Calcium 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:
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
11;
Binding sites:
The binding sites of Calcium 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 Calcium atom.
In total 11 binding sites of Calcium where determined in the
Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay, PDB code: 8irb:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 11 in 8irb
Go back to
Calcium Binding Sites List in 8irb
Calcium binding site 1 out
of 11 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 Calcium with other atoms in the Ca 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:Ca413
b:47.1
occ:0.40
|
CA1
|
A:OEX413
|
0.0
|
47.1
|
0.4
|
|
CA1
|
A:OEX413
|
0.2
|
52.6
|
0.6
|
|
OD1
|
A:ASP170
|
2.3
|
48.9
|
0.6
|
|
O
|
A:HOH513
|
2.4
|
50.9
|
0.4
|
|
O
|
A:ALA344
|
2.4
|
53.4
|
0.6
|
|
OD1
|
A:ASP170
|
2.4
|
44.8
|
0.4
|
|
O
|
A:HOH620
|
2.4
|
48.8
|
0.4
|
|
O
|
A:ALA344
|
2.5
|
51.6
|
0.4
|
|
O2
|
A:OEX413
|
2.5
|
43.6
|
0.6
|
|
O
|
A:HOH513
|
2.5
|
54.2
|
0.6
|
|
O5
|
A:OEX413
|
2.5
|
46.9
|
0.4
|
|
O
|
A:HOH620
|
2.6
|
49.5
|
0.6
|
|
O5
|
A:OEX413
|
2.6
|
47.2
|
0.6
|
|
O1
|
A:OEX413
|
2.6
|
42.8
|
0.4
|
|
O2
|
A:OEX413
|
2.6
|
43.4
|
0.4
|
|
O1
|
A:OEX413
|
2.7
|
43.1
|
0.6
|
|
OE1
|
A:GLU189
|
3.0
|
47.9
|
0.4
|
|
OE1
|
A:GLU189
|
3.1
|
52.5
|
0.6
|
|
CG
|
A:ASP170
|
3.1
|
44.8
|
0.6
|
|
CG
|
A:ASP170
|
3.3
|
42.8
|
0.4
|
|
MN2
|
A:OEX413
|
3.4
|
44.6
|
0.4
|
|
MN2
|
A:OEX413
|
3.4
|
47.8
|
0.6
|
|
C
|
A:ALA344
|
3.4
|
42.6
|
0.6
|
|
C
|
A:ALA344
|
3.5
|
42.5
|
0.4
|
|
MN3
|
A:OEX413
|
3.5
|
47.0
|
0.6
|
|
MN1
|
A:OEX413
|
3.5
|
41.0
|
0.4
|
|
MN3
|
A:OEX413
|
3.5
|
45.8
|
0.4
|
|
MN1
|
A:OEX413
|
3.6
|
45.3
|
0.6
|
|
OD2
|
A:ASP170
|
3.6
|
41.9
|
0.4
|
|
OD2
|
A:ASP170
|
3.6
|
40.7
|
0.6
|
|
OE2
|
A:GLU189
|
3.6
|
45.1
|
0.6
|
|
OE2
|
A:GLU189
|
3.6
|
44.6
|
0.4
|
|
CD
|
A:GLU189
|
3.7
|
47.9
|
0.4
|
|
OXT
|
A:ALA344
|
3.8
|
47.5
|
0.6
|
|
CD
|
A:GLU189
|
3.8
|
47.9
|
0.6
|
|
OXT
|
A:ALA344
|
3.8
|
47.3
|
0.4
|
|
MN4
|
A:OEX413
|
3.8
|
46.0
|
0.4
|
|
O4
|
A:OEX413
|
3.9
|
41.4
|
0.6
|
|
MN4
|
A:OEX413
|
3.9
|
51.5
|
0.6
|
|
O3
|
A:OEX413
|
4.0
|
46.4
|
0.6
|
|
O4
|
A:OEX413
|
4.0
|
41.9
|
0.4
|
|
O3
|
A:OEX413
|
4.0
|
47.3
|
0.4
|
|
O
|
A:HOH587
|
4.1
|
42.4
|
0.4
|
|
CB
|
