Calcium in PDB 6jlk: Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET1)
Enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET1)
All present enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET1):
1.10.3.9;
Protein crystallography data
The structure of Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET1), PDB code: 6jlk
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 /
2.15
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
121.970,
228.720,
286.980,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
14.9 /
19.3
|
Other elements in 6jlk:
The structure of Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET1) also contains other interesting chemical elements:
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
13;
Binding sites:
The binding sites of Calcium atom in the Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET1)
(pdb code 6jlk). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 13 binding sites of Calcium where determined in the
Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET1), PDB code: 6jlk:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 13 in 6jlk
Go back to
Calcium Binding Sites List in 6jlk
Calcium binding site 1 out
of 13 in the Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET1)
 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 (1F State, DATASET1) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca418
b:56.8
occ:0.40
|
CA1
|
A:OEX418
|
0.0
|
56.8
|
0.4
|
|
CA1
|
A:OEX418
|
0.2
|
39.5
|
0.6
|
|
OD1
|
A:ASP170
|
2.2
|
43.6
|
0.6
|
|
OD1
|
A:ASP170
|
2.4
|
44.0
|
0.4
|
|
O
|
A:ALA344
|
2.4
|
46.2
|
0.4
|
|
O
|
A:ALA344
|
2.5
|
42.4
|
0.6
|
|
O
|
A:HOH516
|
2.5
|
45.5
|
0.4
|
|
O5
|
A:OEX418
|
2.5
|
34.3
|
0.6
|
|
O2
|
A:OEX418
|
2.5
|
33.8
|
0.6
|
|
O1
|
A:OEX418
|
2.6
|
36.8
|
0.4
|
|
O5
|
A:OEX418
|
2.6
|
36.5
|
0.4
|
|
O1
|
A:OEX418
|
2.6
|
38.4
|
0.6
|
|
O
|
A:HOH646
|
2.6
|
44.9
|
0.4
|
|
O
|
A:HOH516
|
2.6
|
46.3
|
0.6
|
|
O
|
A:HOH646
|
2.6
|
45.0
|
0.6
|
|
O2
|
A:OEX418
|
2.6
|
30.7
|
0.4
|
|
CG
|
A:ASP170
|
3.0
|
36.2
|
0.6
|
|
OE1
|
A:GLU189
|
3.1
|
35.9
|
0.4
|
|
CG
|
A:ASP170
|
3.1
|
36.9
|
0.4
|
|
OE1
|
A:GLU189
|
3.2
|
41.5
|
0.6
|
|
MN3
|
A:OEX418
|
3.3
|
35.8
|
0.6
|
|
MN3
|
A:OEX418
|
3.3
|
38.3
|
0.4
|
|
OD2
|
A:ASP170
|
3.3
|
35.9
|
0.6
|
|
MN2
|
A:OEX418
|
