Iron in PDB 6jln: Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET2)
Enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET2)
All present enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET2):
1.10.3.9;
Protein crystallography data
The structure of Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET2), PDB code: 6jln
was solved by
M.Suga,
J.R.Shen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
19.99 /
2.40
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
122.040,
228.840,
286.980,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
15.4 /
21.2
|
Other elements in 6jln:
The structure of Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET2) also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET2)
(pdb code 6jln). 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 (1F State, DATASET2), PDB code: 6jln:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 6jln
Go back to
Iron Binding Sites List in 6jln
Iron binding site 1 out
of 8 in the Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET2)
 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 (1F State, DATASET2) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:66.5
occ:0.40
|
FE
|
A:FE2401
|
0.0
|
66.5
|
0.4
|
|
FE
|
A:FE2401
|
0.2
|
65.5
|
0.6
|
|
NE2
|
A:HIS215
|
2.2
|
55.9
|
0.6
|
|
NE2
|
D:HIS214
|
2.2
|
50.7
|
0.6
|
|
O2
|
A:BCT404
|
2.2
|
71.1
|
0.6
|
|
NE2
|
D:HIS214
|
2.3
|
50.8
|
0.4
|
|
NE2
|
A:HIS215
|
2.3
|
55.4
|
0.4
|
|
O2
|
A:BCT404
|
2.4
|
72.6
|
0.4
|
|
NE2
|
D:HIS268
|
2.4
|
55.5
|
0.6
|
|
NE2
|
D:HIS268
|
2.4
|
53.8
|
0.4
|
|
NE2
|
A:HIS272
|
2.4
|
60.3
|
0.4
|
|
NE2
|
A:HIS272
|
2.4
|
60.4
|
0.6
|
|
O1
|
A:BCT404
|
2.5
|
74.7
|
0.4
|
|
C
|
A:BCT404
|
2.7
|
78.2
|
0.4
|
|
O1
|
A:BCT404
|
2.8
|
72.2
|
0.6
|
|
C
|
A:BCT404
|
2.9
|
78.7
|
0.6
|
|
CE1
|
A:HIS215
|
3.0
|
52.8
|
0.6
|
|
CE1
|
A:HIS215
|
3.0
|
53.9
|
0.4
|
|
CE1
|
D:HIS214
|
3.1
|
50.9
|
0.6
|
|
CE1
|
D:HIS214
|
3.1
|
51.4
|
0.4
|
|
CE1
|
D:HIS268
|
3.2
|
49.0
|
0.6
|
|
CE1
|
A:HIS272
|
3.3
|
58.2
|
0.4
|
|
CE1
|
A:HIS272
|
3.3
|
57.7
|
0.6
|
|
CE1
|
D:HIS268
|
3.3
|
50.0
|
0.4
|
|
CD2
|
D:HIS214
|
3.3
|
48.6
|
0.6
|
|
CD2
|
A:HIS215
|
3.3
|
54.5
|
0.6
|
|
CD2
|
D:HIS268
|
3.3
|
52.9
|
0.4
|
|
CD2
|
D:HIS214
