
|
57.1
|
1.0
|
|
C3A
|
A:HEM302
|
4.3
|
63.1
|
1.0
|
|
C3B
|
A:HEM302
|
4.3
|
59.3
|
1.0
|
|
C2A
|
A:HEM302
|
4.3
|
61.7
|
1.0
|
|
CG
|
A:HIS100
|
4.5
|
60.0
|
1.0
|
|
ND1
|
A:HIS202
|
4.5
|
71.3
|
1.0
|
|
ND1
|
A:HIS100
|
4.6
|
68.8
|
1.0
|
|
CG
|
A:HIS202
|
4.6
|
65.5
|
1.0
|
|
Iron binding site 3 out
of 12 in 9es9
Go back to
Iron Binding Sites List in 9es9
Iron binding site 3 out
of 12 in the Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe303
b:90.5
occ:1.00
|
FE
|
A:HEC303
|
0.0
|
90.5
|
1.0
|
|
NC
|
A:HEC303
|
2.0
|
73.1
|
1.0
|
|
NA
|
A:HEC303
|
2.1
|
69.9
|
1.0
|
|
NB
|
A:HEC303
|
2.1
|
68.9
|
1.0
|
|
ND
|
A:HEC303
|
2.1
|
64.5
|
1.0
|
|
O
|
A:HOH402
|
2.8
|
65.0
|
1.0
|
|
C4C
|
A:HEC303
|
3.0
|
63.2
|
1.0
|
|
C1D
|
A:HEC303
|
3.1
|
62.7
|
1.0
|
|
C1A
|
A:HEC303
|
3.1
|
64.7
|
1.0
|
|
C4A
|
A:HEC303
|
3.1
|
59.1
|
1.0
|
|
C4D
|
A:HEC303
|
3.1
|
62.3
|
1.0
|
|
C1B
|
A:HEC303
|
3.1
|
58.2
|
1.0
|
|
C1C
|
A:HEC303
|
3.1
|
62.3
|
1.0
|
|
C4B
|
A:HEC303
|
3.1
|
61.3
|
1.0
|
|
CHD
|
A:HEC303
|
3.4
|
59.8
|
1.0
|
|
CHA
|
A:HEC303
|
3.4
|
61.9
|
1.0
|
|
CHB
|
A:HEC303
|
3.4
|
53.3
|
1.0
|
|
CHC
|
A:HEC303
|
3.5
|
54.9
|
1.0
|
|
CZ
|
B:PHE40
|
4.0
|
44.9
|
1.0
|
|
CE2
|
B:PHE40
|
4.2
|
44.0
|
1.0
|
|
C3C
|
A:HEC303
|
4.3
|
62.0
|
1.0
|
|
C3A
|
A:HEC303
|
4.3
|
65.9
|
1.0
|
|
C2A
|
A:HEC303
|
4.3
|
62.8
|
1.0
|
|
C2D
|
A:HEC303
|
4.3
|
62.8
|
1.0
|
|
C2C
|
A:HEC303
|
4.3
|
60.4
|
1.0
|
|
C2B
|
A:HEC303
|
4.3
|
57.0
|
1.0
|
|
C3D
|
A:HEC303
|
4.3
|
64.6
|
1.0
|
|
C3B
|
A:HEC303
|
4.3
|
62.4
|
1.0
|
|
O1A
|
A:HEM302
|
4.8
|
79.2
|
1.0
|
|
CA
|
A:GLY38
|
4.9
|
62.3
|
1.0
|
|
CE1
|
B:PHE40
|
4.9
|
42.3
|
1.0
|
|
CMA
|
A:HEM302
|
4.9
|
53.2
|
1.0
|
|
O
|
A:TYR34
|
5.0
|
70.4
|
1.0
|
|
N
|
A:GLY38
|
5.0
|
67.7
|
1.0
|
|
Iron binding site 4 out
of 12 in 9es9
Go back to
Iron Binding Sites List in 9es9
Iron binding site 4 out
of 12 in the Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe301
b:96.0
occ:1.00
|
FE
|
C:HEC301
|
0.0
|
96.0
|
1.0
|
|
NA
|
C:HEC301
|
2.0
|
84.1
|
1.0
|
|
NC
|
C:HEC301
|
2.0
|
83.8
|
1.0
|
|
NB
|
C:HEC301
|
2.1
|
82.8
|
1.0
|
|
ND
|
C:HEC301
|
2.1
|