3.3
|
34.7
|
0.6
|
|
OD2
|
A:ASP170
|
3.4
|
41.9
|
0.4
|
|
C
|
A:ALA344
|
3.4
|
48.1
|
0.6
|
|
MN2
|
A:OEX418
|
3.4
|
41.1
|
0.4
|
|
C
|
A:ALA344
|
3.4
|
47.1
|
0.4
|
|
MN1
|
A:OEX418
|
3.5
|
39.6
|
0.6
|
|
MN1
|
A:OEX418
|
3.6
|
32.5
|
0.4
|
|
OXT
|
A:ALA344
|
3.6
|
37.8
|
0.6
|
|
O4
|
A:OEX418
|
3.7
|
30.7
|
0.4
|
|
MN4
|
A:OEX418
|
3.7
|
36.8
|
0.4
|
|
OXT
|
A:ALA344
|
3.7
|
35.5
|
0.4
|
|
MN4
|
A:OEX418
|
3.7
|
40.0
|
0.6
|
|
OE2
|
A:GLU189
|
3.8
|
39.2
|
0.6
|
|
O4
|
A:OEX418
|
3.9
|
37.9
|
0.6
|
|
OE2
|
A:GLU189
|
3.9
|
37.8
|
0.4
|
|
CD
|
A:GLU189
|
3.9
|
35.0
|
0.6
|
|
CD
|
A:GLU189
|
3.9
|
35.4
|
0.4
|
|
O
|
A:HOH524
|
3.9
|
57.5
|
1.0
|
|
O3
|
A:OEX418
|
4.0
|
39.5
|
0.6
|
|
O3
|
A:OEX418
|
4.1
|
43.5
|
0.4
|
|
NH1
|
C:ARG357
|
4.2
|
33.0
|
1.0
|
|
CB
|
A:ASP170
|
4.2
|
31.0
|
0.6
|
|
NH2
|
C:ARG357
|
4.4
|
28.6
|
1.0
|
|
O
|
A:HOH511
|
4.4
|
32.5
|
1.0
|
|
CB
|
A:ASP170
|
4.5
|
27.9
|
0.4
|
|
O
|
A:HOH599
|
4.6
|
35.9
|
0.4
|
|
O
|
A:HOH599
|
4.7
|
37.4
|
0.6
|
|
OH
|
A:TYR161
|
4.7
|
30.4
|
1.0
|
|
CA
|
A:ALA344
|
4.8
|
45.2
|
0.6
|
|
CA
|
A:ALA344
|
4.8
|
47.5
|
0.4
|
|
OE1
|
A:GLN165
|
4.8
|
43.0
|
1.0
|
|
CZ
|
C:ARG357
|
4.8
|
47.4
|
1.0
|
|
OE2
|
C:GLU354
|
4.9
|
35.1
|
0.6
|
|
OE1
|
C:GLU354
|
4.9
|
36.5
|
0.6
|
|
Calcium binding site 2 out
of 13 in 6jlk
Go back to
Calcium Binding Sites List in 6jlk
Calcium binding site 2 out
of 13 in the Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET1)
 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 (1F State, DATASET1) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca418
b:39.5
occ:0.60
|
CA1
|
A:OEX418
|
0.0
|
39.5
|
0.6
|
|
CA1
|
A:OEX418
|
0.2
|
56.8
|
0.4
|
|
O
|
A:HOH516
|
2.3
|
45.5
|
0.4
|
|
OD1
|
A:ASP170
|
2.4
|
43.6
|
0.6
|
|
O
|
A:ALA344
|
2.4
|
46.2
|
0.4
|
|
O
|
A:HOH516
|
2.5
|
46.3
|
0.6
|
|
O
|
A:ALA344
|
2.5
|
42.4
|
0.6
|
|
OD1
|
A:ASP170
|
2.5
|
44.0
|
0.4
|
|
O1
|
A:OEX418
|
2.5
|
36.8
|
0.4
|
|
O
|
A:HOH646
|
2.5
|
44.9
|
0.4
|
|
O1
|
A:OEX418
|
2.5
|
38.4
|
0.6
|
|
O
|
A:HOH646
|
2.6
|
45.0
|
0.6
|
|
O5
|
A:OEX418
|
2.6
|
34.3
|
0.6
|
|
O5
|
A:OEX418
|
2.7
|
36.5
|
0.4
|
|
O2
|
A:OEX418
|
2.7
|
33.8
|
0.6
|
|
O2
|
A:OEX418
|
2.8
|
30.7
|
0.4
|
|
OE1
|
A:GLU189
|
2.9
|
35.9
|
0.4
|
|
OE1
|
A:GLU189
|
3.0
|
41.5
|
0.6
|
|
CG
|
A:ASP170
|
3.1
|
36.2
|
0.6
|
|
CG
|