|
3.4
|
49.2
|
0.4
|
|
CD2
|
D:HIS268
|
3.4
|
52.2
|
0.6
|
|
CD2
|
A:HIS272
|
3.4
|
61.7
|
0.4
|
|
CD2
|
A:HIS215
|
3.5
|
54.4
|
0.4
|
|
CD2
|
A:HIS272
|
3.5
|
62.4
|
0.6
|
|
O3
|
A:BCT404
|
4.1
|
88.2
|
0.4
|
|
O3
|
A:BCT404
|
4.1
|
90.0
|
0.6
|
|
ND1
|
A:HIS215
|
4.2
|
56.8
|
0.6
|
|
ND1
|
A:HIS215
|
4.2
|
56.6
|
0.4
|
|
ND1
|
D:HIS214
|
4.2
|
54.6
|
0.6
|
|
ND1
|
D:HIS214
|
4.3
|
54.3
|
0.4
|
|
CG
|
A:HIS215
|
4.4
|
54.9
|
0.6
|
|
ND1
|
D:HIS268
|
4.4
|
55.5
|
0.6
|
|
CG
|
D:HIS214
|
4.4
|
51.2
|
0.6
|
|
ND1
|
D:HIS268
|
4.4
|
55.1
|
0.4
|
|
ND1
|
A:HIS272
|
4.4
|
58.9
|
0.4
|
|
CG
|
D:HIS214
|
4.4
|
51.2
|
0.4
|
|
ND1
|
A:HIS272
|
4.5
|
59.3
|
0.6
|
|
CG
|
A:HIS215
|
4.5
|
54.6
|
0.4
|
|
CG
|
D:HIS268
|
4.5
|
54.4
|
0.4
|
|
CG
|
D:HIS268
|
4.5
|
54.8
|
0.6
|
|
CG2
|
A:VAL219
|
4.5
|
53.7
|
0.4
|
|
CG
|
A:HIS272
|
4.5
|
58.0
|
0.4
|
|
CG
|
A:HIS272
|
4.6
|
57.8
|
0.6
|
|
CG2
|
A:VAL219
|
4.7
|
53.1
|
0.6
|
|
CG2
|
D:VAL218
|
4.7
|
41.7
|
1.0
|
|
OH
|
D:TYR244
|
4.9
|
58.6
|
0.6
|
|
OH
|
D:TYR244
|
5.0
|
58.9
|
0.4
|
|
Iron binding site 2 out
of 8 in 6jln
Go back to
Iron Binding Sites List in 6jln
Iron binding site 2 out
of 8 in the Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET2)
 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 (1F State, DATASET2) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:65.5
occ:0.60
|
FE
|
A:FE2401
|
0.0
|
65.5
|
0.6
|
|
FE
|
A:FE2401
|
0.2
|
66.5
|
0.4
|
|
NE2
|
D:HIS214
|
2.2
|
50.7
|
0.6
|
|
NE2
|
D:HIS214
|
2.2
|
50.8
|
0.4
|
|
O2
|
A:BCT404
|
2.3
|
71.1
|
0.6
|
|
NE2
|
A:HIS215
|
2.3
|
55.9
|
0.6
|
|
NE2
|
A:HIS272
|
2.3
|
60.3
|
0.4
|
|
NE2
|
A:HIS272
|
2.4
|
60.4
|
0.6
|
|
O2
|
A:BCT404
|
2.4
|
72.6
|
0.4
|
|
O1
|
A:BCT404
|
2.4
|
74.7
|
0.4
|
|
NE2
|
A:HIS215
|
2.4
|
55.4
|
0.4
|
|
NE2
|
D:HIS268
|
2.4
|
53.8
|
0.4
|
|
NE2
|
D:HIS268
|
2.4
|
55.5
|
0.6
|
|
C
|
A:BCT404
|
2.7
|
78.2
|
0.4
|
|
O1
|
A:BCT404
|
2.8
|
72.2
|
0.6
|
|
C
|
A:BCT404
|
2.8
|
78.7
|
0.6
|
|
CE1
|
D:HIS214
|
3.0
|
50.9
|
0.6
|
|
CE1
|
D:HIS214
|
3.0
|
51.4
|
0.4
|
|
CE1
|
A:HIS215
|
3.1
|
52.8
|
0.6
|
|
CE1
|
A:HIS215
|
3.1
|
53.9
|
0.4
|
|
CE1
|
A:HIS272
|
3.2
|
58.2
|
0.4
|
|
CE1
|
D:HIS268
|
3.2
|
49.0
|
0.6
|
|
CE1
|
A:HIS272
|
3.3
|
57.7
|
0.6
|
|