A:ASP170
|
4.2
|
40.6
|
0.6
|
|
NH1
|
C:ARG357
|
4.3
|
42.5
|
0.4
|
|
NH1
|
C:ARG357
|
4.3
|
42.3
|
0.6
|
|
O
|
A:HOH526
|
4.4
|
48.0
|
0.6
|
|
O
|
A:HOH526
|
4.5
|
48.1
|
0.4
|
|
CB
|
A:ASP170
|
4.5
|
41.8
|
0.4
|
|
NH2
|
C:ARG357
|
4.5
|
43.3
|
0.6
|
|
NH2
|
C:ARG357
|
4.6
|
43.7
|
0.4
|
|
O
|
A:HOH587
|
4.6
|
60.5
|
0.6
|
|
OE1
|
A:GLN165
|
4.6
|
49.1
|
0.4
|
|
O
|
A:HOH544
|
4.6
|
43.2
|
0.4
|
|
OE1
|
A:GLN165
|
4.6
|
49.1
|
0.6
|
|
OH
|
A:TYR161
|
4.7
|
43.0
|
0.4
|
|
OH
|
A:TYR161
|
4.8
|
43.3
|
0.6
|
|
CA
|
A:ALA344
|
4.8
|
48.7
|
0.6
|
|
CA
|
A:ALA344
|
4.8
|
48.8
|
0.4
|
|
O
|
A:HOH544
|
4.8
|
45.3
|
0.6
|
|
OE2
|
C:GLU354
|
4.9
|
48.4
|
0.6
|
|
CZ
|
C:ARG357
|
4.9
|
54.0
|
0.6
|
|
CZ
|
C:ARG357
|
4.9
|
53.8
|
0.4
|
|
O
|
A:HOH573
|
4.9
|
58.5
|
0.6
|
|
O
|
A:HOH625
|
4.9
|
50.5
|
0.6
|
|
Calcium binding site 2 out
of 11 in 8irb
Go back to
Calcium Binding Sites List in 8irb
Calcium binding site 2 out
of 11 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 Calcium with other atoms in the Ca 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:Ca413
b:52.6
occ:0.60
|
CA1
|
A:OEX413
|
0.0
|
52.6
|
0.6
|
|
CA1
|
A:OEX413
|
0.2
|
47.1
|
0.4
|
|
O
|
A:HOH513
|
2.4
|
50.9
|
0.4
|
|
O
|
A:HOH620
|
2.4
|
48.8
|
0.4
|
|
O
|
A:HOH513
|
2.5
|
54.2
|
0.6
|
|
O
|
A:ALA344
|
2.5
|
53.4
|
0.6
|
|
OD1
|
A:ASP170
|
2.5
|
48.9
|
0.6
|
|
O1
|
A:OEX413
|
2.5
|
42.8
|
0.4
|
|
O
|
A:HOH620
|
2.5
|
49.5
|
0.6
|
|
O
|
A:ALA344
|
2.5
|
51.6
|
0.4
|
|
O5
|
A:OEX413
|
2.6
|
46.9
|
0.4
|
|
O1
|
A:OEX413
|
2.6
|
43.1
|
0.6
|
|
O5
|
A:OEX413
|
2.6
|
47.2
|
0.6
|
|
O2
|
A:OEX413
|
2.6
|
43.6
|
0.6
|
|
OD1
|
A:ASP170
|
2.6
|
44.8
|
0.4
|
|
O2
|
A:OEX413
|
2.8
|
43.4
|
0.4
|
|
OE1
|
A:GLU189
|
2.8
|
47.9
|
0.4
|
|
OE1
|
A:GLU189
|
2.9
|
52.5
|
0.6
|
|
CG
|
A:ASP170
|
3.3
|
44.8
|
0.6
|
|
MN1
|
A:OEX413
|
3.4
|
41.0
|
0.4
|
|
CG
|
A:ASP170
|
3.4
|
42.8
|
0.4
|
|
MN2
|
A:OEX413
|
3.4
|
44.6
|
0.4
|
|
MN2
|
A:OEX413
|
3.4
|
47.8
|
0.6
|
|
OE2
|
A:GLU189
|
3.5
|
45.1
|
0.6
|
|
OE2
|
A:GLU189
|
3.5
|
44.6
|
0.4
|
|
C
|
A:ALA344
|
3.5
|
42.6
|
0.6
|
|
CD
|
A:GLU189
|
3.5
|
47.9
|
0.4
|
|
MN1
|
A:OEX413
|
3.5
|
45.3
|
0.6
|
|
C
|
A:ALA344
|
3.5
|
42.5
|
0.4
|
|
CD
|
A:GLU189
|
3.5
|
47.9
|
0.6
|
|
MN3
|
A:OEX413
|
3.6
|
47.0
|
0.6
|
|
MN3
|
A:OEX413
|
3.6
|
45.8
|
0.4
|
|