A:ASP170
|
3.3
|
36.9
|
0.4
|
|
MN2
|
A:OEX418
|
3.4
|
34.7
|
0.6
|
|
C
|
A:ALA344
|
3.4
|
48.1
|
0.6
|
|
MN3
|
A:OEX418
|
3.4
|
35.8
|
0.6
|
|
C
|
A:ALA344
|
3.4
|
47.1
|
0.4
|
|
OD2
|
A:ASP170
|
3.5
|
35.9
|
0.6
|
|
MN2
|
A:OEX418
|
3.5
|
41.1
|
0.4
|
|
MN3
|
A:OEX418
|
3.5
|
38.3
|
0.4
|
|
MN1
|
A:OEX418
|
3.5
|
39.6
|
0.6
|
|
OD2
|
A:ASP170
|
3.5
|
41.9
|
0.4
|
|
MN1
|
A:OEX418
|
3.5
|
32.5
|
0.4
|
|
OXT
|
A:ALA344
|
3.6
|
37.8
|
0.6
|
|
OE2
|
A:GLU189
|
3.7
|
39.2
|
0.6
|
|
CD
|
A:GLU189
|
3.7
|
35.0
|
0.6
|
|
CD
|
A:GLU189
|
3.7
|
35.4
|
0.4
|
|
OXT
|
A:ALA344
|
3.8
|
35.5
|
0.4
|
|
OE2
|
A:GLU189
|
3.8
|
37.8
|
0.4
|
|
O
|
A:HOH524
|
3.8
|
57.5
|
1.0
|
|
MN4
|
A:OEX418
|
3.8
|
36.8
|
0.4
|
|
O4
|
A:OEX418
|
3.9
|
30.7
|
0.4
|
|
MN4
|
A:OEX418
|
3.9
|
40.0
|
0.6
|
|
O3
|
A:OEX418
|
4.0
|
39.5
|
0.6
|
|
O4
|
A:OEX418
|
4.1
|
37.9
|
0.6
|
|
O3
|
A:OEX418
|
4.2
|
43.5
|
0.4
|
|
O
|
A:HOH511
|
4.2
|
32.5
|
1.0
|
|
NH1
|
C:ARG357
|
4.3
|
33.0
|
1.0
|
|
CB
|
A:ASP170
|
4.3
|
31.0
|
0.6
|
|
OH
|
A:TYR161
|
4.5
|
30.4
|
1.0
|
|
CB
|
A:ASP170
|
4.6
|
27.9
|
0.4
|
|
NH2
|
C:ARG357
|
4.6
|
28.6
|
1.0
|
|
O
|
A:HOH599
|
4.6
|
35.9
|
0.4
|
|
OE1
|
A:GLN165
|
4.7
|
43.0
|
1.0
|
|
O
|
A:HOH599
|
4.7
|
37.4
|
0.6
|
|
CA
|
A:ALA344
|
4.8
|
45.2
|
0.6
|
|
CA
|
A:ALA344
|
4.8
|
47.5
|
0.4
|
|
CZ
|
C:ARG357
|
5.0
|
47.4
|
1.0
|
|
CG1
|
A:VAL185
|
5.0
|
31.1
|
1.0
|
|
Calcium binding site 3 out
of 13 in 6jlk
Go back to
Calcium Binding Sites List in 6jlk
Calcium binding site 3 out
of 13 in the Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET1)
 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 (1F State, DATASET1) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca601
b:0.3
occ:1.00
|
O
|
B:HOH905
|
2.7
|
94.8
|
1.0
|
|
O
|
O:HOH468
|
2.7
|
1.0
|
1.0
|
|
O
|
B:HOH866
|
2.8
|
77.0
|
1.0
|
|
O
|
B:HOH976
|
2.8
|
60.1
|
1.0
|
|
O
|
B:HOH900
|
3.1
|
51.5
|
1.0
|
|
OD1
|
B:ASN438
|
3.3
|
45.4
|
1.0
|
|
O
|
D:HOH633
|
3.3
|
93.1
|
1.0
|
|
O
|
M:HOH202
|
4.4
|
80.3
|
1.0
|
|
OE1
|
O:GLU181
|
4.4
|
69.4
|
0.5
|
|
CG
|
B:ASN438
|
4.5
|
44.0
|
1.0
|
|
O
|
B:HOH771
|
4.6
|
51.2
|
1.0
|
|
O
|
B:HOH867
|
4.7
|
45.3
|
1.0
|
|
OE2
|
O:GLU181
|
4.9
|
80.7
|
0.5
|
|
OE1
|
O:GLU181
|
5.0
|
71.9
|
0.5
|
|
Calcium binding site 4 out
of 13 in 6jlk
Go back to
Calcium Binding Sites List in 6jlk