85.1
|
1.0
|
|
N
|
C:TYR1
|
2.1
|
73.7
|
1.0
|
|
NE2
|
C:HIS25
|
2.4
|
62.4
|
1.0
|
|
C1A
|
C:HEC301
|
3.0
|
75.7
|
1.0
|
|
C4C
|
C:HEC301
|
3.1
|
77.6
|
1.0
|
|
CE1
|
C:HIS25
|
3.1
|
69.5
|
1.0
|
|
C1C
|
C:HEC301
|
3.1
|
82.9
|
1.0
|
|
C4D
|
C:HEC301
|
3.1
|
75.7
|
1.0
|
|
C4A
|
C:HEC301
|
3.1
|
84.4
|
1.0
|
|
C4B
|
C:HEC301
|
3.1
|
75.0
|
1.0
|
|
C1B
|
C:HEC301
|
3.1
|
78.6
|
1.0
|
|
C1D
|
C:HEC301
|
3.1
|
88.0
|
1.0
|
|
CA
|
C:TYR1
|
3.3
|
72.1
|
1.0
|
|
CHA
|
C:HEC301
|
3.4
|
75.1
|
1.0
|
|
CHD
|
C:HEC301
|
3.4
|
77.8
|
1.0
|
|
CHC
|
C:HEC301
|
3.4
|
81.2
|
1.0
|
|
CHB
|
C:HEC301
|
3.4
|
78.0
|
1.0
|
|
CD2
|
C:HIS25
|
3.5
|
72.6
|
1.0
|
|
C
|
C:TYR1
|
3.9
|
75.1
|
1.0
|
|
O
|
C:TYR1
|
4.0
|
76.3
|
1.0
|
|
C2A
|
C:HEC301
|
4.3
|
77.5
|
1.0
|
|
C3C
|
C:HEC301
|
4.3
|
78.6
|
1.0
|
|
C3A
|
C:HEC301
|
4.3
|
81.0
|
1.0
|
|
C2C
|
C:HEC301
|
4.3
|
83.1
|
1.0
|
|
C3B
|
C:HEC301
|
4.3
|
76.0
|
1.0
|
|
C2B
|
C:HEC301
|
4.3
|
75.1
|
1.0
|
|
ND1
|
C:HIS25
|
4.3
|
67.0
|
1.0
|
|
C3D
|
C:HEC301
|
4.3
|
79.2
|
1.0
|
|
C2D
|
C:HEC301
|
4.3
|
84.7
|
1.0
|
|
CB
|
C:TYR1
|
4.5
|
68.5
|
1.0
|
|
CG
|
C:HIS25
|
4.5
|
71.9
|
1.0
|
|
N
|
C:PRO2
|
4.8
|
76.8
|
1.0
|
|
CG
|
C:TYR1
|
4.9
|
72.4
|
1.0
|
|
CD1
|
C:TYR1
|
4.9
|
80.7
|
1.0
|
|
CD2
|
C:PHE4
|
5.0
|
76.3
|
1.0
|
|
Iron binding site 5 out
of 12 in 9es9
Go back to
Iron Binding Sites List in 9es9
Iron binding site 5 out
of 12 in the Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe202
b:92.4
occ:1.00
|
FE1
|
D:FES202
|
0.0
|
92.4
|
1.0
|
|
ND1
|
D:HIS109
|
2.1
|
73.6
|
1.0
|
|
ND1
|
D:HIS128
|
2.2
|
66.5
|
1.0
|
|
S1
|
D:FES202
|
2.2
|
68.8
|
1.0
|
|
S2
|
D:FES202
|
2.2
|
83.6
|
1.0
|
|
FE2
|
D:FES202
|
2.7
|
105.0
|
1.0
|
|
CE1
|
D:HIS109
|
3.1
|
65.7
|
1.0
|
|
CE1
|
D:HIS128
|
3.1
|
67.0
|
1.0
|
|
CG
|
D:HIS128
|
3.1
|
67.1
|
1.0
|
|
CG
|
D:HIS109
|
3.1
|
75.2
|
1.0
|
|
CB
|
D:HIS128
|
3.4
|
74.0
|
1.0
|
|
CB
|
D:HIS109
|
3.5
|
68.4
|
1.0
|
|
N
|
D:HIS128
|
4.0
|
72.6
|
1.0
|
|
CB
|
D:CYS127
|
4.1
|
70.3
|
1.0
|
|
SG
|
D:CYS125
|
4.2
|
68.6
|
1.0
|
|
NE2
|
D:HIS109
|
4.2
|
65.0
|
1.0
|
|
N
|
D:LEU110
|
4.2
|
73.1
|
1.0
|
|
NE2
|
D:HIS128