OD2
|
A:ASP170
|
3.7
|
40.7
|
0.6
|
|
OD2
|
A:ASP170
|
3.7
|
41.9
|
0.4
|
|
OXT
|
A:ALA344
|
3.8
|
47.5
|
0.6
|
|
OXT
|
A:ALA344
|
3.8
|
47.3
|
0.4
|
|
MN4
|
A:OEX413
|
3.9
|
46.0
|
0.4
|
|
O3
|
A:OEX413
|
4.0
|
46.4
|
0.6
|
|
O
|
A:HOH587
|
4.0
|
42.4
|
0.4
|
|
O3
|
A:OEX413
|
4.0
|
47.3
|
0.4
|
|
O4
|
A:OEX413
|
4.0
|
41.4
|
0.6
|
|
MN4
|
A:OEX413
|
4.1
|
51.5
|
0.6
|
|
O4
|
A:OEX413
|
4.2
|
41.9
|
0.4
|
|
O
|
A:HOH526
|
4.3
|
48.0
|
0.6
|
|
O
|
A:HOH526
|
4.3
|
48.1
|
0.4
|
|
CB
|
A:ASP170
|
4.3
|
40.6
|
0.6
|
|
O
|
A:HOH587
|
4.4
|
60.5
|
0.6
|
|
NH1
|
C:ARG357
|
4.5
|
42.3
|
0.6
|
|
NH1
|
C:ARG357
|
4.5
|
42.5
|
0.4
|
|
OH
|
A:TYR161
|
4.5
|
43.0
|
0.4
|
|
OE1
|
A:GLN165
|
4.6
|
49.1
|
0.4
|
|
OE1
|
A:GLN165
|
4.6
|
49.1
|
0.6
|
|
CB
|
A:ASP170
|
4.6
|
41.8
|
0.4
|
|
OH
|
A:TYR161
|
4.6
|
43.3
|
0.6
|
|
O
|
A:HOH544
|
4.7
|
43.2
|
0.4
|
|
NH2
|
C:ARG357
|
4.8
|
43.3
|
0.6
|
|
NH2
|
C:ARG357
|
4.8
|
43.7
|
0.4
|
|
CA
|
A:ALA344
|
4.8
|
48.7
|
0.6
|
|
CA
|
A:ALA344
|
4.8
|
48.8
|
0.4
|
|
O
|
A:HOH573
|
4.8
|
58.5
|
0.6
|
|
O
|
A:HOH544
|
4.8
|
45.3
|
0.6
|
|
CG
|
A:GLU189
|
4.9
|
45.7
|
0.4
|
|
O
|
A:HOH625
|
5.0
|
50.5
|
0.6
|
|
OD2
|
A:ASP342
|
5.0
|
40.8
|
0.6
|
|
Calcium binding site 3 out
of 11 in 8irb
Go back to
Calcium Binding Sites List in 8irb
Calcium binding site 3 out
of 11 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 Calcium with other atoms in the Ca 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
|
C:Ca524
b:69.8
occ:1.00
|
O
|
C:THR254
|
2.7
|
63.5
|
1.0
|
|
O
|
C:HIS251
|
2.7
|
72.3
|
1.0
|
|
OG1
|
C:THR159
|
2.8
|
64.7
|
1.0
|
|
O
|
C:ASN155
|
2.8
|
69.6
|
1.0
|
|
OD1
|
C:ASN155
|
2.9
|
74.9
|
1.0
|
|
OG1
|
C:THR158
|
2.9
|
61.5
|
1.0
|
|
O
|
C:ILE252
|
3.1
|
59.7
|
1.0
|
|
C
|
C:ILE252
|
3.6
|
76.7
|
1.0
|
|
N
|
C:THR159
|
3.6
|
64.7
|
1.0
|
|
C
|
C:ASN155
|
3.7
|
71.2
|
1.0
|
|
CG
|
C:ASN155
|
3.8
|
73.2
|
1.0
|
|
C
|
C:THR254
|
3.9
|
70.7
|
1.0
|
|
C
|
C:HIS251
|
3.9
|
64.6
|
1.0
|
|
CB
|
C:THR159
|
3.9
|
57.8
|
1.0
|
|
CA
|
C:ILE252
|
4.0
|
65.2
|
1.0
|
|
CB
|
C:THR158
|
4.0
|
70.0
|
1.0
|
|
CA
|
C:THR159
|
4.0
|
64.8
|
1.0
|
|
CA
|
C:ASN155
|
4.0
|
68.0
|
1.0
|
|
C
|
C:THR158
|
4.1
|
69.9
|
1.0
|
|
N
|
C:THR254
|
4.3
|
82.5
|
1.0
|
|
O
|
C:HOH633
|
4.4
|
64.1
|
1.0
|
|
N
|
C:ILE252
|
4.4
|
74.2
|
1.0
|
|