CD2
|
D:HIS214
|
3.3
|
48.6
|
0.6
|
|
CD2
|
D:HIS214
|
3.3
|
49.2
|
0.4
|
|
CE1
|
D:HIS268
|
3.3
|
50.0
|
0.4
|
|
CD2
|
A:HIS272
|
3.4
|
61.7
|
0.4
|
|
CD2
|
A:HIS272
|
3.4
|
62.4
|
0.6
|
|
CD2
|
A:HIS215
|
3.4
|
54.5
|
0.6
|
|
CD2
|
D:HIS268
|
3.4
|
52.9
|
0.4
|
|
CD2
|
D:HIS268
|
3.5
|
52.2
|
0.6
|
|
CD2
|
A:HIS215
|
3.6
|
54.4
|
0.4
|
|
O3
|
A:BCT404
|
4.0
|
88.2
|
0.4
|
|
O3
|
A:BCT404
|
4.1
|
90.0
|
0.6
|
|
ND1
|
D:HIS214
|
4.2
|
54.6
|
0.6
|
|
ND1
|
D:HIS214
|
4.2
|
54.3
|
0.4
|
|
ND1
|
A:HIS215
|
4.3
|
56.8
|
0.6
|
|
CG
|
D:HIS214
|
4.3
|
51.2
|
0.6
|
|
ND1
|
A:HIS215
|
4.4
|
56.6
|
0.4
|
|
CG
|
D:HIS214
|
4.4
|
51.2
|
0.4
|
|
ND1
|
A:HIS272
|
4.4
|
58.9
|
0.4
|
|
ND1
|
A:HIS272
|
4.4
|
59.3
|
0.6
|
|
ND1
|
D:HIS268
|
4.4
|
55.5
|
0.6
|
|
CG
|
A:HIS272
|
4.5
|
58.0
|
0.4
|
|
ND1
|
D:HIS268
|
4.5
|
55.1
|
0.4
|
|
CG
|
A:HIS215
|
4.5
|
54.9
|
0.6
|
|
CG
|
A:HIS272
|
4.5
|
57.8
|
0.6
|
|
CG
|
D:HIS268
|
4.6
|
54.4
|
0.4
|
|
CG2
|
D:VAL218
|
4.6
|
41.7
|
1.0
|
|
CG
|
A:HIS215
|
4.6
|
54.6
|
0.4
|
|
CG
|
D:HIS268
|
4.6
|
54.8
|
0.6
|
|
CG2
|
A:VAL219
|
4.7
|
53.7
|
0.4
|
|
OH
|
D:TYR244
|
4.8
|
58.6
|
0.6
|
|
CG2
|
A:VAL219
|
4.8
|
53.1
|
0.6
|
|
OH
|
D:TYR244
|
4.8
|
58.9
|
0.4
|
|
Iron binding site 3 out
of 8 in 6jln
Go back to
Iron Binding Sites List in 6jln
Iron binding site 3 out
of 8 in the Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET2)
 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 (1F State, DATASET2) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe103
b:88.9
occ:1.00
|
FE
|
E:HEM103
|
0.0
|
88.9
|
1.0
|
|
ND
|
E:HEM103
|
2.0
|
67.9
|
1.0
|
|
NA
|
E:HEM103
|
2.0
|
88.7
|
1.0
|
|
NC
|
E:HEM103
|
2.1
|
73.5
|
1.0
|
|
NB
|
E:HEM103
|
2.1
|
78.5
|
1.0
|
|
NE2
|
F:HIS24
|
2.1
|
0.1
|
1.0
|
|
NE2
|
E:HIS23
|
2.1
|
91.0
|
1.0
|
|
C4D
|
E:HEM103
|
2.9
|
79.9
|
1.0
|
|
C1A
|
E:HEM103
|
2.9
|
91.6
|
1.0
|
|
C1D
|
E:HEM103
|
2.9
|
68.6
|
1.0
|
|
CE1
|
F:HIS24
|
3.0
|
91.7
|
1.0
|
|
CE1
|
E:HIS23
|
3.0
|
88.1
|
1.0
|
|
C4A
|
E:HEM103
|
3.0
|
86.7
|
1.0
|
|
CD2
|
F:HIS24
|
3.1
|
94.9
|
1.0
|
|
C4C
|
E:HEM103
|
3.1
|
77.9
|
1.0
|
|
C1B
|
E:HEM103
|
3.1
|
82.1
|
1.0
|
|
C4B
|
E:HEM103
|
3.1
|
78.6
|
1.0
|
|
CD2
|
E:HIS23
|
3.1
|
91.1
|
1.0
|
|
C1C
|
E:HEM103
|
3.1
|