|
4.2
|
61.8
|
1.0
|
|
CD2
|
D:HIS109
|
4.3
|
71.3
|
1.0
|
|
CD2
|
D:HIS128
|
4.3
|
62.2
|
1.0
|
|
CA
|
D:HIS128
|
4.3
|
69.9
|
1.0
|
|
CB
|
D:LEU110
|
4.4
|
67.0
|
1.0
|
|
SG
|
D:CYS107
|
4.5
|
88.6
|
1.0
|
|
OG
|
D:SER130
|
4.5
|
79.4
|
1.0
|
|
C
|
D:CYS127
|
4.6
|
71.7
|
1.0
|
|
CG
|
D:LEU110
|
4.6
|
67.1
|
1.0
|
|
CD1
|
D:LEU110
|
4.7
|
70.8
|
1.0
|
|
CA
|
D:HIS109
|
4.7
|
66.3
|
1.0
|
|
C
|
D:HIS109
|
4.7
|
69.2
|
1.0
|
|
CA
|
D:LEU110
|
4.9
|
72.3
|
1.0
|
|
CA
|
D:CYS127
|
5.0
|
73.0
|
1.0
|
|
Iron binding site 6 out
of 12 in 9es9
Go back to
Iron Binding Sites List in 9es9
Iron binding site 6 out
of 12 in the Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe202
b:105.0
occ:1.00
|
FE2
|
D:FES202
|
0.0
|
105.0
|
1.0
|
|
S2
|
D:FES202
|
2.2
|
83.6
|
1.0
|
|
S1
|
D:FES202
|
2.2
|
68.8
|
1.0
|
|
SG
|
D:CYS107
|
2.3
|
88.6
|
1.0
|
|
SG
|
D:CYS125
|
2.3
|
68.6
|
1.0
|
|
FE1
|
D:FES202
|
2.7
|
92.4
|
1.0
|
|
CB
|
D:CYS107
|
3.2
|
71.7
|
1.0
|
|
CB
|
D:CYS125
|
3.4
|
60.7
|
1.0
|
|
CB
|
D:HIS109
|
3.9
|
68.4
|
1.0
|
|
OG
|
D:SER130
|
4.1
|
79.4
|
1.0
|
|
CB
|
D:CYS112
|
4.2
|
69.8
|
1.0
|
|
ND1
|
D:HIS109
|
4.3
|
73.6
|
1.0
|
|
CB
|
D:SER130
|
4.5
|
84.5
|
1.0
|
|
CB
|
D:CYS127
|
4.5
|
70.3
|
1.0
|
|
N
|
D:CYS112
|
4.5
|
70.2
|
1.0
|
|
N
|
D:LEU110
|
4.6
|
73.1
|
1.0
|
|
ND1
|
D:HIS128
|
4.6
|
66.5
|
1.0
|
|
CG
|
D:HIS109
|
4.6
|
75.2
|
1.0
|
|
CA
|
D:CYS107
|
4.6
|
70.9
|
1.0
|
|
N
|
D:HIS109
|
4.7
|
72.6
|
1.0
|
|
SG
|
D:CYS112
|
4.8
|
96.7
|
1.0
|
|
N
|
D:HIS128
|
4.8
|
72.6
|
1.0
|
|
CA
|
D:CYS125
|
4.8
|
67.7
|
1.0
|
|
O
|
D:CYS112
|
4.8
|
74.3
|
1.0
|
|
CA
|
D:HIS109
|
4.8
|
66.3
|
1.0
|
|
CA
|
D:CYS112
|
4.9
|
67.0
|
1.0
|
|
N
|
D:GLY111
|
5.0
|
77.8
|
1.0
|
|
Iron binding site 7 out
of 12 in 9es9
Go back to
Iron Binding Sites List in 9es9
Iron binding site 7 out
of 12 in the Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Fe301
b:82.4
occ:1.00
|
FE
|
I:HEM301
|
0.0
|
82.4
|
1.0
|
|
ND
|
I:HEM301
|
2.0
|
70.5
|
1.0
|
|
NB
|
I:HEM301
|
2.0
|
70.9
|
1.0
|
|
NA
|
I:HEM301
|
2.0
|
68.5
|
1.0
|
|
NC
|
I:HEM301
|
2.0
|
71.8
|
1.0
|
|
NE2
|
I:HIS187
|
2.3
|
58.9
|
1.0
|
