Iron in PDB 8irb: Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay
Enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay
All present enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay:
1.10.3.9;
Protein crystallography data
The structure of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay, PDB code: 8irb
was solved by
H.Li,
M.Suga,
J.R.Shen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
19.98 /
2.30
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
125.75,
231.6,
288.28,
90,
90,
90
|
|
R / Rfree (%)
|
14 /
17.7
|
Other elements in 8irb:
The structure of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay
(pdb code 8irb). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay, PDB code: 8irb:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 8irb
Go back to
Iron Binding Sites List in 8irb
Iron binding site 1 out
of 8 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:52.1
occ:0.40
|
FE
|
A:FE2401
|
0.0
|
52.1
|
0.4
|
|
FE
|
A:FE2401
|
0.1
|
51.9
|
0.6
|
|
NE2
|
A:HIS215
|
2.1
|
59.0
|
0.6
|
|
NE2
|
A:HIS215
|
2.1
|
58.9
|
0.4
|
|
O2
|
A:BCT416
|
2.1
|
54.9
|
0.4
|
|
NE2
|
D:HIS214
|
2.1
|
53.0
|
0.4
|
|
NE2
|
D:HIS214
|
2.1
|
53.2
|
0.6
|
|
O1
|
A:BCT416
|
2.2
|
55.9
|
0.4
|
|
NE2
|
D:HIS268
|
2.2
|
49.3
|
0.4
|
|
NE2
|
D:HIS268
|
2.3
|
49.3
|
0.6
|
|
NE2
|
A:HIS272
|
2.3
|
55.5
|
0.4
|
|
NE2
|
A:HIS272
|
2.3
|
55.6
|
0.6
|
|
O2
|
A:BCT416
|
2.4
|
54.0
|
0.6
|
|
O1
|
A:BCT416
|
2.4
|
56.5
|
0.6
|
|
C
|
A:BCT416
|
2.4
|
56.9
|
0.4
|
|
C
|
A:BCT416
|
2.7
|
59.8
|
0.6
|
|
CE1
|
A:HIS215
|
2.9
|
49.4
|
0.4
|
|
CE1
|
A:HIS215
|
2.9
|
49.2
|
0.6
|
|
CE1
|
D:HIS214
|
3.0
|
48.2
|
0.4
|
|
CE1
|
D:HIS214
|
3.1
|
48.2
|
0.6
|
|
CE1
|
A:HIS272
|
3.1
|
49.2
|
0.6
|
|
CE1
|
A:HIS272
|
3.2
|
49.4
|
0.4
|
|
CE1
|
D:HIS268
|
3.2
|
45.6
|
0.4
|
|
CE1
|
D:HIS268
|
3.2
|
45.4
|
0.6
|
|
CD2
|
A:HIS215
|
3.2
|
47.2
|
0.6
|
|
CD2
|
D:HIS214
|
3.2
|
45.4
|
0.6
|
|
CD2
|
D:HIS214
|
3.2
|
45.4
|
0.4
|
|
CD2
|
A:HIS215
|
3.2
|
47.2
|
0.4
|
|
CD2
|
D:HIS268
|
3.3
|
46.6
|
0.4
|
|
CD2
|
D:HIS268
|
3.3
|
46.5
|
0.6
|
|
CD2
|
A:HIS272
|
3.4
