Calcium 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:
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Calcium 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 Calcium atom.
In total 12 binding sites of Calcium where determined in the
Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset, PDB code: 5ws6:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 12 in 5ws6
Go back to
Calcium Binding Sites List in 5ws6
Calcium binding site 1 out
of 12 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca 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:Ca414
b:50.5
occ:0.20
|
CA1
|
A:OEX414
|
0.0
|
50.5
|
0.2
|
|
CA1
|
A:OEY415
|
0.3
|
46.9
|
0.8
|
|
OD1
|
A:ASP170
|
2.2
|
47.9
|
0.8
|
|
OD1
|
A:ASP170
|
2.4
|
46.0
|
0.2
|
|
O5
|
A:OEY415
|
2.4
|
55.7
|
0.8
|
|
O
|
A:ALA344
|
2.4
|
46.3
|
0.2
|
|
O
|
A:HOH620
|
2.5
|
48.5
|
0.8
|
|
O
|
A:HOH550
|
2.5
|
60.0
|
0.2
|
|
O
|
A:ALA344
|
2.6
|
46.1
|
0.8
|
|
O2
|
A:OEY415
|
2.6
|
43.9
|
0.8
|
|
O1
|
A:OEX414
|
2.6
|
47.7
|
0.2
|
|
O5
|
A:OEX414
|
2.6
|
59.1
|
0.2
|
|
O
|
A:HOH620
|
2.6
|
49.5
|
0.2
|
|
O
|
A:HOH550
|
2.6
|
60.5
|
0.8
|
|
O2
|
A:OEX414
|
2.6
|
45.1
|
0.2
|
|
O1
|
A:OEY415
|
2.7
|
48.5
|
0.8
|
|
O6
|
A:OEY415
|
2.9
|
56.7
|
0.4
|
|
OE1
|
A:GLU189
|
3.0
|
49.1
|
0.2
|
|
CG
|
A:ASP170
|
3.0
|
43.3
|
0.8
|
|
OE1
|
A:GLU189
|
3.2
|
49.7
|
0.8
|
|
CG
|
A:ASP170
|
3.2
|
45.3
|
0.2
|
|
C
|
A:ALA344
|
3.4
|
47.4
|
0.2
|
|
MN2
|
A:OEX414
|
3.4
|
49.6
|
0.2
|
|
MN3
|
A:OEY415
|
3.5
|
49.6
|
0.8
|
|
MN2
|
A:OEY415
|
3.5
|
49.8
|
0.8
|
|
OD2
|
A:ASP170
|
3.5
|
50.1
|
0.8
|
|
MN1
|
A:OEY415
|
3.5
|
49.4
|
0.8
|
|
MN3
|
A:OEX414
|
3.5
|
44.9
|
0.2
|
|
OD2
|
A:ASP170
|
3.6
|
47.2
|
0.2
|
|
MN1
|
A:OEX414
|
3.6
|
49.0
|
0.2
|
|
C
|
A:ALA344
|
3.6
|
46.9
|
0.8
|
|
CD
|
A:GLU189
|
3.8
|
49.0
|
0.2
|
|
OE2
|
A:GLU189
|
3.8
|
49.8
|
0.2
|
|
OXT
|
A:ALA344
|
3.8
|
48.4
|
0.2
|
|
MN4
|
A:OEY415
|
3.8
|
54.0
|
0.8
|
|
O4
|
A:OEX414
|
3.8
|
48.1
|
0.2
|
|
MN4
|
A:OEX414
|
3.8
|
55.4
|
0.2
|
|
OE2
|
A:GLU189
|
3.9
|
50.0
|
0.8
|
|
OXT
|
A:ALA344
|
3.9
|
48.7
|
0.8
|
|
CD
|
A:GLU189
|
3.9
|
47.6
|
0.8
|
|
O4
|
A:OEY415