|
NE2
|
I:HIS86
|
2.4
|
51.0
|
1.0
|
|
C1D
|
I:HEM301
|
3.0
|
69.7
|
1.0
|
|
C1B
|
I:HEM301
|
3.1
|
67.8
|
1.0
|
|
C4A
|
I:HEM301
|
3.1
|
62.5
|
1.0
|
|
C4C
|
I:HEM301
|
3.1
|
64.3
|
1.0
|
|
C4B
|
I:HEM301
|
3.1
|
62.7
|
1.0
|
|
C4D
|
I:HEM301
|
3.1
|
64.9
|
1.0
|
|
C1A
|
I:HEM301
|
3.1
|
57.9
|
1.0
|
|
C1C
|
I:HEM301
|
3.1
|
65.4
|
1.0
|
|
CE1
|
I:HIS187
|
3.1
|
56.5
|
1.0
|
|
CE1
|
I:HIS86
|
3.3
|
54.4
|
1.0
|
|
CD2
|
I:HIS86
|
3.4
|
58.9
|
1.0
|
|
CHD
|
I:HEM301
|
3.4
|
68.4
|
1.0
|
|
CHB
|
I:HEM301
|
3.4
|
63.3
|
1.0
|
|
CHC
|
I:HEM301
|
3.4
|
57.9
|
1.0
|
|
CHA
|
I:HEM301
|
3.4
|
56.9
|
1.0
|
|
CD2
|
I:HIS187
|
3.5
|
68.3
|
1.0
|
|
C2D
|
I:HEM301
|
4.3
|
68.7
|
1.0
|
|
C2B
|
I:HEM301
|
4.3
|
66.9
|
1.0
|
|
C3D
|
I:HEM301
|
4.3
|
70.0
|
1.0
|
|
C3B
|
I:HEM301
|
4.3
|
64.7
|
1.0
|
|
C3A
|
I:HEM301
|
4.3
|
65.3
|
1.0
|
|
C3C
|
I:HEM301
|
4.3
|
63.8
|
1.0
|
|
C2A
|
I:HEM301
|
4.3
|
68.0
|
1.0
|
|
C2C
|
I:HEM301
|
4.3
|
61.3
|
1.0
|
|
ND1
|
I:HIS187
|
4.3
|
66.1
|
1.0
|
|
ND1
|
I:HIS86
|
4.4
|
62.1
|
1.0
|
|
CG
|
I:HIS187
|
4.5
|
66.5
|
1.0
|
|
CG
|
I:HIS86
|
4.5
|
62.1
|
1.0
|
|
NE2
|
I:GLN47
|
4.9
|
67.6
|
1.0
|
|
Iron binding site 8 out
of 12 in 9es9
Go back to
Iron Binding Sites List in 9es9
Iron binding site 8 out
of 12 in the Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Fe302
b:84.0
occ:1.00
|
FE
|
I:HEM302
|
0.0
|
84.0
|
1.0
|
|
ND
|
I:HEM302
|
2.0
|
75.1
|
1.0
|
|
NB
|
I:HEM302
|
2.0
|
67.6
|
1.0
|
|
NC
|
I:HEM302
|
2.0
|
74.4
|
1.0
|
|
NA
|
I:HEM302
|
2.0
|
62.1
|
1.0
|
|
NE2
|
I:HIS100
|
2.4
|
51.7
|
1.0
|
|
NE2
|
I:HIS202
|
2.4
|
50.9
|
1.0
|
|
C1D
|
I:HEM302
|
3.0
|
63.4
|
1.0
|
|
C4C
|
I:HEM302
|
3.0
|
63.5
|
1.0
|
|
C1B
|
I:HEM302
|
3.0
|
61.4
|
1.0
|
|
C4A
|
I:HEM302
|
3.0
|
66.5
|
1.0
|
|
C1C
|
I:HEM302
|
3.1
|
65.1
|
1.0
|
|
C4D
|
I:HEM302
|
3.1
|
67.8
|
1.0
|
|
C4B
|
I:HEM302
|
3.1
|
63.0
|
1.0
|
|
C1A
|
I:HEM302
|
3.1
|
57.2
|
1.0
|
|
CD2
|
I:HIS100
|
3.2
|
52.0
|
1.0
|
|
CE1
|
I:HIS202
|
3.3
|
64.3
|
1.0
|
|
CHD
|
I:HEM302
|
3.4
|
58.6
|
1.0
|
|
CHB
|
I:HEM302
|
3.4
|
63.8
|
1.0
|
|
CHC
|
I:HEM302
|
3.4
|
67.4
|
1.0
|
|
CD2
|
I:HIS202
|
3.4
|
59.7
|
