Iron in PDB 5ws6: Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset
Enzymatic activity of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset
All present enzymatic activity of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset:
1.10.3.9;
Protein crystallography data
The structure of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset, PDB code: 5ws6
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)
|
20.00 /
2.35
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
124.960,
230.220,
286.020,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
12.9 /
17.5
|
Other elements in 5ws6:
The structure of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset
(pdb code 5ws6). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the
Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset, PDB code: 5ws6:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iron binding site 1 out
of 8 in 5ws6
Go back to
Iron Binding Sites List in 5ws6
Iron binding site 1 out
of 8 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:62.6
occ:0.20
|
FE
|
A:FE2401
|
0.0
|
62.6
|
0.2
|
|
FE
|
A:FE2401
|
0.2
|
60.9
|
0.8
|
|
NE2
|
A:HIS215
|
2.1
|
53.0
|
0.8
|
|
NE2
|
D:HIS214
|
2.1
|
45.1
|
0.2
|
|
NE2
|
A:HIS215
|
2.1
|
50.2
|
0.2
|
|
NE2
|
D:HIS214
|
2.1
|
46.0
|
0.8
|
|
NE2
|
D:HIS268
|
2.2
|
51.5
|
1.0
|
|
O2
|
A:BCT403
|
2.2
|
58.2
|
0.2
|
|
O1
|
A:BCT403
|
2.2
|
60.5
|
0.2
|
|
NE2
|
A:HIS272
|
2.2
|
56.5
|
0.2
|
|
NE2
|
A:HIS272
|
2.4
|
59.1
|
0.8
|
|
O2
|
A:BCT403
|
2.4
|
55.3
|
0.8
|
|
O1
|
A:BCT403
|
2.5
|
61.5
|
0.8
|
|
C
|
A:BCT403
|
2.5
|
60.7
|
0.2
|
|
C
|
A:BCT403
|
2.8
|
62.5
|
0.8
|
|
CE1
|
A:HIS215
|
2.9
|
47.0
|
0.8
|
|
CE1
|
A:HIS215
|
2.9
|
48.6
|
0.2
|
|
CE1
|
D:HIS214
|
3.0
|
43.9
|
0.2
|
|
CE1
|
A:HIS272
|
3.0
|
54.8
|
0.2
|
|
CE1
|
D:HIS214
|
3.1
|
44.5
|
0.8
|
|
CD2
|
D:HIS268
|
3.1
|
41.8
|
1.0
|
|
CD2
|
D:HIS214
|
3.1
|
44.7
|
0.8
|
|
CE1
|
D:HIS268
|
3.1
|
48.3
|
1.0
|
|
CD2
|
A:HIS215
|
3.2
|
47.0
|
0.8
|
|