|
4.0
|
50.7
|
0.8
|
|
O3
|
A:OEY415
|
4.1
|
46.6
|
0.8
|
|
O3
|
A:OEX414
|
4.2
|
46.3
|
0.2
|
|
CB
|
A:ASP170
|
4.2
|
43.2
|
0.8
|
|
O
|
A:HOH517
|
4.3
|
48.2
|
1.0
|
|
NH1
|
C:ARG357
|
4.3
|
41.0
|
1.0
|
|
CB
|
A:ASP170
|
4.4
|
43.6
|
0.2
|
|
O
|
A:HOH586
|
4.4
|
62.9
|
1.0
|
|
NH2
|
C:ARG357
|
4.5
|
42.9
|
1.0
|
|
O
|
A:HOH575
|
4.5
|
50.9
|
0.8
|
|
OH
|
A:TYR161
|
4.7
|
43.8
|
1.0
|
|
O
|
A:HOH575
|
4.7
|
51.4
|
0.2
|
|
CA
|
A:ALA344
|
4.7
|
47.0
|
0.2
|
|
OE1
|
A:GLN165
|
4.8
|
56.4
|
1.0
|
|
CA
|
A:ALA344
|
4.9
|
45.1
|
0.8
|
|
CZ
|
C:ARG357
|
4.9
|
49.5
|
1.0
|
|
OE1
|
C:GLU354
|
5.0
|
57.4
|
0.8
|
|
Calcium binding site 2 out
of 12 in 5ws6
Go back to
Calcium Binding Sites List in 5ws6
Calcium binding site 2 out
of 12 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca 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:Ca415
b:46.9
occ:0.80
|
CA1
|
A:OEY415
|
0.0
|
46.9
|
0.8
|
|
CA1
|
A:OEX414
|
0.3
|
50.5
|
0.2
|
|
O
|
A:ALA344
|
2.3
|
46.3
|
0.2
|
|
O
|
A:HOH550
|
2.3
|
60.0
|
0.2
|
|
O1
|
A:OEX414
|
2.4
|
47.7
|
0.2
|
|
OD1
|
A:ASP170
|
2.4
|
47.9
|
0.8
|
|
O
|
A:ALA344
|
2.4
|
46.1
|
0.8
|
|
O
|
A:HOH550
|
2.5
|
60.5
|
0.8
|
|
O5
|
A:OEY415
|
2.5
|
55.7
|
0.8
|
|
O1
|
A:OEY415
|
2.5
|
48.5
|
0.8
|
|
O
|
A:HOH620
|
2.6
|
48.5
|
0.8
|
|
OD1
|
A:ASP170
|
2.6
|
46.0
|
0.2
|
|
O2
|
A:OEY415
|
2.6
|
43.9
|
0.8
|
|
O
|
A:HOH620
|
2.7
|
49.5
|
0.2
|
|
O2
|
A:OEX414
|
2.7
|
45.1
|
0.2
|
|
O5
|
A:OEX414
|
2.7
|
59.1
|
0.2
|
|
OE1
|
A:GLU189
|
2.8
|
49.1
|
0.2
|
|
O6
|
A:OEY415
|
2.9
|
56.7
|
0.4
|
|
OE1
|
A:GLU189
|
3.0
|
49.7
|
0.8
|
|
CG
|
A:ASP170
|
3.3
|
43.3
|
0.8
|
|
C
|
A:ALA344
|
3.3
|
47.4
|
0.2
|
|
MN2
|
A:OEX414
|
3.4
|
49.6
|
0.2
|
|
MN2
|
A:OEY415
|
3.4
|
49.8
|
0.8
|
|
MN1
|
A:OEY415
|
3.4
|
49.4
|
0.8
|
|
CG
|
A:ASP170
|
3.4
|
45.3
|
0.2
|
|
C
|
A:ALA344
|
3.4
|
46.9
|
0.8
|
|
MN1
|
A:OEX414
|
3.5
|
49.0
|
0.2
|
|
MN3
|
A:OEY415
|
3.6
|
49.6
|
0.8
|
|
CD
|
A:GLU189
|
3.6
|
49.0
|
0.2
|
|
MN3
|
A:OEX414
|
3.6
|
44.9
|
0.2
|
|
OE2
|
A:GLU189
|
3.6
|
49.8
|
0.2
|
|
OXT
|
A:ALA344
|
3.7
|
48.4
|
0.2
|
|
CD
|
A:GLU189
|
3.8
|
47.6
|
0.8
|
|
OD2
|
A:ASP170