CB
|
C:ASN155
|
4.5
|
70.7
|
1.0
|
|
CA
|
C:THR158
|
4.5
|
62.0
|
1.0
|
|
N
|
C:LEU253
|
4.5
|
73.9
|
1.0
|
|
O
|
C:THR158
|
4.6
|
65.7
|
1.0
|
|
ND2
|
C:ASN155
|
4.7
|
101.8
|
1.0
|
|
CA
|
C:THR254
|
4.7
|
58.4
|
1.0
|
|
N
|
C:THR255
|
4.8
|
67.1
|
1.0
|
|
C
|
C:LEU253
|
4.8
|
77.0
|
1.0
|
|
N
|
C:THR158
|
4.9
|
67.6
|
1.0
|
|
N
|
C:LYS156
|
4.9
|
67.5
|
1.0
|
|
CA
|
C:THR255
|
4.9
|
70.5
|
1.0
|
|
Calcium binding site 4 out
of 11 in 8irb
Go back to
Calcium Binding Sites List in 8irb
Calcium binding site 4 out
of 11 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 Calcium with other atoms in the Ca 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
|
F:Ca104
b:121.4
occ:1.00
|
O
|
F:ARG45
|
3.2
|
69.7
|
1.0
|
|
OXT
|
F:ARG45
|
3.3
|
61.8
|
1.0
|
|
OE2
|
V:GLU2
|
3.5
|
61.8
|
0.5
|
|
OE1
|
V:GLU2
|
3.5
|
57.4
|
0.5
|
|
OE2
|
V:GLU23
|
3.6
|
109.9
|
1.0
|
|
C
|
F:ARG45
|
3.8
|
62.6
|
1.0
|
|
CD
|
V:GLU2
|
3.9
|
70.2
|
0.5
|
|
OE1
|
V:GLU23
|
4.3
|
112.7
|
1.0
|
|
CD
|
V:GLU23
|
4.4
|
96.1
|
1.0
|
|
O
|
A:ALA309
|
4.6
|
58.0
|
1.0
|
|
CB
|
A:ALA309
|
4.9
|
48.7
|
1.0
|
|
Calcium binding site 5 out
of 11 in 8irb
Go back to
Calcium Binding Sites List in 8irb
Calcium binding site 5 out
of 11 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 Calcium with other atoms in the Ca 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
|
O:Ca301
b:100.8
occ:1.00
|
O
|
O:HOH410
|
2.4
|
81.0
|
1.0
|
|
ND2
|
O:ASN200
|
2.5
|
115.6
|
1.0
|
|
O
|
O:THR138
|
2.8
|
97.5
|
1.0
|
|
O
|
O:VAL201
|
2.9
|
85.0
|
1.0
|
|
OD2
|
O:ASP141
|
3.1
|
92.5
|
1.0
|
|
CG
|
O:ASN200
|
3.3
|
96.5
|
1.0
|
|
O
|
O:THR140
|
3.5
|
81.4
|
1.0
|
|
CA
|
O:SER139
|
3.6
|
86.8
|
1.0
|
|
C
|
O:THR138
|
3.6
|
86.8
|
1.0
|
|
OD1
|
O:ASN200
|
3.7
|
104.2
|
1.0
|
|
C
|
O:SER139
|
3.9
|
81.3
|
1.0
|
|
N
|
O:SER139
|
4.0
|
91.2
|
1.0
|
|
C
|
O:VAL201
|
4.0
|
67.6
|
1.0
|
|
N
|
O:VAL201
|
4.1
|
68.8
|
1.0
|
|
CG
|
O:ASP141
|
4.1
|
99.9
|
1.0
|
|
O
|
O:SER139
|
4.3
|
84.6
|
1.0
|
|
C
|
O:ASN200
|
4.3
|
61.1
|
1.0
|
|
N
|
O:THR140
|
4.4
|
90.8
|
1.0
|
|
OD1
|
O:ASP141
|
4.4
|
108.9
|
1.0
|
|
C
|
O:THR140
|
4.4
|
94.6
|
1.0
|
|
CB
|
O:ASN200
|
4.4
|
76.2
|
1.0
|
|
CA
|
O:ASN200
|
4.5
|
67.5
|
1.0
|
|
CA
|
O:VAL201
|
4.5
|
74.9
|
1.0
|
|
CA
|
O:THR138
|
4.8
|
90.2
|
1.0
|
|
CB
|
O:SER139
|
4.8