63.1
|
1.0
|
|
CHA
|
E:HEM103
|
3.3
|
85.4
|
1.0
|
|
CHD
|
E:HEM103
|
3.4
|
73.9
|
1.0
|
|
CHB
|
E:HEM103
|
3.5
|
84.3
|
1.0
|
|
CHC
|
E:HEM103
|
3.5
|
69.7
|
1.0
|
|
ND1
|
F:HIS24
|
4.0
|
81.4
|
1.0
|
|
CG
|
F:HIS24
|
4.1
|
85.1
|
1.0
|
|
ND1
|
E:HIS23
|
4.1
|
83.2
|
1.0
|
|
C2A
|
E:HEM103
|
4.1
|
99.7
|
1.0
|
|
C3D
|
E:HEM103
|
4.1
|
75.8
|
1.0
|
|
C2D
|
E:HEM103
|
4.2
|
70.0
|
1.0
|
|
C3A
|
E:HEM103
|
4.2
|
95.1
|
1.0
|
|
CG
|
E:HIS23
|
4.2
|
86.6
|
1.0
|
|
C3C
|
E:HEM103
|
4.3
|
78.5
|
1.0
|
|
C2C
|
E:HEM103
|
4.3
|
69.5
|
1.0
|
|
C2B
|
E:HEM103
|
4.3
|
82.3
|
1.0
|
|
C3B
|
E:HEM103
|
4.3
|
82.1
|
1.0
|
|
CE2
|
E:TYR19
|
4.9
|
83.4
|
1.0
|
|
NE1
|
F:TRP20
|
5.0
|
95.0
|
1.0
|
|
Iron binding site 4 out
of 8 in 6jln
Go back to
Iron Binding Sites List in 6jln
Iron binding site 4 out
of 8 in the Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET2)
 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 (1F State, DATASET2) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
V:Fe205
b:56.6
occ:1.00
|
FE
|
V:HEM205
|
0.0
|
56.6
|
1.0
|
|
ND
|
V:HEM205
|
2.0
|
65.0
|
1.0
|
|
NA
|
V:HEM205
|
2.0
|
67.4
|
1.0
|
|
NC
|
V:HEM205
|
2.1
|
44.7
|
1.0
|
|
NE2
|
V:HIS41
|
2.1
|
52.9
|
1.0
|
|
NE2
|
V:HIS92
|
2.1
|
59.8
|
1.0
|
|
NB
|
V:HEM205
|
2.1
|
65.2
|
1.0
|
|
C4D
|
V:HEM205
|
2.9
|
44.7
|
1.0
|
|
C1A
|
V:HEM205
|
3.0
|
62.5
|
1.0
|
|
C1D
|
V:HEM205
|
3.0
|
55.6
|
1.0
|
|
C4A
|
V:HEM205
|
3.0
|
62.9
|
1.0
|
|
CD2
|
V:HIS92
|
3.0
|
59.6
|
1.0
|
|
C4C
|
V:HEM205
|
3.1
|
55.2
|
1.0
|
|
CE1
|
V:HIS92
|
3.1
|
59.9
|
1.0
|
|
CD2
|
V:HIS41
|
3.1
|
52.1
|
1.0
|
|
C1B
|
V:HEM205
|
3.1
|
54.4
|
1.0
|
|
CE1
|
V:HIS41
|
3.1
|
56.6
|
1.0
|
|
C4B
|
V:HEM205
|
3.1
|
56.3
|
1.0
|
|
C1C
|
V:HEM205
|
3.1
|
59.0
|
1.0
|
|
CHA
|
V:HEM205
|
3.3
|
45.1
|
1.0
|
|
CHD
|
V:HEM205
|
3.4
|
53.1
|
1.0
|
|
CHB
|
V:HEM205
|
3.5
|
57.4
|
1.0
|
|
CHC
|
V:HEM205
|
3.5
|
52.9
|
1.0
|
|
ND1
|
V:HIS92
|
4.1
|
55.9
|
1.0
|
|
C2A
|
V:HEM205
|
4.2
|
62.9
|
1.0
|
|
CG
|
V:HIS92
|
4.2
|
63.1
|
1.0
|
|
C3D
|
V:HEM205
|
4.2
|
52.1
|
1.0
|
|
ND1
|
V:HIS41
|
4.2
|
49.0
|
1.0
|
|
C3A
|
V:HEM205
|
4.2
|
66.0
|
1.0
|
|
C2D
|
V:HEM205
|
4.2
|
57.0
|
1.0
|
|
CG
|
V:HIS41
|
4.2
|
50.5
|
1.0
|
|
C3C
|
V:HEM205
|
4.3
|
59.7
|
1.0
|
|
C2C