|
3.8
|
50.1
|
0.8
|
|
OE2
|
A:GLU189
|
3.8
|
50.0
|
0.8
|
|
OXT
|
A:ALA344
|
3.8
|
48.7
|
0.8
|
|
OD2
|
A:ASP170
|
3.8
|
47.2
|
0.2
|
|
O4
|
A:OEX414
|
4.1
|
48.1
|
0.2
|
|
MN4
|
A:OEY415
|
4.1
|
54.0
|
0.8
|
|
MN4
|
A:OEX414
|
4.1
|
55.4
|
0.2
|
|
O3
|
A:OEY415
|
4.1
|
46.6
|
0.8
|
|
O
|
A:HOH586
|
4.2
|
62.9
|
1.0
|
|
O3
|
A:OEX414
|
4.2
|
46.3
|
0.2
|
|
O4
|
A:OEY415
|
4.2
|
50.7
|
0.8
|
|
O
|
A:HOH517
|
4.3
|
48.2
|
1.0
|
|
CB
|
A:ASP170
|
4.4
|
43.2
|
0.8
|
|
NH1
|
C:ARG357
|
4.4
|
41.0
|
1.0
|
|
CA
|
A:ALA344
|
4.5
|
47.0
|
0.2
|
|
OH
|
A:TYR161
|
4.6
|
43.8
|
1.0
|
|
OE1
|
A:GLN165
|
4.6
|
56.4
|
1.0
|
|
CB
|
A:ASP170
|
4.6
|
43.6
|
0.2
|
|
NH2
|
C:ARG357
|
4.6
|
42.9
|
1.0
|
|
CA
|
A:ALA344
|
4.7
|
45.1
|
0.8
|
|
O
|
A:HOH575
|
4.7
|
50.9
|
0.8
|
|
O
|
A:HOH575
|
4.9
|
51.4
|
0.2
|
|
OE1
|
C:GLU354
|
5.0
|
57.4
|
0.8
|
|
Calcium binding site 3 out
of 12 in 5ws6
Go back to
Calcium Binding Sites List in 5ws6
Calcium binding site 3 out
of 12 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca 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
|
C:Ca524
b:72.8
occ:1.00
|
O
|
C:THR254
|
2.5
|
62.6
|
1.0
|
|
O
|
C:HIS251
|
2.7
|
74.2
|
1.0
|
|
OG1
|
C:THR159
|
2.8
|
73.6
|
1.0
|
|
OD1
|
C:ASN155
|
2.9
|
85.9
|
1.0
|
|
O
|
C:ASN155
|
2.9
|
67.6
|
1.0
|
|
OG1
|
C:THR158
|
3.0
|
70.8
|
1.0
|
|
O
|
C:ILE252
|
3.1
|
71.1
|
1.0
|
|
C
|
C:ILE252
|
3.6
|
73.6
|
1.0
|
|
N
|
C:THR159
|
3.6
|
63.2
|
1.0
|
|
C
|
C:THR254
|
3.7
|
67.1
|
1.0
|
|
CG
|
C:ASN155
|
3.7
|
87.9
|
1.0
|
|
C
|
C:ASN155
|
3.7
|
65.4
|
1.0
|
|
C
|
C:HIS251
|
3.8
|
63.5
|
1.0
|
|
CA
|
C:ILE252
|
3.9
|
67.0
|
1.0
|
|
CB
|
C:THR159
|
3.9
|
63.3
|
1.0
|
|
CA
|
C:ASN155
|
4.0
|
72.3
|
1.0
|
|
CA
|
C:THR159
|
4.0
|
62.9
|
1.0
|
|
CB
|
C:THR158
|
4.0
|
63.6
|
1.0
|
|
C
|
C:THR158
|
4.1
|
62.5
|
1.0
|
|
N
|
C:THR254
|
4.3
|
69.5
|
1.0
|
|
N
|
C:ILE252
|
4.3
|
65.9
|
1.0
|
|
O
|
C:HOH621
|
4.4
|
69.5
|
1.0
|
|
CB
|
C:ASN155
|
4.5
|
79.7
|
1.0
|
|
N
|
C:LEU253
|
4.5
|
73.6
|
1.0
|
|
CA
|
C:THR158
|
4.5
|
63.7
|
1.0
|
|
ND2
|
C:ASN155
|
4.6
|
95.7
|
1.0
|
|
O
|
C:THR158
|
4.6
|
70.7
|
1.0
|
|
CA
|
C:THR254
|
4.6