|
87.9
|
1.0
|
|
CB
|
O:VAL201
|
4.9
|
73.7
|
1.0
|
|
O
|
O:ASN200
|
4.9
|
76.2
|
1.0
|
|
Calcium binding site 6 out
of 11 in 8irb
Go back to
Calcium Binding Sites List in 8irb
Calcium binding site 6 out
of 11 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 Calcium with other atoms in the Ca 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:Ca412
b:53.1
occ:0.40
|
CA1
|
a:OEX412
|
0.0
|
53.1
|
0.4
|
|
CA1
|
a:OEX412
|
0.3
|
58.0
|
0.6
|
|
OD1
|
a:ASP170
|
2.2
|
54.5
|
0.6
|
|
OD1
|
a:ASP170
|
2.3
|
51.8
|
0.4
|
|
O
|
a:HOH525
|
2.4
|
48.5
|
0.4
|
|
O
|
a:ALA344
|
2.5
|
53.8
|
0.6
|
|
O
|
a:ALA344
|
2.5
|
53.8
|
0.4
|
|
O2
|
a:OEX412
|
2.5
|
46.0
|
0.6
|
|
O
|
a:HOH623
|
2.6
|
54.2
|
0.4
|
|
O1
|
a:OEX412
|
2.6
|
47.1
|
0.4
|
|
O
|
a:HOH525
|
2.6
|
58.6
|
0.6
|
|
O5
|
a:OEX412
|
2.6
|
50.8
|
0.4
|
|
O1
|
a:OEX412
|
2.6
|
47.3
|
0.6
|
|
O2
|
a:OEX412
|
2.6
|
43.9
|
0.4
|
|
O5
|
a:OEX412
|
2.7
|
50.8
|
0.6
|
|
O
|
a:HOH623
|
2.7
|
55.8
|
0.6
|
|
OE1
|
a:GLU189
|
3.0
|
51.1
|
0.4
|
|
OE1
|
a:GLU189
|
3.1
|
57.9
|
0.6
|
|
CG
|
a:ASP170
|
3.1
|
47.8
|
0.6
|
|
CG
|
a:ASP170
|
3.2
|
47.2
|
0.4
|
|
MN2
|
a:OEX412
|
3.4
|
50.2
|
0.4
|
|
MN2
|
a:OEX412
|
3.4
|
50.2
|
0.6
|
|
C
|
a:ALA344
|
3.4
|
53.0
|
0.6
|
|
MN3
|
a:OEX412
|
3.4
|
47.8
|
0.4
|
|
MN3
|
a:OEX412
|
3.4
|
50.1
|
0.6
|
|
C
|
a:ALA344
|
3.5
|
53.0
|
0.4
|
|
MN1
|
a:OEX412
|
3.5
|
48.4
|
0.4
|
|
MN1
|
a:OEX412
|
3.6
|
48.4
|
0.6
|
|
OD2
|
a:ASP170
|
3.6
|
50.0
|
0.4
|
|
OD2
|
a:ASP170
|
3.7
|
50.0
|
0.6
|
|
OXT
|
a:ALA344
|
3.7
|
55.4
|
0.6
|
|
O3
|
a:OEX412
|
3.8
|
45.1
|
0.6
|
|
MN4
|
a:OEX412
|
3.8
|
44.0
|
0.4
|
|
OXT
|
a:ALA344
|
3.8
|
54.5
|
0.4
|
|
O3
|
a:OEX412
|
3.8
|
45.1
|
0.4
|
|
CD
|
a:GLU189
|
3.8
|
50.1
|
0.4
|
|
OE2
|
a:GLU189
|
3.9
|
51.3
|
0.4
|
|
CD
|
a:GLU189
|
3.9
|
50.2
|
0.6
|
|
OE2
|
a:GLU189
|
3.9
|
51.6
|
0.6
|
|
MN4
|
a:OEX412
|
3.9
|
53.1
|
0.6
|
|
O4
|
a:OEX412
|
4.1
|
49.1
|
0.6
|
|
O4
|
a:OEX412
|
4.1
|
48.7
|
0.4
|
|
O
|
a:HOH591
|
4.2
|
47.5
|
0.4
|
|
NH1
|
c:ARG357
|
4.2
|
49.2
|
0.6
|
|
NH1
|
c:ARG357
|
4.2
|
49.4
|
0.4
|
|
CB
|
a:ASP170
|
4.3
|
49.2
|
0.6
|
|
CB
|
a:ASP170
|
4.4
|
49.6
|
0.4
|
|
O
|
a:HOH516
|
4.4
|
52.7
|
0.4
|
|
NH2
|
c:ARG357
|
4.5
|
46.2
|
0.6
|
|
O
|
a:HOH516
|
4.5
|
53.1
|
0.6
|
|
NH2
|
c:ARG357
|
4.5
|
46.4
|
0.4
|
|
OE1
|