CD2
|
D:HIS214
|
3.2
|
44.0
|
0.2
|
|
CD2
|
A:HIS215
|
3.2
|
48.6
|
0.2
|
|
CE1
|
A:HIS272
|
3.3
|
53.3
|
0.8
|
|
CD2
|
A:HIS272
|
3.3
|
54.4
|
0.2
|
|
CD2
|
A:HIS272
|
3.4
|
53.5
|
0.8
|
|
O3
|
A:BCT403
|
3.8
|
69.1
|
0.2
|
|
ND1
|
A:HIS215
|
4.1
|
46.7
|
0.8
|
|
O3
|
A:BCT403
|
4.1
|
78.3
|
0.8
|
|
ND1
|
A:HIS215
|
4.1
|
47.6
|
0.2
|
|
ND1
|
D:HIS214
|
4.1
|
42.0
|
0.2
|
|
ND1
|
A:HIS272
|
4.2
|
53.0
|
0.2
|
|
ND1
|
D:HIS214
|
4.2
|
41.0
|
0.8
|
|
ND1
|
D:HIS268
|
4.2
|
48.0
|
1.0
|
|
CG
|
A:HIS215
|
4.3
|
48.4
|
0.8
|
|
CG
|
D:HIS268
|
4.3
|
47.1
|
1.0
|
|
CG
|
D:HIS214
|
4.3
|
42.5
|
0.8
|
|
CG
|
D:HIS214
|
4.3
|
42.3
|
0.2
|
|
CG
|
A:HIS215
|
4.3
|
47.9
|
0.2
|
|
CG
|
A:HIS272
|
4.4
|
54.1
|
0.2
|
|
ND1
|
A:HIS272
|
4.5
|
51.4
|
0.8
|
|
CG
|
A:HIS272
|
4.5
|
55.4
|
0.8
|
|
CG2
|
A:VAL219
|
4.6
|
48.1
|
1.0
|
|
OH
|
D:TYR244
|
4.8
|
52.4
|
1.0
|
|
CG2
|
D:VAL218
|
4.9
|
43.1
|
1.0
|
|
Iron binding site 2 out
of 8 in 5ws6
Go back to
Iron Binding Sites List in 5ws6
Iron binding site 2 out
of 8 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:60.9
occ:0.80
|
FE
|
A:FE2401
|
0.0
|
60.9
|
0.8
|
|
FE
|
A:FE2401
|
0.2
|
62.6
|
0.2
|
|
NE2
|
D:HIS214
|
2.1
|
45.1
|
0.2
|
|
NE2
|
A:HIS272
|
2.1
|
56.5
|
0.2
|
|
O2
|
A:BCT403
|
2.1
|
58.2
|
0.2
|
|
NE2
|
D:HIS214
|
2.1
|
46.0
|
0.8
|
|
NE2
|
A:HIS215
|
2.2
|
53.0
|
0.8
|
|
O1
|
A:BCT403
|
2.2
|
60.5
|
0.2
|
|
NE2
|
A:HIS215
|
2.2
|
50.2
|
0.2
|
|
NE2
|
A:HIS272
|
2.3
|
59.1
|
0.8
|
|
NE2
|
D:HIS268
|
2.3
|
51.5
|
1.0
|
|
O2
|
A:BCT403
|
2.3
|
55.3
|
0.8
|
|
C
|
A:BCT403
|
2.4
|
60.7
|
0.2
|
|
O1
|
A:BCT403
|
2.4
|
61.5
|
0.8
|
|
C
|
A:BCT403
|
2.7
|
62.5
|
0.8
|
|
CE1
|
A:HIS272
|
2.9
|
54.8
|
0.2
|
|
CE1
|
D:HIS214
|
2.9
|
43.9
|
0.2
|
|
CE1
|
A:HIS215
|
3.0
|
47.0
|
0.8
|
|
CE1
|
A:HIS215
|
3.0
|
48.6
|
0.2
|
|
CE1
|
D:HIS214
|
3.0
|
44.5
|
0.8
|
|
CD2
|
D:HIS214
|
3.1
|
44.7
|
0.8
|
|
CD2
|
D:HIS214
|
3.2
|
44.0
|
0.2
|
|
CE1
|
A:HIS272
|
3.2
|
53.3
|
0.8
|
|
CD2
|
A:HIS272
|
3.2