|
64.7
|
1.0
|
|
N
|
C:THR255
|
4.7
|
68.1
|
1.0
|
|
C
|
C:LEU253
|
4.7
|
73.4
|
1.0
|
|
CA
|
C:THR255
|
4.8
|
68.9
|
1.0
|
|
N
|
C:THR158
|
4.9
|
70.6
|
1.0
|
|
N
|
C:LYS156
|
4.9
|
67.8
|
1.0
|
|
CA
|
C:HIS251
|
4.9
|
61.8
|
1.0
|
|
Calcium binding site 4 out
of 12 in 5ws6
Go back to
Calcium Binding Sites List in 5ws6
Calcium binding site 4 out
of 12 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca 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
|
O:Ca301
b:0.4
occ:1.00
|
ND2
|
O:ASN200
|
2.5
|
0.1
|
1.0
|
|
O
|
O:HOH426
|
2.5
|
85.4
|
1.0
|
|
O
|
O:VAL201
|
3.0
|
90.7
|
1.0
|
|
O
|
O:THR138
|
3.0
|
0.5
|
1.0
|
|
CG
|
O:ASN200
|
3.2
|
0.3
|
1.0
|
|
O
|
O:THR140
|
3.3
|
88.1
|
1.0
|
|
CA
|
O:SER139
|
3.5
|
99.3
|
1.0
|
|
OD1
|
O:ASN200
|
3.5
|
0.4
|
1.0
|
|
C
|
O:THR138
|
3.6
|
96.2
|
1.0
|
|
C
|
O:SER139
|
3.7
|
90.8
|
1.0
|
|
N
|
O:VAL201
|
3.9
|
66.5
|
1.0
|
|
N
|
O:SER139
|
3.9
|
96.5
|
1.0
|
|
C
|
O:VAL201
|
4.0
|
80.4
|
1.0
|
|
O
|
O:SER139
|
4.0
|
90.0
|
1.0
|
|
C
|
O:THR140
|
4.2
|
85.3
|
1.0
|
|
N
|
O:THR140
|
4.2
|
82.5
|
1.0
|
|
C
|
O:ASN200
|
4.3
|
72.2
|
1.0
|
|
CB
|
O:ASN200
|
4.4
|
86.7
|
1.0
|
|
CA
|
O:VAL201
|
4.4
|
74.8
|
1.0
|
|
CA
|
O:ASN200
|
4.4
|
75.7
|
1.0
|
|
CB
|
O:ASP141
|
4.5
|
99.5
|
1.0
|
|
OD2
|
O:ASP141
|
4.7
|
0.5
|
1.0
|
|
CB
|
O:SER139
|
4.8
|
0.3
|
1.0
|
|
CA
|
O:THR138
|
4.8
|
90.1
|
1.0
|
|
CB
|
O:VAL201
|
4.9
|
73.0
|
1.0
|
|
CA
|
O:THR140
|
4.9
|
76.9
|
1.0
|
|
CG
|
O:ASP141
|
4.9
|
0.5
|
1.0
|
|
N
|
O:ASP141
|
5.0
|
82.2
|
1.0
|
|
Calcium binding site 5 out
of 12 in 5ws6
Go back to
Calcium Binding Sites List in 5ws6
Calcium binding site 5 out
of 12 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca 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
|
V:Ca201
b:0.7
occ:1.00
|
O
|
V:HOH360
|
2.5
|
0.2
|
1.0
|
|
OE2
|
V:GLU23
|
2.9
|
86.6
|
1.0
|
|
O
|
V:HOH351
|
3.1
|
77.3
|
1.0
|
|
O
|
A:ALA309
|
3.3
|
62.2
|
1.0
|
|
O
|
F:ARG45
|
3.4
|
72.0
|
1.0
|
|
OXT
|
F:ARG45
|
3.6
|
66.7
|
1.0
|
|
C
|
F:ARG45
|
3.9
|
66.8
|
1.0
|
|
CD
|
V:GLU23
|
3.9
|
94.5
|
1.0
|
|
C
|
A:ALA309
|
4.2
|
56.6
|
1.0
|
|
CA
|
A:ALA309
|
4.4