a:GLN165
|
4.6
|
54.8
|
0.6
|
|
O
|
a:HOH570
|
4.6
|
49.5
|
0.4
|
|
OH
|
a:TYR161
|
4.6
|
50.1
|
0.4
|
|
OE1
|
a:GLN165
|
4.6
|
55.4
|
0.4
|
|
O
|
a:HOH591
|
4.7
|
61.2
|
0.6
|
|
OH
|
a:TYR161
|
4.7
|
50.0
|
0.6
|
|
CA
|
a:ALA344
|
4.7
|
54.0
|
0.6
|
|
O
|
a:HOH576
|
4.8
|
72.5
|
0.6
|
|
CA
|
a:ALA344
|
4.8
|
53.9
|
0.4
|
|
O
|
a:HOH570
|
4.8
|
48.9
|
0.6
|
|
OE2
|
c:GLU354
|
4.9
|
50.6
|
0.6
|
|
CZ
|
c:ARG357
|
4.9
|
53.9
|
0.6
|
|
CZ
|
c:ARG357
|
4.9
|
53.8
|
0.4
|
|
OD1
|
a:ASP342
|
5.0
|
52.9
|
0.4
|
|
Calcium binding site 7 out
of 11 in 8irb
Go back to
Calcium Binding Sites List in 8irb
Calcium binding site 7 out
of 11 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 Calcium with other atoms in the Ca 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
|
a:Ca412
b:58.0
occ:0.60
|
CA1
|
a:OEX412
|
0.0
|
58.0
|
0.6
|
|
CA1
|
a:OEX412
|
0.3
|
53.1
|
0.4
|
|
O
|
a:HOH525
|
2.2
|
48.5
|
0.4
|
|
OD1
|
a:ASP170
|
2.4
|
54.5
|
0.6
|
|
O
|
a:HOH623
|
2.4
|
54.2
|
0.4
|
|
O
|
a:HOH525
|
2.5
|
58.6
|
0.6
|
|
OD1
|
a:ASP170
|
2.5
|
51.8
|
0.4
|
|
O
|
a:ALA344
|
2.5
|
53.8
|
0.6
|
|
O1
|
a:OEX412
|
2.6
|
47.1
|
0.4
|
|
O
|
a:ALA344
|
2.6
|
53.8
|
0.4
|
|
O1
|
a:OEX412
|
2.6
|
47.3
|
0.6
|
|
O
|
a:HOH623
|
2.6
|
55.8
|
0.6
|
|
O5
|
a:OEX412
|
2.7
|
50.8
|
0.4
|
|
O5
|
a:OEX412
|
2.7
|
50.8
|
0.6
|
|
O2
|
a:OEX412
|
2.7
|
46.0
|
0.6
|
|
OE1
|
a:GLU189
|
2.8
|
51.1
|
0.4
|
|
OE1
|
a:GLU189
|
2.9
|
57.9
|
0.6
|
|
O2
|
a:OEX412
|
2.9
|
43.9
|
0.4
|
|
CG
|
a:ASP170
|
3.3
|
47.8
|
0.6
|
|
CG
|
a:ASP170
|
3.4
|
47.2
|
0.4
|
|
MN1
|
a:OEX412
|
3.4
|
48.4
|
0.4
|
|
MN2
|
a:OEX412
|
3.5
|
50.2
|
0.4
|
|
MN2
|
a:OEX412
|
3.5
|
50.2
|
0.6
|
|
C
|
a:ALA344
|
3.5
|
53.0
|
0.6
|
|
MN1
|
a:OEX412
|
3.5
|
48.4
|
0.6
|
|
C
|
a:ALA344
|
3.6
|
53.0
|
0.4
|
|
MN3
|
a:OEX412
|
3.6
|
47.8
|
0.4
|
|
CD
|
a:GLU189
|
3.6
|
50.1
|
0.4
|
|
MN3
|
a:OEX412
|
3.6
|
50.1
|
0.6
|
|
CD
|
a:GLU189
|
3.7
|
50.2
|
0.6
|
|
OE2
|
a:GLU189
|
3.7
|
51.3
|
0.4
|
|
OE2
|
a:GLU189
|
3.7
|
51.6
|
0.6
|
|
OXT
|
a:ALA344
|
3.8
|
55.4
|
0.6
|
|
OD2
|
a:ASP170
|
3.8
|
50.0
|
0.4
|
|
OD2
|
a:ASP170
|
3.8
|
50.0
|
0.6
|
|
O3
|
a:OEX412
|
3.8
|
45.1
|
0.6
|
|
O3
|
a:OEX412
|
3.9
|
45.1
|
0.4
|
|
OXT
|
a:ALA344
|
3.9
|
54.5
|
0.4
|
|
MN4
|
a:OEX412
|
3.9
|
44.0
|
0.4
|
|
O
|
a:HOH591
|
4.0
|
47.5
|