|
54.4
|
0.2
|
|
CE1
|
D:HIS268
|
3.2
|
48.3
|
1.0
|
|
CD2
|
D:HIS268
|
3.3
|
41.8
|
1.0
|
|
CD2
|
A:HIS272
|
3.3
|
53.5
|
0.8
|
|
CD2
|
A:HIS215
|
3.3
|
47.0
|
0.8
|
|
CD2
|
A:HIS215
|
3.3
|
48.6
|
0.2
|
|
O3
|
A:BCT403
|
3.8
|
69.1
|
0.2
|
|
O3
|
A:BCT403
|
4.0
|
78.3
|
0.8
|
|
ND1
|
A:HIS272
|
4.1
|
53.0
|
0.2
|
|
ND1
|
D:HIS214
|
4.1
|
42.0
|
0.2
|
|
ND1
|
D:HIS214
|
4.2
|
41.0
|
0.8
|
|
ND1
|
A:HIS215
|
4.2
|
46.7
|
0.8
|
|
ND1
|
A:HIS215
|
4.2
|
47.6
|
0.2
|
|
CG
|
D:HIS214
|
4.2
|
42.5
|
0.8
|
|
CG
|
D:HIS214
|
4.3
|
42.3
|
0.2
|
|
CG
|
A:HIS272
|
4.3
|
54.1
|
0.2
|
|
ND1
|
A:HIS272
|
4.3
|
51.4
|
0.8
|
|
CG
|
A:HIS215
|
4.3
|
48.4
|
0.8
|
|
ND1
|
D:HIS268
|
4.4
|
48.0
|
1.0
|
|
CG
|
A:HIS215
|
4.4
|
47.9
|
0.2
|
|
CG
|
A:HIS272
|
4.4
|
55.4
|
0.8
|
|
CG
|
D:HIS268
|
4.4
|
47.1
|
1.0
|
|
CG2
|
A:VAL219
|
4.7
|
48.1
|
1.0
|
|
OH
|
D:TYR244
|
4.7
|
52.4
|
1.0
|
|
CG2
|
D:VAL218
|
4.7
|
43.1
|
1.0
|
|
Iron binding site 3 out
of 8 in 5ws6
Go back to
Iron Binding Sites List in 5ws6
Iron binding site 3 out
of 8 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe103
b:77.5
occ:1.00
|
FE
|
E:HEM103
|
0.0
|
77.5
|
1.0
|
|
ND
|
E:HEM103
|
2.0
|
66.3
|
1.0
|
|
NA
|
E:HEM103
|
2.0
|
80.2
|
1.0
|
|
NC
|
E:HEM103
|
2.1
|
68.4
|
1.0
|
|
NE2
|
F:HIS24
|
2.1
|
70.6
|
1.0
|
|
NE2
|
E:HIS23
|
2.1
|
70.6
|
1.0
|
|
NB
|
E:HEM103
|
2.1
|
64.2
|
1.0
|
|
CD2
|
F:HIS24
|
2.9
|
63.3
|
1.0
|
|
C4D
|
E:HEM103
|
2.9
|
72.3
|
1.0
|
|
C1A
|
E:HEM103
|
3.0
|
74.3
|
1.0
|
|
C1D
|
E:HEM103
|
3.0
|
60.1
|
1.0
|
|
CD2
|
E:HIS23
|
3.0
|
70.4
|
1.0
|
|
C4C
|
E:HEM103
|
3.1
|
64.1
|
1.0
|
|
C4A
|
E:HEM103
|
3.1
|
74.8
|
1.0
|
|
C1B
|
E:HEM103
|
3.1
|
71.4
|
1.0
|
|
C4B
|
E:HEM103
|
3.1
|
63.3
|
1.0
|
|
C1C
|
E:HEM103
|
3.1
|
64.1
|
1.0
|
|
CE1
|
E:HIS23
|
3.1
|
66.3
|
1.0
|
|
CE1
|
F:HIS24
|
3.2
|
74.8
|
1.0
|
|
CHA
|
E:HEM103
|
3.3
|
69.7
|
1.0
|
|
CHD
|
E:HEM103
|
3.4
|
62.7
|
1.0
|
|
CHB
|
E:HEM103
|
3.5
|
73.3
|
1.0
|
|
CHC
|
E:HEM103
|
3.5
|
61.3
|
1.0
|
|