1.0
|
|
CHA
|
I:HEM302
|
3.4
|
55.5
|
1.0
|
|
CE1
|
I:HIS100
|
3.5
|
54.3
|
1.0
|
|
C3C
|
I:HEM302
|
4.2
|
62.4
|
1.0
|
|
C2D
|
I:HEM302
|
4.2
|
63.0
|
1.0
|
|
C2C
|
I:HEM302
|
4.2
|
64.3
|
1.0
|
|
C3D
|
I:HEM302
|
4.3
|
63.4
|
1.0
|
|
C2B
|
I:HEM302
|
4.3
|
57.1
|
1.0
|
|
C3A
|
I:HEM302
|
4.3
|
63.1
|
1.0
|
|
C3B
|
I:HEM302
|
4.3
|
59.3
|
1.0
|
|
C2A
|
I:HEM302
|
4.3
|
61.7
|
1.0
|
|
CG
|
I:HIS100
|
4.5
|
60.0
|
1.0
|
|
ND1
|
I:HIS202
|
4.5
|
71.3
|
1.0
|
|
ND1
|
I:HIS100
|
4.6
|
68.8
|
1.0
|
|
CG
|
I:HIS202
|
4.6
|
65.5
|
1.0
|
|
Iron binding site 9 out
of 12 in 9es9
Go back to
Iron Binding Sites List in 9es9
Iron binding site 9 out
of 12 in the Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Fe303
b:90.5
occ:1.00
|
FE
|
I:HEC303
|
0.0
|
90.5
|
1.0
|
|
NC
|
I:HEC303
|
2.0
|
73.1
|
1.0
|
|
NA
|
I:HEC303
|
2.1
|
69.9
|
1.0
|
|
NB
|
I:HEC303
|
2.1
|
68.9
|
1.0
|
|
ND
|
I:HEC303
|
2.1
|
64.5
|
1.0
|
|
O
|
I:HOH402
|
2.8
|
67.5
|
1.0
|
|
C4C
|
I:HEC303
|
3.0
|
63.2
|
1.0
|
|
C1D
|
I:HEC303
|
3.1
|
62.7
|
1.0
|
|
C1A
|
I:HEC303
|
3.1
|
64.7
|
1.0
|
|
C4A
|
I:HEC303
|
3.1
|
59.1
|
1.0
|
|
C4D
|
I:HEC303
|
3.1
|
62.3
|
1.0
|
|
C1B
|
I:HEC303
|
3.1
|
58.2
|
1.0
|
|
C1C
|
I:HEC303
|
3.1
|
62.3
|
1.0
|
|
C4B
|
I:HEC303
|
3.1
|
61.3
|
1.0
|
|
CHD
|
I:HEC303
|
3.4
|
59.8
|
1.0
|
|
CHA
|
I:HEC303
|
3.4
|
61.9
|
1.0
|
|
CHB
|
I:HEC303
|
3.4
|
53.3
|
1.0
|
|
CHC
|
I:HEC303
|
3.5
|
54.9
|
1.0
|
|
CZ
|
J:PHE40
|
4.0
|
44.9
|
1.0
|
|
CE2
|
J:PHE40
|
4.2
|
44.0
|
1.0
|
|
C3C
|
I:HEC303
|
4.3
|
62.0
|
1.0
|
|
C3A
|
I:HEC303
|
4.3
|
65.9
|
1.0
|
|
C2A
|
I:HEC303
|
4.3
|
62.8
|
1.0
|
|
C2D
|
I:HEC303
|
4.3
|
62.8
|
1.0
|
|
C2C
|
I:HEC303
|
4.3
|
60.4
|
1.0
|
|
C2B
|
I:HEC303
|
4.3
|
57.0
|
1.0
|
|
C3D
|
I:HEC303
|
4.3
|
64.6
|
1.0
|
|
C3B
|
I:HEC303
|
4.3
|
62.4
|
1.0
|
|
O1A
|
I:HEM302
|
4.8
|
79.2
|
1.0
|
|
CA
|
I:GLY38
|
4.9
|
62.3
|
1.0
|
|
CE1
|
J:PHE40
|
4.9
|
42.3
|
1.0
|
|
CMA
|
I:HEM302
|
4.9
|
53.2
|
1.0
|
|
O
|
I:TYR34
|
5.0
|
70.4
|
1.0
|
|
N
|
I:GLY38
|
5.0
|
67.7
|
1.0
|
|
Iron binding site 10 out
of 12 in 9es9
Go back to
Iron Binding Sites List in 9es9
Iron binding site 10 out