Calcium binding site 4 out
of 13 in the Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET1)
 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 (1F State, DATASET1) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca526
b:70.9
occ:1.00
|
OG1
|
C:THR159
|
2.6
|
69.9
|
1.0
|
|
O
|
C:ASN155
|
2.7
|
68.2
|
1.0
|
|
O
|
C:HIS251
|
2.7
|
64.2
|
1.0
|
|
O
|
C:THR254
|
2.8
|
62.9
|
1.0
|
|
OD1
|
C:ASN155
|
2.9
|
74.6
|
1.0
|
|
O
|
C:ILE252
|
3.0
|
66.5
|
1.0
|
|
OG1
|
C:THR158
|
3.0
|
57.6
|
1.0
|
|
N
|
C:THR159
|
3.5
|
52.3
|
1.0
|
|
C
|
C:ILE252
|
3.5
|
75.3
|
1.0
|
|
C
|
C:ASN155
|
3.6
|
66.2
|
1.0
|
|
CG
|
C:ASN155
|
3.8
|
71.2
|
1.0
|
|
CB
|
C:THR159
|
3.8
|
65.2
|
1.0
|
|
CA
|
C:THR159
|
3.8
|
61.1
|
1.0
|
|
C
|
C:HIS251
|
3.8
|
67.6
|
1.0
|
|
CA
|
C:ILE252
|
3.9
|
69.5
|
1.0
|
|
CA
|
C:ASN155
|
3.9
|
66.8
|
1.0
|
|
C
|
C:THR158
|
3.9
|
58.5
|
1.0
|
|
C
|
C:THR254
|
4.0
|
65.5
|
1.0
|
|
CB
|
C:THR158
|
4.0
|
53.1
|
1.0
|
|
N
|
C:THR254
|
4.3
|
63.9
|
1.0
|
|
N
|
C:ILE252
|
4.3
|
66.0
|
1.0
|
|
O
|
C:HOH654
|
4.4
|
61.0
|
1.0
|
|
CA
|
C:THR158
|
4.5
|
60.3
|
1.0
|
|
CB
|
C:ASN155
|
4.5
|
62.5
|
1.0
|
|
N
|
C:LEU253
|
4.5
|
81.8
|
1.0
|
|
O
|
C:THR158
|
4.5
|
57.9
|
1.0
|
|
ND2
|
C:ASN155
|
4.7
|
86.0
|
1.0
|
|
N
|
C:LYS156
|
4.7
|
60.4
|
1.0
|
|
CA
|
C:THR254
|
4.8
|
63.9
|
1.0
|
|
N
|
C:THR158
|
4.8
|
59.7
|
1.0
|
|
CG2
|
C:THR159
|
4.8
|
52.5
|
1.0
|
|
C
|
C:LEU253
|
4.9
|
76.7
|
1.0
|
|
N
|
C:THR255
|
4.9
|
68.1
|
1.0
|
|
Calcium binding site 5 out
of 13 in 6jlk
Go back to
Calcium Binding Sites List in 6jlk
Calcium binding site 5 out
of 13 in the Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET1)
 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 (1F State, DATASET1) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca104
b:84.2
occ:1.00
|
O
|
V:HOH393
|
2.6
|
70.3
|
1.0
|
|
O
|
F:HOH207
|
2.7
|
69.5
|
1.0
|
|
O
|
F:ARG45
|
2.8
|
52.5
|
1.0
|
|
O3
|
A:GOL422
|
2.8
|
68.6
|
1.0
|
|
OXT
|
F:ARG45
|
2.8
|
51.6
|
1.0
|
|
O2
|
A:GOL422
|
2.8
|
82.4
|
1.0
|
|
O
|
F:HOH208
|
3.0
|
74.4
|
1.0
|
|
C3
|
A:GOL422
|
3.0
|
72.0
|
1.0
|
|
C
|
F:ARG45
|
3.2
|
52.8
|
1.0
|
|
C2
|
A:GOL422
|
3.5
|
73.4
|
1.0
|
|
O
|
V:HOH384
|
3.5
|
70.7
|
1.0
|
|
O
|
F:HOH203
|
4.3
|
72.5
|
1.0
|
|
OE2
|
V:GLU23
|
4.3
|
0.6
|
1.0
|
|
O
|
A:HOH570
|