|
57.1
|
1.0
|
|
OE1
|
V:GLU23
|
4.5
|
0.8
|
1.0
|
|
NH1
|
F:ARG45
|
4.6
|
59.1
|
1.0
|
|
CB
|
V:LEU3
|
4.6
|
66.2
|
1.0
|
|
CB
|
A:ALA309
|
4.7
|
42.5
|
1.0
|
|
CG
|
F:ARG45
|
4.8
|
58.8
|
1.0
|
|
Calcium binding site 6 out
of 12 in 5ws6
Go back to
Calcium Binding Sites List in 5ws6
Calcium binding site 6 out
of 12 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca 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:Ca412
b:61.2
occ:0.20
|
CA1
|
a:OEX412
|
0.0
|
61.2
|
0.2
|
|
CA1
|
a:OEY413
|
0.2
|
58.0
|
0.8
|
|
OD1
|
a:ASP170
|
2.2
|
52.6
|
0.8
|
|
O
|
a:ALA344
|
2.3
|
50.9
|
0.8
|
|
OD1
|
a:ASP170
|
2.3
|
51.4
|
0.2
|
|
O
|
a:HOH515
|
2.4
|
56.4
|
0.8
|
|
O
|
a:ALA344
|
2.4
|
51.7
|
0.2
|
|
O
|
a:HOH515
|
2.5
|
57.0
|
0.2
|
|
O1
|
a:OEX412
|
2.6
|
74.1
|
0.2
|
|
O
|
a:HOH598
|
2.6
|
60.5
|
0.2
|
|
O5
|
a:OEX412
|
2.6
|
56.3
|
0.2
|
|
O
|
a:HOH598
|
2.6
|
60.9
|
0.8
|
|
O1
|
a:OEY413
|
2.6
|
74.7
|
0.8
|
|
O2
|
a:OEY413
|
2.6
|
50.9
|
0.8
|
|
O2
|
a:OEX412
|
2.6
|
50.5
|
0.2
|
|
O5
|
a:OEY413
|
2.7
|
57.4
|
0.8
|
|
OE1
|
a:GLU189
|
3.0
|
55.9
|
0.2
|
|
CG
|
a:ASP170
|
3.1
|
50.0
|
0.8
|
|
OE1
|
a:GLU189
|
3.1
|
58.1
|
0.8
|
|
O6
|
a:OEY413
|
3.2
|
54.5
|
0.4
|
|
CG
|
a:ASP170
|
3.2
|
49.8
|
0.2
|
|
C
|
a:ALA344
|
3.3
|
53.8
|
0.8
|
|
C
|
a:ALA344
|
3.4
|
52.9
|
0.2
|
|
MN2
|
a:OEY413
|
3.4
|
54.9
|
0.8
|
|
MN2
|
a:OEX412
|
3.4
|
55.1
|
0.2
|
|
MN3
|
a:OEX412
|
3.5
|
51.5
|
0.2
|
|
OD2
|
a:ASP170
|
3.5
|
51.5
|
0.2
|
|
OD2
|
a:ASP170
|
3.5
|
52.8
|
0.8
|
|
MN3
|
a:OEY413
|
3.5
|
53.1
|
0.8
|
|
MN1
|
a:OEY413
|
3.6
|
56.0
|
0.8
|
|
MN1
|
a:OEX412
|
3.6
|
56.3
|
0.2
|
|
OXT
|
a:ALA344
|
3.6
|
51.6
|
0.8
|
|
OXT
|
a:ALA344
|
3.7
|
51.7
|
0.2
|
|
OE2
|
a:GLU189
|
3.8
|
55.3
|
0.2
|
|
CD
|
a:GLU189
|
3.8
|
54.5
|
0.2
|
|
MN4
|
a:OEX412
|
3.9
|
56.1
|
0.2
|
|
OE2
|
a:GLU189
|
3.9
|
57.1
|
0.8
|
|
CD
|
a:GLU189
|
3.9
|
52.4
|
0.8
|
|
MN4
|
a:OEY413
|
4.0
|
56.6
|
0.8
|
|
O4
|
a:OEX412
|
4.1
|
50.0
|
0.2
|
|
NH1
|
c:ARG357
|
4.1
|
51.2
|
1.0
|
|
O3
|
a:OEY413
|
4.2
|
53.6
|
0.8
|
|
O4
|
a:OEY413
|
4.2
|
50.3
|
0.8
|
|
O
|
a:HOH594
|
4.2
|
78.6
|
1.0
|
|
O3
|
a:OEX412
|