CG
|
F:HIS24
|
4.1
|
72.0
|
1.0
|
|
C2A
|
E:HEM103
|
4.2
|
75.0
|
1.0
|
|
C3D
|
E:HEM103
|
4.2
|
71.8
|
1.0
|
|
C2D
|
E:HEM103
|
4.2
|
64.8
|
1.0
|
|
CG
|
E:HIS23
|
4.2
|
65.4
|
1.0
|
|
ND1
|
E:HIS23
|
4.2
|
69.1
|
1.0
|
|
C3A
|
E:HEM103
|
4.2
|
78.5
|
1.0
|
|
ND1
|
F:HIS24
|
4.2
|
76.9
|
1.0
|
|
C3C
|
E:HEM103
|
4.3
|
65.7
|
1.0
|
|
C2C
|
E:HEM103
|
4.3
|
61.0
|
1.0
|
|
C2B
|
E:HEM103
|
4.3
|
73.0
|
1.0
|
|
C3B
|
E:HEM103
|
4.3
|
73.9
|
1.0
|
|
CE2
|
E:TYR19
|
4.9
|
70.8
|
1.0
|
|
NE1
|
F:TRP20
|
5.0
|
84.7
|
1.0
|
|
Iron binding site 4 out
of 8 in 5ws6
Go back to
Iron Binding Sites List in 5ws6
Iron binding site 4 out
of 8 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
V:Fe203
b:57.5
occ:1.00
|
FE
|
V:HEC203
|
0.0
|
57.5
|
1.0
|
|
ND
|
V:HEC203
|
2.0
|
60.9
|
1.0
|
|
NA
|
V:HEC203
|
2.0
|
53.4
|
1.0
|
|
NE2
|
V:HIS41
|
2.1
|
44.2
|
1.0
|
|
NE2
|
V:HIS92
|
2.1
|
44.2
|
1.0
|
|
NC
|
V:HEC203
|
2.1
|
45.9
|
1.0
|
|
NB
|
V:HEC203
|
2.1
|
54.5
|
1.0
|
|
C4D
|
V:HEC203
|
2.9
|
49.5
|
1.0
|
|
C1D
|
V:HEC203
|
3.0
|
46.6
|
1.0
|
|
C1A
|
V:HEC203
|
3.0
|
57.3
|
1.0
|
|
CD2
|
V:HIS41
|
3.0
|
46.0
|
1.0
|
|
C4A
|
V:HEC203
|
3.0
|
54.0
|
1.0
|
|
C4C
|
V:HEC203
|
3.0
|
47.9
|
1.0
|
|
CE1
|
V:HIS92
|
3.0
|
46.7
|
1.0
|
|
C1B
|
V:HEC203
|
3.1
|
50.2
|
1.0
|
|
CD2
|
V:HIS92
|
3.1
|
44.6
|
1.0
|
|
C4B
|
V:HEC203
|
3.1
|
51.8
|
1.0
|
|
CE1
|
V:HIS41
|
3.1
|
52.7
|
1.0
|
|
C1C
|
V:HEC203
|
3.1
|
55.5
|
1.0
|
|
CHA
|
V:HEC203
|
3.4
|
52.8
|
1.0
|
|
CHD
|
V:HEC203
|
3.4
|
52.9
|
1.0
|
|
CHB
|
V:HEC203
|
3.5
|
56.5
|
1.0
|
|
CHC
|
V:HEC203
|
3.5
|
55.7
|
1.0
|
|
ND1
|
V:HIS92
|
4.2
|
47.8
|
1.0
|
|
C3D
|
V:HEC203
|
4.2
|
54.1
|
1.0
|
|
C2A
|
V:HEC203
|
4.2
|
55.4
|
1.0
|
|
C2D
|
V:HEC203
|
4.2
|
46.5
|
1.0
|
|
CG
|
V:HIS41
|
4.2
|
53.1
|
1.0
|
|
ND1
|
V:HIS41
|
4.2
|
55.0
|
1.0
|
|
CG
|
V:HIS92
|
4.2
|
53.2
|
1.0
|
|
C3A
|
V:HEC203
|
4.2
|
50.6
|
1.0
|
|
C3C
|
V:HEC203
|
4.3
|
56.6
|
1.0
|
|
C2B
|
V:HEC203
|
4.3
|
52.3
|
1.0
|
|
C2C
|
V:HEC203
|