4.6
|
65.3
|
1.0
|
|
CA
|
F:ARG45
|
4.7
|
52.0
|
1.0
|
|
C1
|
A:GOL422
|
4.7
|
74.4
|
1.0
|
|
O
|
A:ALA309
|
4.8
|
49.4
|
1.0
|
|
CB
|
A:ALA309
|
4.9
|
47.1
|
1.0
|
|
OE1
|
V:GLU23
|
4.9
|
0.1
|
1.0
|
|
CD
|
V:GLU23
|
5.0
|
99.3
|
1.0
|
|
Calcium binding site 6 out
of 13 in 6jlk
Go back to
Calcium Binding Sites List in 6jlk
Calcium binding site 6 out
of 13 in the Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET1)
 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 (1F State, DATASET1) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
O:Ca302
b:81.8
occ:1.00
|
O
|
O:VAL201
|
2.4
|
67.2
|
1.0
|
|
O
|
O:THR138
|
2.4
|
67.2
|
1.0
|
|
O
|
O:HOH517
|
2.5
|
59.1
|
1.0
|
|
O
|
O:HOH529
|
2.5
|
64.5
|
1.0
|
|
OD1
|
O:ASN200
|
2.5
|
93.3
|
1.0
|
|
O
|
O:HOH548
|
2.8
|
71.5
|
1.0
|
|
O
|
O:HOH553
|
2.9
|
79.0
|
1.0
|
|
CG
|
O:ASN200
|
3.4
|
90.5
|
1.0
|
|
C
|
O:VAL201
|
3.5
|
59.6
|
1.0
|
|
C
|
O:THR138
|
3.6
|
62.8
|
1.0
|
|
ND2
|
O:ASN200
|
3.8
|
1.0
|
1.0
|
|
CA
|
O:ALA202
|
4.3
|
59.8
|
1.0
|
|
N
|
O:VAL201
|
4.3
|
51.5
|
1.0
|
|
N
|
O:ALA202
|
4.4
|
60.6
|
1.0
|
|
CA
|
O:THR138
|
4.4
|
62.5
|
1.0
|
|
N
|
O:SER139
|
4.5
|
73.3
|
1.0
|
|
CA
|
O:VAL201
|
4.5
|
52.0
|
1.0
|
|
C
|
O:ASN200
|
4.5
|
50.1
|
1.0
|
|
CB
|
O:THR138
|
4.6
|
65.4
|
1.0
|
|
CA
|
O:SER139
|
4.6
|
62.4
|
1.0
|
|
CB
|
O:ASN200
|
4.7
|
70.5
|
1.0
|
|
O
|
O:HOH456
|
4.8
|
76.5
|
1.0
|
|
O
|
O:ASN200
|
4.8
|
60.2
|
1.0
|
|
O
|
O:THR140
|
4.9
|
74.0
|
1.0
|
|
CA
|
O:ASN200
|
5.0
|
55.2
|
1.0
|
|
Calcium binding site 7 out
of 13 in 6jlk
Go back to
Calcium Binding Sites List in 6jlk
Calcium binding site 7 out
of 13 in the Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET1)
 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 (1F State, DATASET1) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Ca416
b:52.3
occ:0.40
|
CA1
|
a:OEX416
|
0.0
|
52.3
|
0.4
|
|
CA1
|
a:OEX416
|
0.2
|
46.4
|
0.6
|
|
OD1
|
a:ASP170
|
2.2
|
40.9
|
0.6
|
|
O
|
a:ALA344
|
2.3
|
42.2
|
0.6
|
|
OD1
|
a:ASP170
|
2.4
|
42.8
|
0.4
|
|
O
|
a:ALA344
|
2.4
|
44.6
|
0.4
|
|
O
|
a:HOH532
|
2.5
|
46.3
|
0.4
|
|
O2
|
a:OEX416
|
2.5
|
41.4
|
0.6
|
|
O
|
a:HOH532
|
2.5
|
46.9
|
0.6
|
|
O1
|
a:OEX416
|
2.6
|
39.4
|
0.4
|
|
O
|
a:HOH633
|
2.6
|
44.9
|
0.4
|
|
O5
|
a:OEX416
|
2.6
|
35.9
|
0.4
|
|
O2
|
a:OEX416
|
2.6
|
40.2
|