4.2
|
54.9
|
0.2
|
|
CB
|
a:ASP170
|
4.3
|
45.2
|
0.8
|
|
O
|
a:HOH501
|
4.4
|
51.5
|
1.0
|
|
CB
|
a:ASP170
|
4.4
|
45.7
|
0.2
|
|
NH2
|
c:ARG357
|
4.4
|
43.6
|
1.0
|
|
OH
|
a:TYR161
|
4.5
|
50.6
|
1.0
|
|
OE1
|
a:GLN165
|
4.5
|
55.0
|
1.0
|
|
CA
|
a:ALA344
|
4.7
|
55.0
|
0.8
|
|
O
|
a:HOH545
|
4.7
|
44.3
|
0.2
|
|
CA
|
a:ALA344
|
4.7
|
54.6
|
0.2
|
|
O
|
a:HOH545
|
4.8
|
44.8
|
0.8
|
|
CZ
|
c:ARG357
|
4.8
|
54.1
|
1.0
|
|
CB
|
a:GLN165
|
5.0
|
51.9
|
1.0
|
|
OE1
|
c:GLU354
|
5.0
|
50.3
|
0.8
|
|
Calcium binding site 7 out
of 12 in 5ws6
Go back to
Calcium Binding Sites List in 5ws6
Calcium binding site 7 out
of 12 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca 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
|
a:Ca413
b:58.0
occ:0.80
|
CA1
|
a:OEY413
|
0.0
|
58.0
|
0.8
|
|
CA1
|
a:OEX412
|
0.2
|
61.2
|
0.2
|
|
OD1
|
a:ASP170
|
2.4
|
52.6
|
0.8
|
|
O
|
a:ALA344
|
2.4
|
50.9
|
0.8
|
|
O1
|
a:OEX412
|
2.4
|
74.1
|
0.2
|
|
O5
|
a:OEX412
|
2.5
|
56.3
|
0.2
|
|
O
|
a:HOH515
|
2.5
|
56.4
|
0.8
|
|
O1
|
a:OEY413
|
2.5
|
74.7
|
0.8
|
|
O
|
a:HOH598
|
2.5
|
60.5
|
0.2
|
|
OD1
|
a:ASP170
|
2.5
|
51.4
|
0.2
|
|
O
|
a:HOH598
|
2.5
|
60.9
|
0.8
|
|
O
|
a:ALA344
|
2.6
|
51.7
|
0.2
|
|
O
|
a:HOH515
|
2.6
|
57.0
|
0.2
|
|
O5
|
a:OEY413
|
2.6
|
57.4
|
0.8
|
|
O2
|
a:OEY413
|
2.7
|
50.9
|
0.8
|
|
O2
|
a:OEX412
|
2.7
|
50.5
|
0.2
|
|
OE1
|
a:GLU189
|
2.9
|
55.9
|
0.2
|
|
O6
|
a:OEY413
|
3.0
|
54.5
|
0.4
|
|
OE1
|
a:GLU189
|
3.0
|
58.1
|
0.8
|
|
CG
|
a:ASP170
|
3.2
|
50.0
|
0.8
|
|
CG
|
a:ASP170
|
3.3
|
49.8
|
0.2
|
|
MN2
|
a:OEY413
|
3.4
|
54.9
|
0.8
|
|
MN2
|
a:OEX412
|
3.4
|
55.1
|
0.2
|
|
C
|
a:ALA344
|
3.4
|
53.8
|
0.8
|
|
MN1
|
a:OEY413
|
3.4
|
56.0
|
0.8
|
|
MN3
|
a:OEX412
|
3.4
|
51.5
|
0.2
|
|
MN1
|
a:OEX412
|
3.5
|
56.3
|
0.2
|
|
MN3
|
a:OEY413
|
3.5
|
53.1
|
0.8
|
|
C
|
a:ALA344
|
3.5
|
52.9
|
0.2
|
|
OD2
|
a:ASP170
|
3.6
|
51.5
|
0.2
|
|
OD2
|
a:ASP170
|
3.6
|
52.8
|
0.8
|
|
OE2
|
a:GLU189
|
3.6
|
55.3
|
0.2
|
|
CD
|
a:GLU189
|
3.6
|
54.5
|
0.2
|
|
OXT
|
a:ALA344
|
3.7
|
51.6
|
0.8
|
|
OE2
|
a:GLU189
|
3.7
|
57.1
|
0.8
|
|
CD
|
a:GLU189
|
3.7
|
52.4
|
0.8
|
|
OXT
|