4.3
|
58.1
|
1.0
|
|
C3B
|
V:HEC203
|
4.3
|
52.9
|
1.0
|
|
CE1
|
V:TYR75
|
4.8
|
53.1
|
1.0
|
|
Iron binding site 5 out
of 8 in 5ws6
Go back to
Iron Binding Sites List in 5ws6
Iron binding site 5 out
of 8 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Fe401
b:61.0
occ:0.20
|
FE
|
a:FE2401
|
0.0
|
61.0
|
0.2
|
|
FE
|
a:FE2401
|
0.0
|
60.8
|
0.8
|
|
NE2
|
a:HIS215
|
2.1
|
55.7
|
0.2
|
|
NE2
|
a:HIS215
|
2.1
|
58.5
|
0.8
|
|
NE2
|
d:HIS214
|
2.2
|
49.9
|
0.2
|
|
O2
|
a:BCT420
|
2.2
|
63.8
|
0.2
|
|
NE2
|
d:HIS214
|
2.2
|
51.5
|
0.8
|
|
NE2
|
a:HIS272
|
2.2
|
52.4
|
0.2
|
|
O1
|
a:BCT420
|
2.3
|
58.8
|
0.2
|
|
NE2
|
d:HIS268
|
2.3
|
53.8
|
1.0
|
|
NE2
|
a:HIS272
|
2.3
|
52.7
|
0.8
|
|
O2
|
a:BCT420
|
2.3
|
63.8
|
0.8
|
|
O1
|
a:BCT420
|
2.4
|
54.7
|
0.8
|
|
C
|
a:BCT420
|
2.5
|
63.8
|
0.2
|
|
C
|
a:BCT420
|
2.7
|
64.1
|
0.8
|
|
CE1
|
a:HIS215
|
2.9
|
55.6
|
0.2
|
|
CE1
|
a:HIS215
|
3.0
|
54.0
|
0.8
|
|
CE1
|
a:HIS272
|
3.1
|
52.0
|
0.2
|
|
CE1
|
d:HIS214
|
3.1
|
51.8
|
0.2
|
|
CE1
|
d:HIS214
|
3.1
|
51.5
|
0.8
|
|
CD2
|
d:HIS214
|
3.2
|
43.4
|
0.8
|
|
CD2
|
d:HIS214
|
3.2
|
46.8
|
0.2
|
|
CE1
|
d:HIS268
|
3.2
|
61.8
|
1.0
|
|
CE1
|
a:HIS272
|
3.2
|
49.3
|
0.8
|
|
CD2
|
a:HIS215
|
3.2
|
54.4
|
0.2
|
|
CD2
|
a:HIS272
|
3.3
|
52.6
|
0.2
|
|
CD2
|
a:HIS215
|
3.3
|
53.2
|
0.8
|
|
CD2
|
a:HIS272
|
3.3
|
53.1
|
0.8
|
|
CD2
|
d:HIS268
|
3.3
|
54.1
|
1.0
|
|
O3
|
a:BCT420
|
3.8
|
68.9
|
0.2
|
|
O3
|
a:BCT420
|
4.0
|
72.8
|
0.8
|
|
ND1
|
a:HIS215
|
4.1
|
55.4
|
0.2
|
|
ND1
|
a:HIS215
|
4.1
|
57.1
|
0.8
|
|
ND1
|
d:HIS214
|
4.2
|
51.7
|
0.2
|
|
ND1
|
a:HIS272
|
4.2
|
54.4
|
0.2
|
|
ND1
|
d:HIS214
|
4.2
|
54.1
|
0.8
|
|
CG
|
a:HIS215
|
4.3
|
53.3
|
0.2
|
|
CG
|
d:HIS214
|
4.3
|
47.6
|
0.2
|
|
CG
|
d:HIS214
|
4.3
|
47.6
|
0.8
|
|
CG
|
a:HIS215
|
4.3
|
53.6
|
0.8
|
|
ND1
|
d:HIS268
|
4.3
|
51.5
|
1.0
|
|
ND1
|
a:HIS272
|
4.3
|
57.7
|
0.8
|
|
CG
|
a:HIS272
|
4.4
|
53.1
|
0.2
|
|
CG
|
a:HIS272
|
4.4
|
53.2
|
0.8
|
|
CG
|
d:HIS268
|
4.4
|
51.2
|