|
47.7
|
0.4
|
|
CD2
|
A:HIS272
|
3.5
|
47.6
|
0.6
|
|
O3
|
A:BCT416
|
3.7
|
61.5
|
0.4
|
|
O3
|
A:BCT416
|
4.0
|
69.2
|
0.6
|
|
ND1
|
A:HIS215
|
4.1
|
52.1
|
0.4
|
|
ND1
|
A:HIS215
|
4.1
|
52.0
|
0.6
|
|
ND1
|
D:HIS214
|
4.2
|
43.1
|
0.4
|
|
ND1
|
D:HIS214
|
4.2
|
43.0
|
0.6
|
|
CG
|
A:HIS215
|
4.3
|
53.5
|
0.6
|
|
CG
|
A:HIS215
|
4.3
|
53.5
|
0.4
|
|
CG
|
D:HIS214
|
4.3
|
48.2
|
0.4
|
|
CG
|
D:HIS214
|
4.3
|
48.2
|
0.6
|
|
ND1
|
D:HIS268
|
4.3
|
50.1
|
0.4
|
|
ND1
|
A:HIS272
|
4.3
|
51.5
|
0.6
|
|
ND1
|
D:HIS268
|
4.3
|
50.0
|
0.6
|
|
ND1
|
A:HIS272
|
4.3
|
51.6
|
0.4
|
|
CG
|
D:HIS268
|
4.4
|
46.9
|
0.4
|
|
CG
|
D:HIS268
|
4.4
|
46.8
|
0.6
|
|
CG
|
A:HIS272
|
4.5
|
57.2
|
0.4
|
|
CG
|
A:HIS272
|
4.5
|
57.3
|
0.6
|
|
CG2
|
A:VAL219
|
4.6
|
55.6
|
0.4
|
|
CG2
|
A:VAL219
|
4.7
|
55.6
|
0.6
|
|
CG2
|
D:VAL218
|
4.9
|
49.5
|
0.6
|
|
OH
|
D:TYR244
|
4.9
|
63.7
|
0.6
|
|
OH
|
A:TYR246
|
4.9
|
79.8
|
0.6
|
|
CG2
|
D:VAL218
|
4.9
|
49.4
|
0.4
|
|
OH
|
D:TYR244
|
5.0
|
63.7
|
0.4
|
|
Iron binding site 2 out
of 8 in 8irb
Go back to
Iron Binding Sites List in 8irb
Iron binding site 2 out
of 8 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:51.9
occ:0.60
|
FE
|
A:FE2401
|
0.0
|
51.9
|
0.6
|
|
FE
|
A:FE2401
|
0.1
|
52.1
|
0.4
|
|
O2
|
A:BCT416
|
2.1
|
54.9
|
0.4
|
|
NE2
|
D:HIS214
|
2.1
|
53.0
|
0.4
|
|
NE2
|
D:HIS214
|
2.1
|
53.2
|
0.6
|
|
NE2
|
A:HIS215
|
2.1
|
59.0
|
0.6
|
|
NE2
|
A:HIS215
|
2.2
|
58.9
|
0.4
|
|
O1
|
A:BCT416
|
2.2
|
55.9
|
0.4
|
|
NE2
|
D:HIS268
|
2.3
|
49.3
|
0.4
|
|
NE2
|
A:HIS272
|
2.3
|
55.5
|
0.4
|
|
NE2
|
D:HIS268
|
2.3
|
49.3
|
0.6
|
|
O2
|
A:BCT416
|
2.3
|
54.0
|
0.6
|
|
NE2
|
A:HIS272
|
2.3
|
55.6
|
0.6
|
|
O1
|
A:BCT416
|
2.4
|
56.5
|
0.6
|
|
C
|
A:BCT416
|
2.4
|
56.9
|
0.4
|
|
C
|
A:BCT416
|
2.6
|
59.8
|
0.6
|
|
CE1
|
A:HIS215
|
3.0
|
49.4
|
0.4
|
|
CE1
|
A:HIS215
|
3.0
|
49.2
|
0.6
|
|
CE1
|
D:HIS214
|
3.0
|
48.2
|
0.4
|
|
CE1
|
D:HIS214
|
3.0
|
48.2
|
0.6
|
|
CE1
|
A:HIS272
|
3.1
|
49.2
|
0.6
|
|
CE1
|
A:HIS272
|
3.1
|
49.4
|
0.4
|
|
CE1
|
D:HIS268
|
3.2
|
45.6
|
0.4
|
|
CE1
|
D:HIS268
|
3.2
|
45.4
|
0.6
|
|
CD2
|
D:HIS214