|
V:HEM205
|
4.3
|
62.4
|
1.0
|
|
C2B
|
V:HEM205
|
4.3
|
53.3
|
1.0
|
|
C3B
|
V:HEM205
|
4.3
|
58.4
|
1.0
|
|
CE1
|
V:TYR75
|
4.7
|
56.8
|
1.0
|
|
Iron binding site 5 out
of 8 in 6jln
Go back to
Iron Binding Sites List in 6jln
Iron binding site 5 out
of 8 in the Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET2)
 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 (1F State, DATASET2) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Fe406
b:62.6
occ:0.40
|
FE
|
a:FE2406
|
0.0
|
62.6
|
0.4
|
|
FE
|
a:FE2406
|
0.1
|
62.4
|
0.6
|
|
O2
|
d:BCT401
|
1.8
|
85.7
|
0.6
|
|
NE2
|
a:HIS215
|
2.2
|
55.9
|
0.6
|
|
NE2
|
a:HIS215
|
2.2
|
54.3
|
0.4
|
|
NE2
|
d:HIS214
|
2.3
|
48.5
|
0.6
|
|
O2
|
d:BCT401
|
2.3
|
88.8
|
0.4
|
|
NE2
|
d:HIS268
|
2.3
|
50.8
|
0.6
|
|
NE2
|
d:HIS214
|
2.3
|
49.7
|
0.4
|
|
C
|
d:BCT401
|
2.4
|
88.4
|
0.6
|
|
O1
|
d:BCT401
|
2.4
|
85.5
|
0.6
|
|
NE2
|
a:HIS272
|
2.4
|
56.7
|
0.6
|
|
NE2
|
a:HIS272
|
2.4
|
56.3
|
0.4
|
|
NE2
|
d:HIS268
|
2.4
|
51.0
|
0.4
|
|
O1
|
d:BCT401
|
2.5
|
86.5
|
0.4
|
|
C
|
d:BCT401
|
2.7
|
90.2
|
0.4
|
|
CE1
|
a:HIS215
|
2.9
|
47.7
|
0.6
|
|
CE1
|
a:HIS215
|
3.0
|
48.6
|
0.4
|
|
CE1
|
d:HIS214
|
3.1
|
54.7
|
0.6
|
|
CE1
|
d:HIS214
|
3.2
|
54.3
|
0.4
|
|
CE1
|
a:HIS272
|
3.2
|
53.8
|
0.4
|
|
CE1
|
d:HIS268
|
3.2
|
44.7
|
0.6
|
|
CE1
|
a:HIS272
|
3.2
|
52.7
|
0.6
|
|
CD2
|
a:HIS215
|
3.3
|
53.7
|
0.6
|
|
CD2
|
d:HIS268
|
3.4
|
52.9
|
0.4
|
|
CD2
|
d:HIS214
|
3.4
|
50.4
|
0.6
|
|
CE1
|
d:HIS268
|
3.4
|
46.5
|
0.4
|
|
CD2
|
a:HIS215
|
3.4
|
53.9
|
0.4
|
|
CD2
|
d:HIS268
|
3.4
|
52.6
|
0.6
|
|
CD2
|
d:HIS214
|
3.4
|
50.0
|
0.4
|
|
CD2
|
a:HIS272
|
3.4
|
55.2
|
0.6
|
|
CD2
|
a:HIS272
|
3.5
|
55.2
|
0.4
|
|
O3
|
d:BCT401
|
3.7
|
93.1
|
0.6
|
|
O3
|
d:BCT401
|
4.1
|
94.6
|
0.4
|
|
ND1
|
a:HIS215
|
4.1
|
47.8
|
0.6
|
|
ND1
|
a:HIS215
|
4.2
|
49.3
|
0.4
|
|
ND1
|
d:HIS214
|
4.3
|
53.3
|
0.6
|
|
CG
|
a:HIS215
|
4.3
|
54.0
|
0.6
|
|
ND1
|
d:HIS214
|
4.4
|
52.7
|
0.4
|
|
ND1
|
d:HIS268
|
4.4
|
51.0
|
0.6
|
|
ND1
|
a:HIS272
|
4.4
|
56.2
|
0.4
|
|
CG
|
a:HIS215
|
4.4
|
53.2
|
0.4
|
|
ND1
|
a:HIS272
|
4.4
|
56.6
|
0.6
|
|
CG
|
d:HIS214
|
4.4
|
49.4
|
0.6
|
|
CG2
|
a:VAL219
|
4.5
|
52.4
|
0.4
|
|
CG
|
d:HIS268
|
4.5
|
52.2
|
0.6
|
|
ND1
|
d:HIS268