1.0
|
|
CG2
|
a:VAL219
|
4.5
|
49.7
|
1.0
|
|
CG2
|
d:VAL218
|
4.8
|
46.1
|
1.0
|
|
OH
|
d:TYR244
|
4.8
|
61.3
|
1.0
|
|
Iron binding site 6 out
of 8 in 5ws6
Go back to
Iron Binding Sites List in 5ws6
Iron binding site 6 out
of 8 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Fe401
b:60.8
occ:0.80
|
FE
|
a:FE2401
|
0.0
|
60.8
|
0.8
|
|
FE
|
a:FE2401
|
0.0
|
61.0
|
0.2
|
|
NE2
|
a:HIS215
|
2.1
|
55.7
|
0.2
|
|
NE2
|
a:HIS215
|
2.1
|
58.5
|
0.8
|
|
O2
|
a:BCT420
|
2.2
|
63.8
|
0.2
|
|
NE2
|
d:HIS214
|
2.2
|
49.9
|
0.2
|
|
NE2
|
d:HIS214
|
2.2
|
51.5
|
0.8
|
|
NE2
|
a:HIS272
|
2.2
|
52.4
|
0.2
|
|
NE2
|
d:HIS268
|
2.3
|
53.8
|
1.0
|
|
NE2
|
a:HIS272
|
2.3
|
52.7
|
0.8
|
|
O1
|
a:BCT420
|
2.3
|
58.8
|
0.2
|
|
O2
|
a:BCT420
|
2.3
|
63.8
|
0.8
|
|
O1
|
a:BCT420
|
2.4
|
54.7
|
0.8
|
|
C
|
a:BCT420
|
2.5
|
63.8
|
0.2
|
|
C
|
a:BCT420
|
2.7
|
64.1
|
0.8
|
|
CE1
|
a:HIS215
|
2.9
|
55.6
|
0.2
|
|
CE1
|
a:HIS215
|
2.9
|
54.0
|
0.8
|
|
CE1
|
a:HIS272
|
3.1
|
52.0
|
0.2
|
|
CE1
|
d:HIS214
|
3.1
|
51.8
|
0.2
|
|
CE1
|
d:HIS214
|
3.1
|
51.5
|
0.8
|
|
CD2
|
a:HIS215
|
3.2
|
54.4
|
0.2
|
|
CD2
|
d:HIS214
|
3.2
|
43.4
|
0.8
|
|
CD2
|
d:HIS214
|
3.2
|
46.8
|
0.2
|
|
CE1
|
d:HIS268
|
3.2
|
61.8
|
1.0
|
|
CE1
|
a:HIS272
|
3.2
|
49.3
|
0.8
|
|
CD2
|
a:HIS215
|
3.2
|
53.2
|
0.8
|
|
CD2
|
d:HIS268
|
3.3
|
54.1
|
1.0
|
|
CD2
|
a:HIS272
|
3.3
|
52.6
|
0.2
|
|
CD2
|
a:HIS272
|
3.3
|
53.1
|
0.8
|
|
O3
|
a:BCT420
|
3.9
|
68.9
|
0.2
|
|
ND1
|
a:HIS215
|
4.0
|
55.4
|
0.2
|
|
O3
|
a:BCT420
|
4.1
|
72.8
|
0.8
|
|
ND1
|
a:HIS215
|
4.1
|
57.1
|
0.8
|
|
CG
|
a:HIS215
|
4.2
|
53.3
|
0.2
|
|
ND1
|
a:HIS272
|
4.2
|
54.4
|
0.2
|
|
ND1
|
d:HIS214
|
4.3
|
51.7
|
0.2
|
|
ND1
|
d:HIS214
|
4.3
|
54.1
|
0.8
|
|
CG
|
a:HIS215
|
4.3
|
53.6
|
0.8
|
|
CG
|
d:HIS214
|
4.3
|
47.6
|
0.2
|
|
CG
|
d:HIS214
|
4.3
|
47.6
|
0.8
|
|
ND1
|
d:HIS268
|
4.3
|
51.5
|
1.0
|
|
ND1
|
a:HIS272
|
4.4
|
57.7
|
0.8
|
|
CG
|
a:HIS272
|
4.4
|
53.1
|
0.2
|
|
CG
|
d:HIS268
|
4.4
|
51.2
|
1.0
|
|
CG
|