of 12 in the Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 10 of Cryo-Em Structure of Spinacia Oleracea Cytochrome B6F Complex with Inhibitor Dbmib Bound at Plastoquinol Oxidation Site within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Fe301
b:96.0
occ:1.00
|
FE
|
K:HEC301
|
0.0
|
96.0
|
1.0
|
|
NA
|
K:HEC301
|
2.0
|
84.1
|
1.0
|
|
NC
|
K:HEC301
|
2.0
|
83.8
|
1.0
|
|
NB
|
K:HEC301
|
2.1
|
82.8
|
1.0
|
|
ND
|
K:HEC301
|
2.1
|
85.1
|
1.0
|
|
N
|
K:TYR1
|
2.1
|
73.7
|
1.0
|
|
NE2
|
K:HIS25
|
2.4
|
62.4
|
1.0
|
|
C1A
|
K:HEC301
|
3.0
|
75.7
|
1.0
|
|
C4C
|
K:HEC301
|
3.1
|
77.6
|
1.0
|
|
CE1
|
K:HIS25
|
3.1
|
69.5
|
1.0
|
|
C1C
|
K:HEC301
|
3.1
|
82.9
|
1.0
|
|
C4D
|
K:HEC301
|
3.1
|
75.7
|
1.0
|
|
C4A
|
K:HEC301
|
3.1
|
84.4
|
1.0
|
|
C4B
|
K:HEC301
|
3.1
|
75.0
|
1.0
|
|
C1B
|
K:HEC301
|
3.1
|
78.6
|
1.0
|
|
C1D
|
K:HEC301
|
3.1
|
88.0
|
1.0
|
|
CA
|
K:TYR1
|
3.3
|
72.1
|
1.0
|
|
CHA
|
K:HEC301
|
3.4
|
75.1
|
1.0
|
|
CHD
|
K:HEC301
|
3.4
|
77.8
|
1.0
|
|
CHC
|
K:HEC301
|
3.4
|
81.2
|
1.0
|
|
CHB
|
K:HEC301
|
3.4
|
78.0
|
1.0
|
|
CD2
|
K:HIS25
|
3.5
|
72.6
|
1.0
|
|
C
|
K:TYR1
|
3.9
|
75.1
|
1.0
|
|
O
|
K:TYR1
|
4.0
|
76.3
|
1.0
|
|
C2A
|
K:HEC301
|
4.3
|
77.5
|
1.0
|
|
C3C
|
K:HEC301
|
4.3
|
78.6
|
1.0
|
|
C3A
|
K:HEC301
|
4.3
|
81.0
|
1.0
|
|
C2C
|
K:HEC301
|
4.3
|
83.1
|
1.0
|
|
C3B
|
K:HEC301
|
4.3
|
76.0
|
1.0
|
|
C2B
|
K:HEC301
|
4.3
|
75.1
|
1.0
|
|
ND1
|
K:HIS25
|
4.3
|
67.0
|
1.0
|
|
C3D
|
K:HEC301
|
4.3
|
79.2
|
1.0
|
|
C2D
|
K:HEC301
|
4.3
|
84.7
|
1.0
|
|
CB
|
K:TYR1
|
4.5
|
68.5
|
1.0
|
|
CG
|
K:HIS25
|
4.5
|
71.9
|
1.0
|
|
N
|
K:PRO2
|
4.8
|
76.8
|
1.0
|
|
CG
|
K:TYR1
|
4.9
|
72.4
|
1.0
|
|
CD1
|
K:TYR1
|
4.9
|
80.7
|
1.0
|
|
CD2
|
K:PHE4
|
5.0
|
76.3
|
1.0
|
|
Reference:
S.Pintscher,
R.Pietras,
B.Mielecki,
M.Szwalec,
A.Wojcik-Augustyn,
P.Indyka,
M.Rawski,
L.Koziej,
M.Jaciuk,
G.Wazny,
S.Glatt,
A.Osyczka.
Molecular Basis of Plastoquinone Reduction in Plant Cytochrome B 6 F. Nat.Plants 2024.
ISSN: ESSN 2055-0278
PubMed: 39362993
DOI: 10.1038/S41477-024-01804-X
Page generated: Thu Oct 31 21:02:03 2024
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