|
4.5
|
50.5
|
0.4
|
|
CG
|
d:HIS214
|
4.5
|
49.6
|
0.4
|
|
CG
|
d:HIS268
|
4.5
|
52.0
|
0.4
|
|
CG
|
a:HIS272
|
4.5
|
56.0
|
0.6
|
|
CG
|
a:HIS272
|
4.6
|
55.8
|
0.4
|
|
CG2
|
a:VAL219
|
4.7
|
52.0
|
0.6
|
|
CG2
|
d:VAL218
|
4.8
|
46.3
|
1.0
|
|
OH
|
d:TYR244
|
4.9
|
59.7
|
0.6
|
|
OH
|
d:TYR244
|
5.0
|
60.3
|
0.4
|
|
Iron binding site 6 out
of 8 in 6jln
Go back to
Iron Binding Sites List in 6jln
Iron binding site 6 out
of 8 in the Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET2)
 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 (1F State, DATASET2) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Fe406
b:62.4
occ:0.60
|
FE
|
a:FE2406
|
0.0
|
62.4
|
0.6
|
|
FE
|
a:FE2406
|
0.1
|
62.6
|
0.4
|
|
O2
|
d:BCT401
|
1.7
|
85.7
|
0.6
|
|
NE2
|
a:HIS215
|
2.1
|
55.9
|
0.6
|
|
NE2
|
a:HIS215
|
2.2
|
54.3
|
0.4
|
|
O2
|
d:BCT401
|
2.3
|
88.8
|
0.4
|
|
NE2
|
d:HIS268
|
2.3
|
50.8
|
0.6
|
|
C
|
d:BCT401
|
2.3
|
88.4
|
0.6
|
|
NE2
|
d:HIS214
|
2.4
|
48.5
|
0.6
|
|
NE2
|
a:HIS272
|
2.4
|
56.7
|
0.6
|
|
NE2
|
d:HIS268
|
2.4
|
51.0
|
0.4
|
|
NE2
|
a:HIS272
|
2.4
|
56.3
|
0.4
|
|
O1
|
d:BCT401
|
2.4
|
85.5
|
0.6
|
|
NE2
|
d:HIS214
|
2.4
|
49.7
|
0.4
|
|
O1
|
d:BCT401
|
2.5
|
86.5
|
0.4
|
|
C
|
d:BCT401
|
2.7
|
90.2
|
0.4
|
|
CE1
|
a:HIS215
|
2.8
|
47.7
|
0.6
|
|
CE1
|
a:HIS215
|
2.9
|
48.6
|
0.4
|
|
CE1
|
a:HIS272
|
3.2
|
53.8
|
0.4
|
|
CE1
|
d:HIS214
|
3.2
|
54.7
|
0.6
|
|
CE1
|
a:HIS272
|
3.2
|
52.7
|
0.6
|
|
CE1
|
d:HIS268
|
3.2
|
44.7
|
0.6
|
|
CD2
|
a:HIS215
|
3.3
|
53.7
|
0.6
|
|
CD2
|
a:HIS215
|
3.3
|
53.9
|
0.4
|
|
CE1
|
d:HIS214
|
3.3
|
54.3
|
0.4
|
|
CD2
|
d:HIS268
|
3.3
|
52.9
|
0.4
|
|
CD2
|
d:HIS268
|
3.4
|
52.6
|
0.6
|
|
CE1
|
d:HIS268
|
3.4
|
46.5
|
0.4
|
|
CD2
|
d:HIS214
|
3.4
|
50.4
|
0.6
|
|
CD2
|
a:HIS272
|
3.5
|
55.2
|
0.6
|
|
CD2
|
d:HIS214
|
3.5
|
50.0
|
0.4
|
|
CD2
|
a:HIS272
|
3.5
|
55.2
|
0.4
|
|
O3
|
d:BCT401
|
3.6
|
93.1
|
0.6
|
|
ND1
|
a:HIS215
|
4.0
|
47.8
|
0.6
|
|
O3
|
d:BCT401
|
4.1
|
94.6
|
0.4
|
|
ND1
|
a:HIS215
|
4.1
|
49.3
|
0.4
|
|
CG
|
a:HIS215
|
4.3
|
54.0
|
0.6
|
|
CG
|
a:HIS215
|
4.3
|
53.2
|
0.4
|
|
CG2
|
a:VAL219
|
4.4
|
52.4
|
0.4
|
|
ND1
|
d:HIS268
|
4.4
|
51.0
|
0.6
|
|
ND1
|
a:HIS272
|
4.4
|
56.2
|
0.4
|
|
ND1
|
d:HIS214
|
4.4
|
53.3
|