a:HIS272
|
4.4
|
53.2
|
0.8
|
|
CG2
|
a:VAL219
|
4.5
|
49.7
|
1.0
|
|
CG2
|
d:VAL218
|
4.8
|
46.1
|
1.0
|
|
OH
|
d:TYR244
|
4.9
|
61.3
|
1.0
|
|
Iron binding site 7 out
of 8 in 5ws6
Go back to
Iron Binding Sites List in 5ws6
Iron binding site 7 out
of 8 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
e:Fe102
b:89.2
occ:1.00
|
FE
|
e:HEM102
|
0.0
|
89.2
|
1.0
|
|
ND
|
e:HEM102
|
2.0
|
67.1
|
1.0
|
|
NA
|
e:HEM102
|
2.0
|
0.1
|
1.0
|
|
NC
|
e:HEM102
|
2.1
|
78.2
|
1.0
|
|
NE2
|
f:HIS24
|
2.1
|
79.3
|
1.0
|
|
NE2
|
e:HIS23
|
2.1
|
95.7
|
1.0
|
|
NB
|
e:HEM102
|
2.1
|
84.1
|
1.0
|
|
CD2
|
f:HIS24
|
2.9
|
79.0
|
1.0
|
|
C4D
|
e:HEM102
|
2.9
|
77.6
|
1.0
|
|
C1D
|
e:HEM102
|
3.0
|
71.5
|
1.0
|
|
C1A
|
e:HEM102
|
3.0
|
95.8
|
1.0
|
|
CD2
|
e:HIS23
|
3.0
|
93.0
|
1.0
|
|
C4C
|
e:HEM102
|
3.0
|
72.5
|
1.0
|
|
C4A
|
e:HEM102
|
3.1
|
0.6
|
1.0
|
|
CE1
|
e:HIS23
|
3.1
|
88.0
|
1.0
|
|
C1B
|
e:HEM102
|
3.1
|
94.0
|
1.0
|
|
C4B
|
e:HEM102
|
3.1
|
86.9
|
1.0
|
|
C1C
|
e:HEM102
|
3.1
|
78.2
|
1.0
|
|
CE1
|
f:HIS24
|
3.2
|
87.4
|
1.0
|
|
CHA
|
e:HEM102
|
3.4
|
80.8
|
1.0
|
|
CHD
|
e:HEM102
|
3.4
|
71.2
|
1.0
|
|
CHB
|
e:HEM102
|
3.5
|
95.2
|
1.0
|
|
CHC
|
e:HEM102
|
3.5
|
81.1
|
1.0
|
|
CG
|
f:HIS24
|
4.1
|
78.1
|
1.0
|
|
ND1
|
e:HIS23
|
4.1
|
90.7
|
1.0
|
|
CG
|
e:HIS23
|
4.1
|
90.1
|
1.0
|
|
C3D
|
e:HEM102
|
4.2
|
83.9
|
1.0
|
|
C2D
|
e:HEM102
|
4.2
|
76.4
|
1.0
|
|
C2A
|
e:HEM102
|
4.2
|
0.8
|
1.0
|
|
ND1
|
f:HIS24
|
4.2
|
89.7
|
1.0
|
|
C3A
|
e:HEM102
|
4.2
|
0.8
|
1.0
|
|
C3C
|
e:HEM102
|
4.2
|
81.8
|
1.0
|
|
C2C
|
e:HEM102
|
4.3
|
81.0
|
1.0
|
|
C2B
|
e:HEM102
|
4.3
|
94.1
|
1.0
|
|
C3B
|
e:HEM102
|
4.3
|
95.6
|
1.0
|
|
CE2
|
e:TYR19
|
4.8
|
88.3
|
1.0
|
|
Iron binding site 8 out
of 8 in 5ws6
Go back to
Iron Binding Sites List in 5ws6
Iron binding site 8 out
of 8 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset
 Mono view
 Stereo pair view
|
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
v:Fe203
b:66.7
occ:1.00
|
FE
|
v:HEC203