0.4
|
|
O1
|
a:OEX416
|
2.6
|
41.0
|
0.6
|
|
O
|
a:HOH633
|
2.7
|
45.3
|
0.6
|
|
O5
|
a:OEX416
|
2.7
|
37.1
|
0.6
|
|
CG
|
a:ASP170
|
3.1
|
43.2
|
0.6
|
|
OE1
|
a:GLU189
|
3.1
|
48.9
|
0.4
|
|
CG
|
a:ASP170
|
3.1
|
41.8
|
0.4
|
|
OE1
|
a:GLU189
|
3.2
|
53.0
|
0.6
|
|
MN2
|
a:OEX416
|
3.3
|
38.3
|
0.6
|
|
C
|
a:ALA344
|
3.3
|
47.7
|
0.6
|
|
MN3
|
a:OEX416
|
3.4
|
39.1
|
0.6
|
|
OD2
|
a:ASP170
|
3.4
|
43.2
|
0.4
|
|
MN2
|
a:OEX416
|
3.4
|
36.9
|
0.4
|
|
C
|
a:ALA344
|
3.4
|
46.7
|
0.4
|
|
MN3
|
a:OEX416
|
3.5
|
36.4
|
0.4
|
|
OD2
|
a:ASP170
|
3.5
|
40.5
|
0.6
|
|
MN1
|
a:OEX416
|
3.6
|
37.8
|
0.4
|
|
MN1
|
a:OEX416
|
3.6
|
38.6
|
0.6
|
|
OXT
|
a:ALA344
|
3.6
|
39.7
|
0.6
|
|
OXT
|
a:ALA344
|
3.7
|
37.8
|
0.4
|
|
MN4
|
a:OEX416
|
3.8
|
43.9
|
0.6
|
|
MN4
|
a:OEX416
|
3.8
|
37.2
|
0.4
|
|
O4
|
a:OEX416
|
3.9
|
34.5
|
0.4
|
|
O
|
a:HOH515
|
3.9
|
52.7
|
1.0
|
|
OE2
|
a:GLU189
|
3.9
|
43.0
|
0.6
|
|
CD
|
a:GLU189
|
3.9
|
46.9
|
0.4
|
|
CD
|
a:GLU189
|
4.0
|
47.2
|
0.6
|
|
O4
|
a:OEX416
|
4.0
|
34.4
|
0.6
|
|
OE2
|
a:GLU189
|
4.0
|
41.6
|
0.4
|
|
O3
|
a:OEX416
|
4.1
|
32.1
|
0.6
|
|
NH1
|
c:ARG357
|
4.1
|
38.4
|
0.6
|
|
O3
|
a:OEX416
|
4.2
|
40.9
|
0.4
|
|
NH1
|
c:ARG357
|
4.2
|
37.9
|
0.4
|
|
CB
|
a:ASP170
|
4.3
|
38.0
|
0.6
|
|
CB
|
a:ASP170
|
4.4
|
38.7
|
0.4
|
|
NH2
|
c:ARG357
|
4.4
|
37.8
|
0.6
|
|
NH2
|
c:ARG357
|
4.5
|
38.7
|
0.4
|
|
OH
|
a:TYR161
|
4.6
|
38.4
|
1.0
|
|
O
|
a:HOH542
|
4.6
|
38.9
|
0.4
|
|
O
|
a:HOH513
|
4.6
|
38.0
|
1.0
|
|
OE1
|
a:GLN165
|
4.6
|
37.2
|
1.0
|
|
CA
|
a:ALA344
|
4.7
|
49.6
|
0.6
|
|
O
|
a:HOH542
|
4.7
|
38.9
|
0.6
|
|
CA
|
a:ALA344
|
4.8
|
49.4
|
0.4
|
|
CZ
|
c:ARG357
|
4.8
|
39.2
|
0.6
|
|
OE2
|
c:GLU354
|
4.8
|
37.3
|
0.6
|
|
CZ
|
c:ARG357
|
4.8
|
38.4
|
0.4
|
|
OE1
|
c:GLU354
|
4.9
|
39.9
|
0.6
|
|
Calcium binding site 8 out
of 13 in 6jlk
Go back to
Calcium Binding Sites List in 6jlk
Calcium binding site 8 out
of 13 in the Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET1)
 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 (1F State, DATASET1) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
a:Ca416
b:46.4
occ:0.60
|
CA1
|
a:OEX416
|
0.0
|
46.4
|
0.6
|
|
CA1
|
a:OEX416
|
0.2
|
52.3
|
0.4
|
|
O
|
a:HOH532
|
2.4
|
46.3
|
0.4
|
|
O
|
a:ALA344
|
2.4
|
42.2
|
0.6
|
|
OD1
|
a:ASP170
|
2.4
|
40.9
|
0.6
|
|
O
|