|
3.2
|
45.4
|
0.6
|
|
CD2
|
D:HIS214
|
3.2
|
45.4
|
0.4
|
|
CD2
|
A:HIS215
|
3.2
|
47.2
|
0.6
|
|
CD2
|
A:HIS215
|
3.3
|
47.2
|
0.4
|
|
CD2
|
D:HIS268
|
3.3
|
46.6
|
0.4
|
|
CD2
|
D:HIS268
|
3.4
|
46.5
|
0.6
|
|
CD2
|
A:HIS272
|
3.4
|
47.7
|
0.4
|
|
CD2
|
A:HIS272
|
3.4
|
47.6
|
0.6
|
|
O3
|
A:BCT416
|
3.7
|
61.5
|
0.4
|
|
O3
|
A:BCT416
|
4.0
|
69.2
|
0.6
|
|
ND1
|
D:HIS214
|
4.2
|
43.1
|
0.4
|
|
ND1
|
A:HIS215
|
4.2
|
52.1
|
0.4
|
|
ND1
|
A:HIS215
|
4.2
|
52.0
|
0.6
|
|
ND1
|
D:HIS214
|
4.2
|
43.0
|
0.6
|
|
CG
|
D:HIS214
|
4.3
|
48.2
|
0.4
|
|
CG
|
D:HIS214
|
4.3
|
48.2
|
0.6
|
|
ND1
|
A:HIS272
|
4.3
|
51.5
|
0.6
|
|
ND1
|
A:HIS272
|
4.3
|
51.6
|
0.4
|
|
CG
|
A:HIS215
|
4.3
|
53.5
|
0.6
|
|
ND1
|
D:HIS268
|
4.3
|
50.1
|
0.4
|
|
CG
|
A:HIS215
|
4.3
|
53.5
|
0.4
|
|
ND1
|
D:HIS268
|
4.3
|
50.0
|
0.6
|
|
CG
|
D:HIS268
|
4.4
|
46.9
|
0.4
|
|
CG
|
A:HIS272
|
4.4
|
57.2
|
0.4
|
|
CG
|
D:HIS268
|
4.5
|
46.8
|
0.6
|
|
CG
|
A:HIS272
|
4.5
|
57.3
|
0.6
|
|
CG2
|
A:VAL219
|
4.7
|
55.6
|
0.4
|
|
CG2
|
A:VAL219
|
4.7
|
55.6
|
0.6
|
|
CG2
|
D:VAL218
|
4.8
|
49.5
|
0.6
|
|
OH
|
D:TYR244
|
4.8
|
63.7
|
0.6
|
|
CG2
|
D:VAL218
|
4.9
|
49.4
|
0.4
|
|
OH
|
A:TYR246
|
4.9
|
79.8
|
0.6
|
|
OH
|
D:TYR244
|
4.9
|
63.7
|
0.4
|
|
Iron binding site 3 out
of 8 in 8irb
Go back to
Iron Binding Sites List in 8irb
Iron binding site 3 out
of 8 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe102
b:64.0
occ:1.00
|
FE
|
F:HEM102
|
0.0
|
64.0
|
1.0
|
|
ND
|
F:HEM102
|
2.0
|
59.5
|
1.0
|
|
NA
|
F:HEM102
|
2.0
|
69.9
|
1.0
|
|
NE2
|
E:HIS23
|
2.1
|
68.2
|
1.0
|
|
NE2
|
F:HIS24
|
2.1
|
64.7
|
1.0
|
|
NC
|
F:HEM102
|
2.1
|
66.9
|
1.0
|
|
NB
|
F:HEM102
|
2.1
|
63.6
|
1.0
|
|
C4D
|
F:HEM102
|
2.9
|
72.5
|
1.0
|
|
C1A
|
F:HEM102
|
3.0
|
69.6
|
1.0
|
|
C1D
|
F:HEM102
|
3.0
|
66.7
|
1.0
|
|
CE1
|
E:HIS23
|
3.0
|
73.6
|
1.0
|
|
CD2
|
F:HIS24
|
3.0
|
63.5
|
1.0
|
|
C4A
|
F:HEM102
|
3.1
|
66.7
|
1.0
|
|
C4C
|
F:HEM102
|
3.1
|
65.7
|
1.0
|
|
C1B
|
F:HEM102
|
3.1
|
65.6
|
1.0
|
|
C4B
|
F:HEM102
|
3.1
|
64.4
|
1.0
|
|
CE1
|
F:HIS24
|
3.1
|
61.7
|
1.0
|
|
C1C
|
F:HEM102
|
3.1
|
67.8
|
1.0
|
|
CD2