0.4
|
|
MN4
|
a:OEX412
|
4.1
|
53.1
|
0.6
|
|
O
|
a:HOH516
|
4.2
|
52.7
|
0.4
|
|
O4
|
a:OEX412
|
4.3
|
49.1
|
0.6
|
|
O
|
a:HOH516
|
4.3
|
53.1
|
0.6
|
|
O4
|
a:OEX412
|
4.3
|
48.7
|
0.4
|
|
CB
|
a:ASP170
|
4.4
|
49.2
|
0.6
|
|
NH1
|
c:ARG357
|
4.4
|
49.2
|
0.6
|
|
NH1
|
c:ARG357
|
4.4
|
49.4
|
0.4
|
|
OH
|
a:TYR161
|
4.4
|
50.1
|
0.4
|
|
OH
|
a:TYR161
|
4.5
|
50.0
|
0.6
|
|
CB
|
a:ASP170
|
4.5
|
49.6
|
0.4
|
|
O
|
a:HOH591
|
4.5
|
61.2
|
0.6
|
|
OE1
|
a:GLN165
|
4.5
|
54.8
|
0.6
|
|
OE1
|
a:GLN165
|
4.6
|
55.4
|
0.4
|
|
O
|
a:HOH576
|
4.6
|
72.5
|
0.6
|
|
O
|
a:HOH570
|
4.7
|
49.5
|
0.4
|
|
CA
|
a:ALA344
|
4.8
|
54.0
|
0.6
|
|
NH2
|
c:ARG357
|
4.8
|
46.2
|
0.6
|
|
NH2
|
c:ARG357
|
4.8
|
46.4
|
0.4
|
|
CA
|
a:ALA344
|
4.8
|
53.9
|
0.4
|
|
O
|
a:HOH570
|
4.8
|
48.9
|
0.6
|
|
Calcium binding site 8 out
of 11 in 8irb
Go back to
Calcium Binding Sites List in 8irb
Calcium binding site 8 out
of 11 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 Calcium with other atoms in the Ca 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
|
c:Ca524
b:77.1
occ:1.00
|
OG1
|
c:THR159
|
2.6
|
71.2
|
1.0
|
|
O
|
c:THR254
|
2.6
|
66.8
|
1.0
|
|
O
|
c:HIS251
|
2.7
|
70.5
|
1.0
|
|
O
|
c:ASN155
|
2.9
|
69.1
|
1.0
|
|
OG1
|
c:THR158
|
3.1
|
75.7
|
1.0
|
|
O
|
c:ILE252
|
3.1
|
80.2
|
1.0
|
|
OD1
|
c:ASN155
|
3.5
|
103.8
|
1.0
|
|
CG
|
c:ASN155
|
3.6
|
89.0
|
1.0
|
|
N
|
c:THR159
|
3.6
|
71.9
|
1.0
|
|
ND2
|
c:ASN155
|
3.6
|
110.3
|
1.0
|
|
C
|
c:ILE252
|
3.7
|
74.6
|
1.0
|
|
C
|
c:ASN155
|
3.7
|
73.4
|
1.0
|
|
CB
|
c:THR159
|
3.7
|
70.4
|
1.0
|
|
C
|
c:HIS251
|
3.8
|
83.5
|
1.0
|
|
C
|
c:THR254
|
3.8
|
70.9
|
1.0
|
|
CB
|
c:THR158
|
3.9
|
67.8
|
1.0
|
|
CA
|
c:THR159
|
3.9
|
73.4
|
1.0
|
|
CA
|
c:ASN155
|
3.9
|
79.7
|
1.0
|
|
C
|
c:THR158
|
4.0
|
73.2
|
1.0
|
|
CA
|
c:ILE252
|
4.0
|
68.9
|
1.0
|
|
N
|
c:THR254
|
4.3
|
78.2
|
1.0
|
|
O
|
c:HOH692
|
4.3
|
75.1
|
1.0
|
|
CB
|
c:ASN155
|
4.4
|
80.0
|
1.0
|
|
N
|
c:ILE252
|
4.4
|
68.4
|
1.0
|
|
CA
|
c:THR158
|
4.4
|
69.0
|
1.0
|
|
O
|
c:THR158
|
4.5
|
70.2
|
1.0
|
|
N
|
c:LEU253
|
4.6
|
80.4
|
1.0
|
|
CA
|
c:THR254
|
4.7
|
74.7
|
1.0
|
|
N
|
c:THR255
|
4.8
|
65.1
|
1.0
|
|
C
|
c:LEU253
|
4.8
|
76.9
|
1.0
|
|
N
|
c:THR158
|
4.9
|
63.7
|
1.0
|
|
CA
|
c:THR255
|
4.9
|
67.8
|
1.0
|
|
N
|
c:LYS156
|
4.9
|
68.4
|
1.0
|
|