a:ALA344
|
3.8
|
51.7
|
0.2
|
|
MN4
|
a:OEX412
|
3.8
|
56.1
|
0.2
|
|
MN4
|
a:OEY413
|
4.0
|
56.6
|
0.8
|
|
O3
|
a:OEY413
|
4.1
|
53.6
|
0.8
|
|
O4
|
a:OEX412
|
4.1
|
50.0
|
0.2
|
|
O3
|
a:OEX412
|
4.1
|
54.9
|
0.2
|
|
O
|
a:HOH594
|
4.2
|
78.6
|
1.0
|
|
O4
|
a:OEY413
|
4.2
|
50.3
|
0.8
|
|
O
|
a:HOH501
|
4.3
|
51.5
|
1.0
|
|
NH1
|
c:ARG357
|
4.3
|
51.2
|
1.0
|
|
CB
|
a:ASP170
|
4.5
|
45.2
|
0.8
|
|
OH
|
a:TYR161
|
4.5
|
50.6
|
1.0
|
|
CB
|
a:ASP170
|
4.5
|
45.7
|
0.2
|
|
NH2
|
c:ARG357
|
4.6
|
43.6
|
1.0
|
|
O
|
a:HOH545
|
4.6
|
44.3
|
0.2
|
|
OE1
|
a:GLN165
|
4.6
|
55.0
|
1.0
|
|
O
|
a:HOH545
|
4.7
|
44.8
|
0.8
|
|
CA
|
a:ALA344
|
4.8
|
55.0
|
0.8
|
|
CA
|
a:ALA344
|
4.8
|
54.6
|
0.2
|
|
CZ
|
c:ARG357
|
5.0
|
54.1
|
1.0
|
|
OE1
|
c:GLU354
|
5.0
|
50.3
|
0.8
|
|
OE2
|
c:GLU354
|
5.0
|
51.1
|
0.2
|
|
Calcium binding site 8 out
of 12 in 5ws6
Go back to
Calcium Binding Sites List in 5ws6
Calcium binding site 8 out
of 12 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca 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
|
b:Ca626
b:0.4
occ:1.00
|
O
|
b:HOH872
|
2.7
|
94.3
|
1.0
|
|
O
|
m:HOH207
|
2.7
|
85.6
|
1.0
|
|
O
|
b:HOH767
|
3.3
|
78.8
|
1.0
|
|
OD1
|
b:ASN438
|
3.5
|
81.6
|
1.0
|
|
OE2
|
o:GLU181
|
4.0
|
0.0
|
1.0
|
|
OE1
|
o:GLU181
|
4.1
|
0.2
|
1.0
|
|
O
|
b:HOH818
|
4.4
|
62.3
|
1.0
|
|
CD
|
o:GLU181
|
4.5
|
0.7
|
1.0
|
|
CG
|
b:ASN438
|
4.6
|
74.6
|
1.0
|
|
O
|
b:SER439
|
4.7
|
51.5
|
1.0
|
|
OE2
|
m:GLU2
|
4.9
|
95.0
|
1.0
|
|
O
|
b:HOH841
|
5.0
|
71.4
|
1.0
|
|
Calcium binding site 9 out
of 12 in 5ws6
Go back to
Calcium Binding Sites List in 5ws6
Calcium binding site 9 out
of 12 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
c:Ca524
b:79.0
occ:1.00
|
O
|
c:HIS251
|
2.7
|
72.9
|
1.0
|
|
OG1
|
c:THR159
|
2.7
|
84.6
|
1.0
|
|
O
|
c:THR254
|
2.7
|
72.5
|
1.0
|
|
O
|
c:ASN155
|
2.9
|
76.7
|
1.0
|
|
O
|
c:ILE252
|
3.0
|
85.0
|
1.0
|
|
OG1
|
c:THR158
|
3.0
|
77.0
|
1.0
|
|
OD1
|
c:ASN155
|
3.0
|
94.7
|
1.0
|
|
C
|
c:ILE252
|
3.5
|
87.2
|
1.0
|
|
N
|
c:THR159
|
3.6
|
75.6
|
1.0
|
|
CG
|
c:ASN155
|
3.7
|
91.6
|
1.0
|
|
C
|
c:ASN155
|
3.7
|
77.2
|
1.0
|
|
C