0.6
|
|
ND1
|
a:HIS272
|
4.4
|
56.6
|
0.6
|
|
CG
|
d:HIS268
|
4.5
|
52.2
|
0.6
|
|
ND1
|
d:HIS214
|
4.5
|
52.7
|
0.4
|
|
ND1
|
d:HIS268
|
4.5
|
50.5
|
0.4
|
|
CG
|
d:HIS268
|
4.5
|
52.0
|
0.4
|
|
CG
|
d:HIS214
|
4.5
|
49.4
|
0.6
|
|
CG
|
a:HIS272
|
4.6
|
56.0
|
0.6
|
|
CG
|
a:HIS272
|
4.6
|
55.8
|
0.4
|
|
CG2
|
a:VAL219
|
4.6
|
52.0
|
0.6
|
|
CG
|
d:HIS214
|
4.6
|
49.6
|
0.4
|
|
CG2
|
d:VAL218
|
4.9
|
46.3
|
1.0
|
|
OH
|
d:TYR244
|
5.0
|
59.7
|
0.6
|
|
Iron binding site 7 out
of 8 in 6jln
Go back to
Iron Binding Sites List in 6jln
Iron binding site 7 out
of 8 in the Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET2)
 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 (1F State, DATASET2) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
f:Fe101
b:84.4
occ:1.00
|
FE
|
f:HEM101
|
0.0
|
84.4
|
1.0
|
|
ND
|
f:HEM101
|
2.0
|
67.4
|
1.0
|
|
NA
|
f:HEM101
|
2.0
|
94.6
|
1.0
|
|
NC
|
f:HEM101
|
2.1
|
72.0
|
1.0
|
|
NE2
|
e:HIS23
|
2.1
|
84.8
|
1.0
|
|
NE2
|
f:HIS24
|
2.1
|
82.0
|
1.0
|
|
NB
|
f:HEM101
|
2.1
|
88.1
|
1.0
|
|
C4D
|
f:HEM101
|
2.9
|
74.6
|
1.0
|
|
C1D
|
f:HEM101
|
3.0
|
74.6
|
1.0
|
|
C1A
|
f:HEM101
|
3.0
|
98.0
|
1.0
|
|
CD2
|
f:HIS24
|
3.0
|
84.8
|
1.0
|
|
C4A
|
f:HEM101
|
3.0
|
93.3
|
1.0
|
|
CE1
|
e:HIS23
|
3.1
|
82.2
|
1.0
|
|
C4C
|
f:HEM101
|
3.1
|
66.6
|
1.0
|
|
CD2
|
e:HIS23
|
3.1
|
82.3
|
1.0
|
|
C1B
|
f:HEM101
|
3.1
|
90.6
|
1.0
|
|
C4B
|
f:HEM101
|
3.1
|
88.6
|
1.0
|
|
CE1
|
f:HIS24
|
3.1
|
76.9
|
1.0
|
|
C1C
|
f:HEM101
|
3.1
|
78.3
|
1.0
|
|
CHA
|
f:HEM101
|
3.4
|
83.5
|
1.0
|
|
CHD
|
f:HEM101
|
3.4
|
70.0
|
1.0
|
|
CHB
|
f:HEM101
|
3.5
|
96.0
|
1.0
|
|
CHC
|
f:HEM101
|
3.5
|
82.3
|
1.0
|
|
CG
|
f:HIS24
|
4.1
|
78.0
|
1.0
|
|
ND1
|
e:HIS23
|
4.1
|
71.4
|
1.0
|
|
ND1
|
f:HIS24
|
4.2
|
82.7
|
1.0
|
|
C2A
|
f:HEM101
|
4.2
|
0.5
|
1.0
|
|
C3D
|
f:HEM101
|
4.2
|
85.2
|
1.0
|
|
CG
|
e:HIS23
|
4.2
|
75.6
|
1.0
|
|
C2D
|
f:HEM101
|
4.2
|
87.9
|
1.0
|
|
C3A
|
f:HEM101
|
4.2
|
99.0
|
1.0
|
|
C3C
|
f:HEM101
|
4.3
|
81.5
|
1.0
|
|
C2C
|
f:HEM101
|
4.3
|
85.1
|
1.0
|
|
C2B
|
f:HEM101
|
4.3
|
92.2
|
1.0
|
|
C3B
|
f:HEM101
|
4.3
|
90.1
|
1.0
|
|
CE2
|
e:TYR19
|
4.9
|
77.5
|
1.0
|
|
NE1
|
f:TRP20
|
4.9
|
91.6
|
1.0
|
|
Iron binding site 8 out
of 8 in 6jln
Go back to