|
E:HIS23
|
3.1
|
75.8
|
1.0
|
|
CHA
|
F:HEM102
|
3.4
|
61.8
|
1.0
|
|
CHD
|
F:HEM102
|
3.4
|
54.1
|
1.0
|
|
CHB
|
F:HEM102
|
3.5
|
64.8
|
1.0
|
|
CHC
|
F:HEM102
|
3.5
|
54.7
|
1.0
|
|
ND1
|
E:HIS23
|
4.1
|
64.1
|
1.0
|
|
C2A
|
F:HEM102
|
4.2
|
68.3
|
1.0
|
|
C3D
|
F:HEM102
|
4.2
|
59.8
|
1.0
|
|
CG
|
F:HIS24
|
4.2
|
71.3
|
1.0
|
|
ND1
|
F:HIS24
|
4.2
|
67.3
|
1.0
|
|
C2D
|
F:HEM102
|
4.2
|
59.5
|
1.0
|
|
C3A
|
F:HEM102
|
4.2
|
74.5
|
1.0
|
|
CG
|
E:HIS23
|
4.2
|
70.4
|
1.0
|
|
C3C
|
F:HEM102
|
4.3
|
64.2
|
1.0
|
|
C2C
|
F:HEM102
|
4.3
|
62.2
|
1.0
|
|
C2B
|
F:HEM102
|
4.3
|
65.3
|
1.0
|
|
C3B
|
F:HEM102
|
4.3
|
71.3
|
1.0
|
|
CE1
|
E:TYR19
|
4.9
|
70.6
|
1.0
|
|
NE1
|
F:TRP20
|
5.0
|
70.9
|
1.0
|
|
Iron binding site 4 out
of 8 in 8irb
Go back to
Iron Binding Sites List in 8irb
Iron binding site 4 out
of 8 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
V:Fe201
b:50.8
occ:1.00
|
FE
|
V:HEC201
|
0.0
|
50.8
|
1.0
|
|
NA
|
V:HEC201
|
2.0
|
51.4
|
1.0
|
|
NB
|
V:HEC201
|
2.0
|
56.2
|
1.0
|
|
NC
|
V:HEC201
|
2.1
|
53.5
|
1.0
|
|
NE2
|
V:HIS41
|
2.1
|
49.8
|
1.0
|
|
NE2
|
V:HIS92
|
2.1
|
47.4
|
1.0
|
|
ND
|
V:HEC201
|
2.1
|
54.0
|
1.0
|
|
CD2
|
V:HIS92
|
3.0
|
49.4
|
1.0
|
|
C4A
|
V:HEC201
|
3.0
|
55.2
|
1.0
|
|
C1B
|
V:HEC201
|
3.0
|
45.9
|
1.0
|
|
C1A
|
V:HEC201
|
3.0
|
60.1
|
1.0
|
|
CE1
|
V:HIS41
|
3.1
|
53.1
|
1.0
|
|
CD2
|
V:HIS41
|
3.1
|
49.3
|
1.0
|
|
C1D
|
V:HEC201
|
3.1
|
53.1
|
1.0
|
|
C4B
|
V:HEC201
|
3.1
|
53.5
|
1.0
|
|
C4D
|
V:HEC201
|
3.1
|
52.7
|
1.0
|
|
C4C
|
V:HEC201
|
3.1
|
51.9
|
1.0
|
|
C1C
|
V:HEC201
|
3.1
|
56.5
|
1.0
|
|
CE1
|
V:HIS92
|
3.1
|
47.8
|
1.0
|
|
CHB
|
V:HEC201
|
3.4
|
57.6
|
1.0
|
|
CHD
|
V:HEC201
|
3.4
|
53.5
|
1.0
|
|
CHA
|
V:HEC201
|
3.4
|
49.4
|
1.0
|
|
CHC
|
V:HEC201
|
3.5
|
53.9
|
1.0
|
|
CG
|
V:HIS92
|
4.1
|
54.6
|
1.0
|
|
ND1
|
V:HIS41
|
4.2
|
48.6
|
1.0
|
|
ND1
|
V:HIS92
|
4.2
|
46.9
|
1.0
|
|
CG
|
V:HIS41
|
4.2
|
49.4
|
1.0
|
|
C3A
|
V:HEC201
|
4.2
|
57.6
|
1.0
|
|
C2B
|
V:HEC201
|
4.2
|
50.6
|
1.0
|
|
C2A
|
V:HEC201
|
4.3
|
48.8
|
1.0
|
|
C3B
|
V:HEC201
|
4.3
|
47.5
|
1.0
|
|
C3D
|
V:HEC201
|
4.3
|
57.5