|
c:HIS251
|
3.8
|
79.5
|
1.0
|
|
CB
|
c:THR159
|
3.9
|
77.5
|
1.0
|
|
CA
|
c:ILE252
|
3.9
|
75.3
|
1.0
|
|
CA
|
c:THR159
|
3.9
|
75.9
|
1.0
|
|
CB
|
c:THR158
|
3.9
|
70.2
|
1.0
|
|
C
|
c:THR254
|
3.9
|
78.0
|
1.0
|
|
C
|
c:THR158
|
4.0
|
71.9
|
1.0
|
|
CA
|
c:ASN155
|
4.0
|
78.0
|
1.0
|
|
N
|
c:ILE252
|
4.3
|
74.2
|
1.0
|
|
N
|
c:THR254
|
4.3
|
80.3
|
1.0
|
|
ND2
|
c:ASN155
|
4.4
|
93.6
|
1.0
|
|
CA
|
c:THR158
|
4.5
|
67.8
|
1.0
|
|
O
|
c:THR158
|
4.5
|
72.9
|
1.0
|
|
CB
|
c:ASN155
|
4.5
|
86.6
|
1.0
|
|
N
|
c:LEU253
|
4.5
|
88.4
|
1.0
|
|
O
|
c:HOH658
|
4.6
|
81.4
|
1.0
|
|
CA
|
c:THR254
|
4.7
|
76.2
|
1.0
|
|
C
|
c:LEU253
|
4.8
|
82.4
|
1.0
|
|
N
|
c:THR158
|
4.9
|
71.2
|
1.0
|
|
N
|
c:THR255
|
4.9
|
75.6
|
1.0
|
|
N
|
c:LYS156
|
4.9
|
78.8
|
1.0
|
|
Calcium binding site 10 out
of 12 in 5ws6
Go back to
Calcium Binding Sites List in 5ws6
Calcium binding site 10 out
of 12 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
c:Ca525
b:92.2
occ:1.00
|
OE1
|
c:GLU29
|
2.3
|
91.9
|
1.0
|
|
OD2
|
c:ASP27
|
2.3
|
68.8
|
1.0
|
|
O
|
c:PHE22
|
2.4
|
96.5
|
1.0
|
|
OG
|
c:SER30
|
2.4
|
89.0
|
1.0
|
|
O
|
c:THR24
|
2.6
|
86.3
|
1.0
|
|
OD1
|
c:ASP27
|
2.8
|
66.4
|
1.0
|
|
CG
|
c:ASP27
|
2.9
|
75.4
|
1.0
|
|
O
|
c:HOH702
|
3.0
|
0.1
|
1.0
|
|
C
|
c:PHE22
|
3.3
|
88.5
|
1.0
|
|
CD
|
c:GLU29
|
3.5
|
94.4
|
1.0
|
|
CB
|
c:SER30
|
3.7
|
73.4
|
1.0
|
|
C
|
c:THR24
|
3.8
|
89.6
|
1.0
|
|
CB
|
c:PHE22
|
3.8
|
96.7
|
1.0
|
|
CA
|
c:PHE22
|
3.8
|
98.4
|
1.0
|
|
OE2
|
c:GLU29
|
4.0
|
0.8
|
1.0
|
|
N
|
c:SER30
|
4.2
|
70.0
|
1.0
|
|
O
|
c:HOH625
|
4.3
|
82.0
|
1.0
|
|
C
|
c:ALA23
|
4.4
|
0.7
|
1.0
|
|
N
|
c:THR24
|
4.4
|
94.5
|
1.0
|
|
CB
|
c:ASP27
|
4.4
|
76.1
|
1.0
|
|
N
|
c:ALA23
|
4.4
|
90.1
|
1.0
|
|
O
|
c:ALA23
|
4.5
|
0.2
|
1.0
|
|
CA
|
c:SER30
|
4.5
|
68.3
|
1.0
|
|
CB
|
c:GLU29
|
4.6
|
79.7
|
1.0
|
|
CA
|
c:ASN25
|
4.6
|
82.2
|
1.0
|
|
CG
|
c:GLU29
|
4.6
|
87.7
|
1.0
|
|
N
|
c:ASN25
|
4.7
|
86.4
|
1.0
|
|
CA
|
c:THR24
|
4.7
|
91.3
|
1.0
|
|
CA
|
c:ALA23
|
4.8
|
99.5
|
1.0
|
|
CG
|
c:PHE22
|
5.0
|
96.7
|
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: Mon Jul 15 13:26:33 2024
|