a:HOH532
|
2.4
|
46.9
|
0.6
|
|
O
|
a:HOH633
|
2.5
|
44.9
|
0.4
|
|
O
|
a:ALA344
|
2.5
|
44.6
|
0.4
|
|
O1
|
a:OEX416
|
2.5
|
39.4
|
0.4
|
|
OD1
|
a:ASP170
|
2.5
|
42.8
|
0.4
|
|
O
|
a:HOH633
|
2.6
|
45.3
|
0.6
|
|
O1
|
a:OEX416
|
2.6
|
41.0
|
0.6
|
|
O5
|
a:OEX416
|
2.6
|
35.9
|
0.4
|
|
O2
|
a:OEX416
|
2.7
|
41.4
|
0.6
|
|
O5
|
a:OEX416
|
2.7
|
37.1
|
0.6
|
|
O2
|
a:OEX416
|
2.8
|
40.2
|
0.4
|
|
OE1
|
a:GLU189
|
2.9
|
48.9
|
0.4
|
|
OE1
|
a:GLU189
|
3.0
|
53.0
|
0.6
|
|
CG
|
a:ASP170
|
3.2
|
43.2
|
0.6
|
|
CG
|
a:ASP170
|
3.3
|
41.8
|
0.4
|
|
MN2
|
a:OEX416
|
3.4
|
38.3
|
0.6
|
|
C
|
a:ALA344
|
3.4
|
47.7
|
0.6
|
|
MN2
|
a:OEX416
|
3.5
|
36.9
|
0.4
|
|
MN1
|
a:OEX416
|
3.5
|
37.8
|
0.4
|
|
MN3
|
a:OEX416
|
3.5
|
39.1
|
0.6
|
|
C
|
a:ALA344
|
3.5
|
46.7
|
0.4
|
|
OD2
|
a:ASP170
|
3.5
|
43.2
|
0.4
|
|
MN1
|
a:OEX416
|
3.5
|
38.6
|
0.6
|
|
MN3
|
a:OEX416
|
3.6
|
36.4
|
0.4
|
|
OD2
|
a:ASP170
|
3.6
|
40.5
|
0.6
|
|
CD
|
a:GLU189
|
3.7
|
46.9
|
0.4
|
|
OXT
|
a:ALA344
|
3.7
|
39.7
|
0.6
|
|
CD
|
a:GLU189
|
3.7
|
47.2
|
0.6
|
|
OE2
|
a:GLU189
|
3.7
|
43.0
|
0.6
|
|
OXT
|
a:ALA344
|
3.8
|
37.8
|
0.4
|
|
O
|
a:HOH515
|
3.8
|
52.7
|
1.0
|
|
OE2
|
a:GLU189
|
3.8
|
41.6
|
0.4
|
|
MN4
|
a:OEX416
|
3.9
|
43.9
|
0.6
|
|
MN4
|
a:OEX416
|
3.9
|
37.2
|
0.4
|
|
O4
|
a:OEX416
|
4.1
|
34.5
|
0.4
|
|
O3
|
a:OEX416
|
4.1
|
32.1
|
0.6
|
|
O4
|
a:OEX416
|
4.1
|
34.4
|
0.6
|
|
O3
|
a:OEX416
|
4.2
|
40.9
|
0.4
|
|
NH1
|
c:ARG357
|
4.4
|
38.4
|
0.6
|
|
O
|
a:HOH513
|
4.4
|
38.0
|
1.0
|
|
CB
|
a:ASP170
|
4.4
|
38.0
|
0.6
|
|
NH1
|
c:ARG357
|
4.4
|
37.9
|
0.4
|
|
OH
|
a:TYR161
|
4.4
|
38.4
|
1.0
|
|
CB
|
a:ASP170
|
4.5
|
38.7
|
0.4
|
|
O
|
a:HOH542
|
4.6
|
38.9
|
0.4
|
|
OE1
|
a:GLN165
|
4.6
|
37.2
|
1.0
|
|
NH2
|
c:ARG357
|
4.7
|
37.8
|
0.6
|
|
O
|
a:HOH542
|
4.7
|
38.9
|
0.6
|
|
CA
|
a:ALA344
|
4.7
|
49.6
|
0.6
|
|
NH2
|
c:ARG357
|
4.7
|
38.7
|
0.4
|
|
CA
|
a:ALA344
|
4.8
|
49.4
|
0.4
|
|
OE2
|
c:GLU354
|
5.0
|
37.3
|
0.6
|
|
O
|
a:HOH587
|
5.0
|
53.6
|
1.0
|
|
Calcium binding site 9 out
of 13 in 6jlk
Go back to
Calcium Binding Sites List in 6jlk
Calcium binding site 9 out
of 13 in the Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET1)
 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 (1F State, DATASET1) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
b:Ca609
b:0.6