CG2
|
c:THR159
|
5.0
|
53.5
|
1.0
|
|
O
|
c:LYS154
|
5.0
|
74.7
|
1.0
|
|
Calcium binding site 9 out
of 11 in 8irb
Go back to
Calcium Binding Sites List in 8irb
Calcium binding site 9 out
of 11 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 Calcium with other atoms in the Ca binding
site number 9 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
|
c:Ca525
b:78.7
occ:1.00
|
OE1
|
c:GLU29
|
2.4
|
75.0
|
1.0
|
|
O
|
c:PHE22
|
2.5
|
88.4
|
1.0
|
|
OD2
|
c:ASP27
|
2.5
|
69.6
|
1.0
|
|
O
|
c:HOH721
|
2.5
|
75.2
|
1.0
|
|
OG
|
c:SER30
|
2.5
|
93.0
|
1.0
|
|
O
|
c:THR24
|
2.5
|
74.4
|
1.0
|
|
OD1
|
c:ASP27
|
2.7
|
67.1
|
1.0
|
|
CG
|
c:ASP27
|
3.0
|
75.9
|
1.0
|
|
C
|
c:PHE22
|
3.5
|
74.6
|
1.0
|
|
CB
|
c:SER30
|
3.5
|
59.9
|
1.0
|
|
CD
|
c:GLU29
|
3.6
|
71.9
|
1.0
|
|
C
|
c:THR24
|
3.8
|
76.5
|
1.0
|
|
N
|
c:SER30
|
4.0
|
66.6
|
1.0
|
|
CB
|
c:PHE22
|
4.0
|
77.5
|
1.0
|
|
CA
|
c:PHE22
|
4.0
|
86.3
|
1.0
|
|
OE2
|
c:GLU29
|
4.2
|
98.3
|
1.0
|
|
O
|
c:HOH638
|
4.3
|
78.7
|
1.0
|
|
CA
|
c:SER30
|
4.3
|
72.3
|
1.0
|
|
C
|
c:ALA23
|
4.4
|
81.2
|
1.0
|
|
N
|
c:THR24
|
4.4
|
76.8
|
1.0
|
|
CB
|
c:ASP27
|
4.5
|
79.2
|
1.0
|
|
N
|
c:ALA23
|
4.5
|
80.7
|
1.0
|
|
O
|
c:ALA23
|
4.6
|
85.5
|
1.0
|
|
CA
|
c:ASN25
|
4.6
|
75.3
|
1.0
|
|
CB
|
c:GLU29
|
4.6
|
76.9
|
1.0
|
|
N
|
c:ASN25
|
4.6
|
71.3
|
1.0
|
|
CG
|
c:GLU29
|
4.7
|
73.1
|
1.0
|
|
CA
|
c:THR24
|
4.7
|
83.3
|
1.0
|
|
C
|
c:GLU29
|
4.9
|
64.8
|
1.0
|
|
CA
|
c:ALA23
|
4.9
|
88.6
|
1.0
|
|
Calcium binding site 10 out
of 11 in 8irb
Go back to
Calcium Binding Sites List in 8irb
Calcium binding site 10 out
of 11 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 Calcium with other atoms in the Ca binding
site number 10 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:Ca103
b:121.2
occ:1.00
|
O
|
v:HOH314
|
2.6
|
89.9
|
1.0
|
|
OE2
|
v:GLU23
|
3.0
|
123.4
|
1.0
|
|
OXT
|
f:ARG45
|
3.1
|
80.8
|
1.0
|
|
O
|
f:ARG45
|
3.3
|
79.2
|
1.0
|
|
C
|
f:ARG45
|
3.6
|
79.5
|
1.0
|
|
CD
|
v:GLU23
|
4.0
|
120.0
|
1.0
|
|
O
|
a:ALA309
|
4.1
|
68.8
|
1.0
|
|
OE1
|
v:GLU23
|
4.4
|
125.5
|
1.0
|
|
OE1
|
v:GLU2
|
4.6
|
104.2
|
1.0
|
|
C
|
a:ALA309
|
4.9
|
70.3
|
1.0
|
|
CA
|
a:ALA309
|
4.9
|
73.7
|
1.0
|
|
CB
|
a:ALA309
|
4.9
|
63.1
|
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: Thu Jul 10 05:18:07 2025
|