|
1.0
|
|
C2D
|
V:HEC201
|
4.3
|
51.3
|
1.0
|
|
C2C
|
V:HEC201
|
4.3
|
55.9
|
1.0
|
|
C3C
|
V:HEC201
|
4.3
|
55.9
|
1.0
|
|
CE2
|
V:TYR75
|
4.8
|
49.1
|
1.0
|
|
Iron binding site 5 out
of 8 in 8irb
Go back to
Iron Binding Sites List in 8irb
Iron binding site 5 out
of 8 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Fe401
b:55.2
occ:0.40
|
FE
|
a:FE2401
|
0.0
|
55.2
|
0.4
|
|
FE
|
a:FE2401
|
0.1
|
55.8
|
0.6
|
|
NE2
|
a:HIS215
|
2.1
|
57.8
|
0.4
|
|
O2
|
d:BCT401
|
2.1
|
56.6
|
0.4
|
|
NE2
|
a:HIS215
|
2.2
|
57.7
|
0.6
|
|
NE2
|
d:HIS214
|
2.2
|
53.3
|
0.4
|
|
NE2
|
d:HIS214
|
2.2
|
53.3
|
0.6
|
|
NE2
|
d:HIS268
|
2.3
|
56.1
|
0.4
|
|
NE2
|
a:HIS272
|
2.3
|
55.0
|
0.4
|
|
NE2
|
d:HIS268
|
2.3
|
56.1
|
0.6
|
|
NE2
|
a:HIS272
|
2.4
|
54.8
|
0.6
|
|
O1
|
d:BCT401
|
2.4
|
56.4
|
0.4
|
|
O2
|
d:BCT401
|
2.5
|
63.7
|
0.6
|
|
C
|
d:BCT401
|
2.6
|
67.0
|
0.4
|
|
O1
|
d:BCT401
|
2.6
|
57.5
|
0.6
|
|
C
|
d:BCT401
|
2.9
|
68.0
|
0.6
|
|
CE1
|
a:HIS215
|
3.0
|
55.6
|
0.4
|
|
CE1
|
a:HIS215
|
3.0
|
55.5
|
0.6
|
|
CE1
|
d:HIS214
|
3.2
|
55.0
|
0.4
|
|
CE1
|
d:HIS214
|
3.2
|
55.1
|
0.6
|
|
CD2
|
d:HIS214
|
3.2
|
47.9
|
0.6
|
|
CD2
|
d:HIS214
|
3.2
|
48.0
|
0.4
|
|
CD2
|
a:HIS215
|
3.2
|
59.5
|
0.4
|
|
CE1
|
a:HIS272
|
3.2
|
49.3
|
0.4
|
|
CE1
|
d:HIS268
|
3.2
|
58.2
|
0.4
|
|
CD2
|
a:HIS215
|
3.3
|
59.5
|
0.6
|
|
CE1
|
d:HIS268
|
3.3
|
58.3
|
0.6
|
|
CD2
|
d:HIS268
|
3.3
|
55.0
|
0.4
|
|
CE1
|
a:HIS272
|
3.3
|
49.1
|
0.6
|
|
CD2
|
a:HIS272
|
3.3
|
52.2
|
0.4
|
|
CD2
|
d:HIS268
|
3.3
|
54.9
|
0.6
|
|
CD2
|
a:HIS272
|
3.4
|
52.2
|
0.6
|
|
O3
|
d:BCT401
|
3.9
|
76.6
|
0.4
|
|
ND1
|
a:HIS215
|
4.1
|
55.8
|
0.4
|
|
ND1
|
a:HIS215
|
4.2
|
55.6
|
0.6
|
|
O3
|
d:BCT401
|
4.2
|
81.4
|
0.6
|
|
CG
|
a:HIS215
|
4.3
|
60.3
|
0.4
|
|
ND1
|
d:HIS214
|
4.3
|
52.1
|
0.4
|
|
ND1
|
d:HIS214
|
4.3
|
52.0
|
0.6
|
|
CG
|
a:HIS215
|
4.3
|
60.4
|
0.6
|
|
CG
|
d:HIS214
|
4.3
|
54.6
|
0.6
|
|
CG
|
d:HIS214
|
4.4
|
54.5
|
0.4
|
|
ND1
|
a:HIS272
|
4.4
|
62.2
|
0.4
|
|
ND1
|
d:HIS268
|
4.4
|
52.9
|
0.4
|
|
ND1
|
d:HIS268
|
4.4
|
52.9
|
0.6
|
|
ND1
|
a:HIS272
|
4.4
|
62.2
|
0.6
|
|
CG
|