Iron Binding Sites List in 6jln
Iron binding site 8 out
of 8 in the Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET2)
 Mono view
 Stereo pair view
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|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET2) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
v:Fe206
b:59.6
occ:1.00
|
FE
|
v:HEM206
|
0.0
|
59.6
|
1.0
|
|
ND
|
v:HEM206
|
1.9
|
67.2
|
1.0
|
|
NA
|
v:HEM206
|
2.0
|
67.0
|
1.0
|
|
NE2
|
v:HIS41
|
2.1
|
57.7
|
1.0
|
|
NC
|
v:HEM206
|
2.1
|
75.6
|
1.0
|
|
NE2
|
v:HIS92
|
2.1
|
58.5
|
1.0
|
|
NB
|
v:HEM206
|
2.1
|
74.2
|
1.0
|
|
C4D
|
v:HEM206
|
2.9
|
65.6
|
1.0
|
|
CD2
|
v:HIS41
|
2.9
|
65.9
|
1.0
|
|
C1D
|
v:HEM206
|
2.9
|
73.0
|
1.0
|
|
C1A
|
v:HEM206
|
3.0
|
65.5
|
1.0
|
|
C4A
|
v:HEM206
|
3.0
|
64.3
|
1.0
|
|
C4C
|
v:HEM206
|
3.0
|
71.3
|
1.0
|
|
CD2
|
v:HIS92
|
3.1
|
57.2
|
1.0
|
|
C1B
|
v:HEM206
|
3.1
|
59.7
|
1.0
|
|
CE1
|
v:HIS92
|
3.1
|
58.7
|
1.0
|
|
C4B
|
v:HEM206
|
3.1
|
69.5
|
1.0
|
|
C1C
|
v:HEM206
|
3.1
|
74.6
|
1.0
|
|
CE1
|
v:HIS41
|
3.2
|
61.3
|
1.0
|
|
CHA
|
v:HEM206
|
3.4
|
61.7
|
1.0
|
|
CHD
|
v:HEM206
|
3.4
|
67.2
|
1.0
|
|
CHB
|
v:HEM206
|
3.5
|
63.7
|
1.0
|
|
CHC
|
v:HEM206
|
3.5
|
74.6
|
1.0
|
|
CG
|
v:HIS41
|
4.1
|
55.7
|
1.0
|
|
C3D
|
v:HEM206
|
4.2
|
64.3
|
1.0
|
|
C2D
|
v:HEM206
|
4.2
|
71.6
|
1.0
|
|
C2A
|
v:HEM206
|
4.2
|
65.5
|
1.0
|
|
ND1
|
v:HIS41
|
4.2
|
63.0
|
1.0
|
|
ND1
|
v:HIS92
|
4.2
|
60.9
|
1.0
|
|
C3A
|
v:HEM206
|
4.2
|
63.7
|
1.0
|
|
CG
|
v:HIS92
|
4.2
|
62.0
|
1.0
|
|
C3C
|
v:HEM206
|
4.3
|
72.5
|
1.0
|
|
C2C
|
v:HEM206
|
4.3
|
71.0
|
1.0
|
|
C2B
|
v:HEM206
|
4.3
|
63.8
|
1.0
|
|
C3B
|
v:HEM206
|
4.4
|
63.1
|
1.0
|
|
CE1
|
v:TYR75
|
4.9
|
54.8
|
1.0
|
|
Reference:
M.Suga,
F.Akita,
K.Yamashita,
Y.Nakajima,
G.Ueno,
H.Li,
T.Yamane,
K.Hirata,
Y.Umena,
S.Yonekura,
L.J.Yu,
H.Murakami,
T.Nomura,
T.Kimura,
M.Kubo,
S.Baba,
T.Kumasaka,
K.Tono,
M.Yabashi,
H.Isobe,
K.Yamaguchi,
M.Yamamoto,
H.Ago,
J.R.Shen.
An Oxyl/Oxo Mechanism For Oxygen-Oxygen Coupling in Psii Revealed By An X-Ray Free-Electron Laser. Science V. 366 334 2019.
ISSN: ESSN 1095-9203
PubMed: 31624207
DOI: 10.1126/SCIENCE.AAX6998
Page generated: Tue Aug 6 23:22:21 2024
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