occ:1.00
|
O
|
o:HOH431
|
2.5
|
0.4
|
1.0
|
|
O
|
b:HOH721
|
2.8
|
64.9
|
1.0
|
|
O
|
m:HOH215
|
2.8
|
63.8
|
1.0
|
|
O
|
b:HOH891
|
3.0
|
54.4
|
1.0
|
|
OD1
|
b:ASN438
|
3.3
|
48.6
|
1.0
|
|
OE1
|
o:GLU181
|
4.2
|
87.6
|
0.5
|
|
O
|
b:HOH779
|
4.4
|
48.8
|
1.0
|
|
CG
|
b:ASN438
|
4.5
|
44.6
|
1.0
|
|
O
|
m:HOH208
|
4.6
|
59.8
|
1.0
|
|
O
|
o:HOH482
|
4.7
|
71.5
|
1.0
|
|
O
|
b:SER439
|
4.7
|
33.7
|
1.0
|
|
O
|
b:HOH770
|
4.7
|
73.5
|
1.0
|
|
OE2
|
m:GLU2
|
4.7
|
86.5
|
1.0
|
|
O
|
o:HOH553
|
4.7
|
65.0
|
1.0
|
|
OE1
|
b:GLU435
|
4.8
|
78.9
|
0.5
|
|
OE2
|
o:GLU181
|
4.9
|
71.3
|
0.5
|
|
O
|
b:HOH788
|
4.9
|
46.2
|
1.0
|
|
CD
|
o:GLU181
|
5.0
|
78.3
|
0.5
|
|
Calcium binding site 10 out
of 13 in 6jlk
Go back to
Calcium Binding Sites List in 6jlk
Calcium binding site 10 out
of 13 in the Xfel Structure of Cyanobacterial Photosystem II (1F State, DATASET1)
 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 (1F State, DATASET1) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
c:Ca504
b:67.7
occ:1.00
|
O
|
c:HIS251
|
2.6
|
71.9
|
1.0
|
|
O
|
c:ASN155
|
2.6
|
66.0
|
1.0
|
|
OG1
|
c:THR159
|
2.7
|
67.0
|
1.0
|
|
O
|
c:THR254
|
2.7
|
63.3
|
1.0
|
|
OG1
|
c:THR158
|
2.9
|
62.5
|
1.0
|
|
N
|
c:THR159
|
3.2
|
56.8
|
1.0
|
|
OD1
|
c:ASN155
|
3.3
|
78.4
|
1.0
|
|
O
|
c:ILE252
|
3.3
|
61.9
|
1.0
|
|
C
|
c:ASN155
|
3.6
|
62.8
|
1.0
|
|
CA
|
c:THR159
|
3.7
|
62.6
|
1.0
|
|
C
|
c:ILE252
|
3.7
|
75.9
|
1.0
|
|
C
|
c:HIS251
|
3.7
|
73.4
|
1.0
|
|
CB
|
c:THR159
|
3.7
|
62.0
|
1.0
|
|
C
|
c:THR158
|
3.8
|
63.0
|
1.0
|
|
CB
|
c:THR158
|
3.8
|
52.6
|
1.0
|
|
CA
|
c:ILE252
|
3.9
|
66.0
|
1.0
|
|
C
|
c:THR254
|
3.9
|
63.9
|
1.0
|
|
CG
|
c:ASN155
|
4.0
|
72.4
|
1.0
|
|
CA
|
c:ASN155
|
4.0
|
67.6
|
1.0
|
|
CA
|
c:THR158
|
4.3
|
60.2
|
1.0
|
|
N
|
c:ILE252
|
4.3
|
73.3
|
1.0
|
|
N
|
c:THR254
|
4.3
|
63.7
|
1.0
|
|
O
|
c:THR158
|
4.4
|
60.0
|
1.0
|
|
O
|
c:HOH669
|
4.6
|
63.6
|
1.0
|
|
N
|
c:LEU253
|
4.6
|
81.3
|
1.0
|
|
CB
|
c:ASN155
|
4.6
|
59.8
|
1.0
|
|
N
|
c:THR158
|
4.7
|
56.4
|
1.0
|
|
ND2
|
c:ASN155
|
4.7
|
81.5
|
1.0
|
|
CA
|
c:THR254
|
4.8
|
61.1
|
1.0
|
|
N
|
c:LYS156
|
4.8
|
60.4
|
1.0
|
|
CG2
|
c:THR159
|
4.8
|
54.4
|
1.0
|
|
N
|
c:THR255
|
4.9
|
61.8
|
1.0
|
|
CA
|
c:HIS251
|
4.9
|
66.8
|
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 Jul 16 09:52:46 2024
|