d:HIS268
|
4.4
|
55.0
|
0.4
|
|
CG
|
a:HIS272
|
4.4
|
52.3
|
0.4
|
|
CG
|
d:HIS268
|
4.5
|
55.1
|
0.6
|
|
CG
|
a:HIS272
|
4.5
|
52.1
|
0.6
|
|
CG2
|
a:VAL219
|
4.6
|
56.7
|
0.4
|
|
CG2
|
a:VAL219
|
4.7
|
57.0
|
0.6
|
|
CG2
|
d:VAL218
|
4.8
|
50.1
|
0.6
|
|
CG2
|
d:VAL218
|
4.9
|
50.0
|
0.4
|
|
OH
|
d:TYR244
|
5.0
|
60.3
|
0.6
|
|
OH
|
d:TYR244
|
5.0
|
60.5
|
0.4
|
|
Iron binding site 6 out
of 8 in 8irb
Go back to
Iron Binding Sites List in 8irb
Iron binding site 6 out
of 8 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Fe401
b:55.8
occ:0.60
|
FE
|
a:FE2401
|
0.0
|
55.8
|
0.6
|
|
FE
|
a:FE2401
|
0.1
|
55.2
|
0.4
|
|
O2
|
d:BCT401
|
2.1
|
56.6
|
0.4
|
|
NE2
|
a:HIS215
|
2.1
|
57.8
|
0.4
|
|
NE2
|
a:HIS215
|
2.2
|
57.7
|
0.6
|
|
NE2
|
d:HIS214
|
2.2
|
53.3
|
0.4
|
|
NE2
|
d:HIS214
|
2.2
|
53.3
|
0.6
|
|
NE2
|
a:HIS272
|
2.3
|
55.0
|
0.4
|
|
NE2
|
a:HIS272
|
2.3
|
54.8
|
0.6
|
|
NE2
|
d:HIS268
|
2.4
|
56.1
|
0.4
|
|
NE2
|
d:HIS268
|
2.4
|
56.1
|
0.6
|
|
O1
|
d:BCT401
|
2.5
|
56.4
|
0.4
|
|
O2
|
d:BCT401
|
2.5
|
63.7
|
0.6
|
|
C
|
d:BCT401
|
2.6
|
67.0
|
0.4
|
|
O1
|
d:BCT401
|
2.6
|
57.5
|
0.6
|
|
C
|
d:BCT401
|
2.9
|
68.0
|
0.6
|
|
CE1
|
a:HIS215
|
3.0
|
55.6
|
0.4
|
|
CE1
|
a:HIS215
|
3.0
|
55.5
|
0.6
|
|
CE1
|
a:HIS272
|
3.2
|
49.3
|
0.4
|
|
CE1
|
d:HIS214
|
3.2
|
55.0
|
0.4
|
|
CE1
|
d:HIS214
|
3.2
|
55.1
|
0.6
|
|
CD2
|
d:HIS214
|
3.2
|
47.9
|
0.6
|
|
CD2
|
d:HIS214
|
3.2
|
48.0
|
0.4
|
|
CD2
|
a:HIS215
|
3.2
|
59.5
|
0.4
|
|
CE1
|
a:HIS272
|
3.3
|
49.1
|
0.6
|
|
CD2
|
a:HIS272
|
3.3
|
52.2
|
0.4
|
|
CD2
|
a:HIS215
|
3.3
|
59.5
|
0.6
|
|
CE1
|
d:HIS268
|
3.3
|
58.2
|
0.4
|
|
CD2
|
a:HIS272
|
3.3
|
52.2
|
0.6
|
|
CE1
|
d:HIS268
|
3.3
|
58.3
|
0.6
|
|
CD2
|
d:HIS268
|
3.4
|
55.0
|
0.4
|
|
CD2
|
d:HIS268
|
3.4
|
54.9
|
0.6
|
|
O3
|
d:BCT401
|
3.9
|
76.6
|
0.4
|
|
ND1
|
a:HIS215
|
4.1
|
55.8
|
0.4
|
|
ND1
|
a:HIS215
|
4.2
|
55.6
|
0.6
|
|
O3
|
d:BCT401
|
4.2
|
81.4
|
0.6
|
|
CG
|
a:HIS215
|
4.3
|
60.3
|
0.4
|
|
ND1
|
d:HIS214
|
4.3
|
52.1
|
0.4
|
|
ND1
|
d:HIS214
|
4.3
|
52.0
|
0.6
|
|
ND1
|
a:HIS272
|
4.3
|
62.2
|
0.4
|
|
CG
|
a:HIS215
|
4.3
|
60.4
|