|
0.0
|
66.7
|
1.0
|
|
ND
|
v:HEC203
|
2.0
|
62.4
|
1.0
|
|
NA
|
v:HEC203
|
2.0
|
62.5
|
1.0
|
|
NE2
|
v:HIS41
|
2.1
|
54.4
|
1.0
|
|
NE2
|
v:HIS92
|
2.1
|
64.6
|
1.0
|
|
NC
|
v:HEC203
|
2.1
|
61.9
|
1.0
|
|
NB
|
v:HEC203
|
2.1
|
68.0
|
1.0
|
|
C4D
|
v:HEC203
|
2.9
|
61.5
|
1.0
|
|
C1D
|
v:HEC203
|
2.9
|
59.0
|
1.0
|
|
C1A
|
v:HEC203
|
2.9
|
58.7
|
1.0
|
|
CE1
|
v:HIS92
|
3.0
|
62.8
|
1.0
|
|
C4A
|
v:HEC203
|
3.0
|
64.4
|
1.0
|
|
CD2
|
v:HIS41
|
3.0
|
56.9
|
1.0
|
|
C4C
|
v:HEC203
|
3.0
|
66.4
|
1.0
|
|
C1B
|
v:HEC203
|
3.1
|
64.6
|
1.0
|
|
C4B
|
v:HEC203
|
3.1
|
64.1
|
1.0
|
|
CE1
|
v:HIS41
|
3.1
|
59.2
|
1.0
|
|
CD2
|
v:HIS92
|
3.1
|
61.9
|
1.0
|
|
C1C
|
v:HEC203
|
3.1
|
63.6
|
1.0
|
|
CHA
|
v:HEC203
|
3.3
|
52.2
|
1.0
|
|
CHD
|
v:HEC203
|
3.4
|
54.9
|
1.0
|
|
CHB
|
v:HEC203
|
3.5
|
62.8
|
1.0
|
|
CHC
|
v:HEC203
|
3.5
|
71.3
|
1.0
|
|
ND1
|
v:HIS92
|
4.1
|
68.5
|
1.0
|
|
C2A
|
v:HEC203
|
4.1
|
65.2
|
1.0
|
|
C3D
|
v:HEC203
|
4.2
|
62.8
|
1.0
|
|
ND1
|
v:HIS41
|
4.2
|
57.8
|
1.0
|
|
CG
|
v:HIS41
|
4.2
|
58.8
|
1.0
|
|
C2D
|
v:HEC203
|
4.2
|
68.8
|
1.0
|
|
C3A
|
v:HEC203
|
4.2
|
65.4
|
1.0
|
|
CG
|
v:HIS92
|
4.2
|
63.0
|
1.0
|
|
C3C
|
v:HEC203
|
4.3
|
69.6
|
1.0
|
|
C2B
|
v:HEC203
|
4.3
|
60.5
|
1.0
|
|
C2C
|
v:HEC203
|
4.3
|
65.0
|
1.0
|
|
C3B
|
v:HEC203
|
4.3
|
66.3
|
1.0
|
|
CE1
|
v:TYR75
|
4.9
|
69.0
|
1.0
|
|
Reference:
M.Suga,
F.Akita,
M.Sugahara,
M.Kubo,
Y.Nakajima,
T.Nakane,
K.Yamashita,
Y.Umena,
M.Nakabayashi,
T.Yamane,
T.Nakano,
M.Suzuki,
T.Masuda,
S.Inoue,
T.Kimura,
T.Nomura,
S.Yonekura,
L.J.Yu,
T.Sakamoto,
T.Motomura,
J.H.Chen,
Y.Kato,
T.Noguchi,
K.Tono,
Y.Joti,
T.Kameshima,
T.Hatsui,
E.Nango,
R.Tanaka,
H.Naitow,
Y.Matsuura,
A.Yamashita,
M.Yamamoto,
O.Nureki,
M.Yabashi,
T.Ishikawa,
S.Iwata,
J.R.Shen.
Light-Induced Structural Changes and the Site of O=O Bond Formation in Psii Caught By Xfel. Nature V. 543 131 2017.
ISSN: ESSN 1476-4687
PubMed: 28219079
DOI: 10.1038/NATURE21400
Page generated: Sun Dec 13 16:16:33 2020
|