0.6
|
|
CG
|
d:HIS214
|
4.4
|
54.6
|
0.6
|
|
CG
|
d:HIS214
|
4.4
|
54.5
|
0.4
|
|
ND1
|
a:HIS272
|
4.4
|
62.2
|
0.6
|
|
CG
|
a:HIS272
|
4.4
|
52.3
|
0.4
|
|
ND1
|
d:HIS268
|
4.4
|
52.9
|
0.4
|
|
CG
|
a:HIS272
|
4.5
|
52.1
|
0.6
|
|
ND1
|
d:HIS268
|
4.5
|
52.9
|
0.6
|
|
CG
|
d:HIS268
|
4.5
|
55.0
|
0.4
|
|
CG
|
d:HIS268
|
4.5
|
55.1
|
0.6
|
|
CG2
|
a:VAL219
|
4.6
|
56.7
|
0.4
|
|
CG2
|
a:VAL219
|
4.7
|
57.0
|
0.6
|
|
CG2
|
d:VAL218
|
4.8
|
50.1
|
0.6
|
|
CG2
|
d:VAL218
|
4.8
|
50.0
|
0.4
|
|
OH
|
d:TYR244
|
5.0
|
60.3
|
0.6
|
|
OH
|
d:TYR244
|
5.0
|
60.5
|
0.4
|
|
Iron binding site 7 out
of 8 in 8irb
Go back to
Iron Binding Sites List in 8irb
Iron binding site 7 out
of 8 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
f:Fe101
b:74.5
occ:1.00
|
FE
|
f:HEM101
|
0.0
|
74.5
|
1.0
|
|
ND
|
f:HEM101
|
2.0
|
67.7
|
1.0
|
|
NA
|
f:HEM101
|
2.0
|
96.1
|
1.0
|
|
NC
|
f:HEM101
|
2.1
|
76.0
|
1.0
|
|
NE2
|
e:HIS23
|
2.1
|
82.5
|
1.0
|
|
NE2
|
f:HIS24
|
2.1
|
79.0
|
1.0
|
|
NB
|
f:HEM101
|
2.1
|
62.3
|
1.0
|
|
C4D
|
f:HEM101
|
2.9
|
80.5
|
1.0
|
|
C1D
|
f:HEM101
|
3.0
|
66.9
|
1.0
|
|
CD2
|
f:HIS24
|
3.0
|
71.2
|
1.0
|
|
C1A
|
f:HEM101
|
3.0
|
83.0
|
1.0
|
|
CE1
|
e:HIS23
|
3.0
|
81.0
|
1.0
|
|
C4C
|
f:HEM101
|
3.1
|
63.6
|
1.0
|
|
C4A
|
f:HEM101
|
3.1
|
90.0
|
1.0
|
|
C1B
|
f:HEM101
|
3.1
|
83.8
|
1.0
|
|
C4B
|
f:HEM101
|
3.1
|
73.1
|
1.0
|
|
CD2
|
e:HIS23
|
3.1
|
78.5
|
1.0
|
|
C1C
|
f:HEM101
|
3.1
|
70.3
|
1.0
|
|
CE1
|
f:HIS24
|
3.1
|
69.4
|
1.0
|
|
CHA
|
f:HEM101
|
3.4
|
74.9
|
1.0
|
|
CHD
|
f:HEM101
|
3.4
|
58.5
|
1.0
|
|
CHB
|
f:HEM101
|
3.5
|
82.1
|
1.0
|
|
CHC
|
f:HEM101
|
3.5
|
66.2
|
1.0
|
|
CG
|
f:HIS24
|
4.1
|
74.3
|
1.0
|
|
ND1
|
e:HIS23
|
4.1
|
86.8
|
1.0
|
|
C3D
|
f:HEM101
|
4.2
|
77.6
|
1.0
|
|
ND1
|
f:HIS24
|
4.2
|
80.9
|
1.0
|
|
C2D
|
f:HEM101
|
4.2
|
78.7
|
1.0
|
|
CG
|
e:HIS23
|
4.2
|
83.5
|
1.0
|
|
C2A
|
f:HEM101
|
4.2
|
92.3
|
1.0
|
|
C3A
|
f:HEM101
|
4.2
|
95.0
|
1.0
|
|
C3C
|
f:HEM101
|
4.3
|
73.4
|
1.0
|
|
C2C
|
f:HEM101
|
4.3
|
80.9
|
1.0
|
|
C2B
|
f:HEM101
|
4.3
|
85.9
|
1.0
|
|
C3B
|
f:HEM101
|
4.3
|
78.2
|
1.0
|
|
CE1
|
e:TYR19
|
4.9
|
76.3
|
1.0
|
|
Iron binding site 8 out
of 8 in 8irb
Go back to
Iron Binding Sites List in 8irb
Iron binding site 8 out
of 8 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
v:Fe201
b:60.5
occ:1.00
|
FE
|
v:HEC201
|
0.0
|
60.5
|
1.0
|
|
NA
|
v:HEC201
|
2.0
|
63.4
|
1.0
|
|
NC
|
v:HEC201
|
2.0
|
65.8
|
1.0
|
|
NB
|
v:HEC201
|
2.0
|
61.0
|
1.0
|
|
NE2
|
v:HIS92
|
2.1
|
63.2
|
1.0
|
|
NE2
|
v:HIS41
|
2.1
|
55.3
|
1.0
|
|
ND
|
v:HEC201
|
2.1
|
60.4
|
1.0
|
|
C1A
|
v:HEC201
|
3.0
|
56.0
|
1.0
|
|
CE1
|
v:HIS92
|
3.0
|
53.5
|
1.0
|
|
C4A
|
v:HEC201
|
3.0
|
60.6
|
1.0
|
|
C1C
|
v:HEC201
|
3.0
|
65.1
|
1.0
|
|
CD2
|
v:HIS41
|
3.0
|
54.4
|
1.0
|
|
CE1
|
v:HIS41
|
3.0
|
60.2
|
1.0
|
|
C4B
|
v:HEC201
|
3.1
|
59.2
|
1.0
|
|
C4D
|
v:HEC201
|
3.1
|
65.4
|
1.0
|
|
C1B
|
v:HEC201
|
3.1
|
55.1
|
1.0
|
|
CD2
|
v:HIS92
|
3.1
|
60.4
|
1.0
|
|
C4C
|
v:HEC201
|
3.1
|
71.5
|
1.0
|
|
C1D
|
v:HEC201
|
3.1
|
61.3
|
1.0
|
|
CHA
|
v:HEC201
|
3.4
|
52.4
|
1.0
|
|
CHC
|
v:HEC201
|
3.4
|
65.6
|
1.0
|
|
CHB
|
v:HEC201
|
3.4
|
65.7
|
1.0
|
|
CHD
|
v:HEC201
|
3.5
|
56.2
|
1.0
|
|
ND1
|
v:HIS92
|
4.1
|
65.1
|
1.0
|
|
ND1
|
v:HIS41
|
4.1
|
57.5
|
1.0
|
|
CG
|
v:HIS41
|
4.2
|
71.6
|
1.0
|
|
CG
|
v:HIS92
|
4.2
|
65.1
|
1.0
|
|
C2A
|
v:HEC201
|
4.2
|
62.4
|
1.0
|
|
C3A
|
v:HEC201
|
4.2
|
64.7
|
1.0
|
|
C2C
|
v:HEC201
|
4.3
|
60.4
|
1.0
|
|
C2B
|
v:HEC201
|
4.3
|
52.5
|
1.0
|
|
C3B
|
v:HEC201
|
4.3
|
51.6
|
1.0
|
|
C3D
|
v:HEC201
|
4.3
|
62.8
|
1.0
|
|
C3C
|
v:HEC201
|
4.3
|
63.6
|
1.0
|
|
C2D
|
v:HEC201
|
4.3
|
70.2
|
1.0
|
|
CE1
|
v:TYR75
|
4.9
|
56.0
|
1.0
|
|
Reference:
H.Li,
Y.Nakajima,
E.Nango,
S.Owada,
D.Yamada,
K.Hashimoto,
F.Luo,
R.Tanaka,
F.Akita,
K.Kato,
J.M.Kang,
Y.Saitoh,
S.Kishi,
H.Yu,
N.Matsubara,
H.Fujii,
M.Sugahara,
M.Suzuki,
T.Masuda,
T.Kimura,
T.N.Thao,
S.Yonekura,
L.J.Yu,
T.Tosha,
K.Tono,
Y.Joti,
T.Hatsui,
M.Yabashi,
M.Kubo,
S.Iwata,
H.Isobe,
K.Yamaguchi,
M.Suga,
J.R.Shen.
Oxygen-Evolving Photosystem II Structures During S1-S2-S3 Transitions. Nature 2024.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-023-06987-5
Page generated: Sat Aug 10 06:00:58 2024
|
