Magnesium in PDB 8irc: Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)
Enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)
All present enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation):
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 (Single Conformation), PDB code: 8irc
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)
|
19.99 /
2.25
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
125.77,
231.76,
288.58,
90,
90,
90
|
R / Rfree (%)
|
14.1 /
17.6
|
Other elements in 8irc:
The structure of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation) also contains other interesting chemical elements:
Magnesium Binding Sites:
Magnesium binding site 1 out
of 72 in 8irc
Go back to
Magnesium Binding Sites List in 8irc
Magnesium binding site 1 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg404
b:42.5
occ:1.00
|
MG
|
A:CLA404
|
0.0
|
42.5
|
1.0
|
ND
|
A:CLA404
|
2.0
|
45.4
|
1.0
|
NB
|
A:CLA404
|
2.1
|
42.4
|
1.0
|
NC
|
A:CLA404
|
2.1
|
45.1
|
1.0
|
NA
|
A:CLA404
|
2.1
|
42.8
|
1.0
|
NE2
|
A:HIS198
|
2.2
|
41.7
|
1.0
|
C4D
|
A:CLA404
|
3.0
|
43.0
|
1.0
|
C1C
|
A:CLA404
|
3.0
|
41.1
|
1.0
|
C1B
|
A:CLA404
|
3.0
|
40.3
|
1.0
|
CE1
|
A:HIS198
|
3.0
|
42.8
|
1.0
|
C4A
|
A:CLA404
|
3.1
|
45.7
|
1.0
|
C1A
|
A:CLA404
|
3.1
|
44.1
|
1.0
|
C4B
|
A:CLA404
|
3.1
|
38.4
|
1.0
|
C4C
|
A:CLA404
|
3.1
|
39.4
|
1.0
|
C1D
|
A:CLA404
|
3.3
|
40.8
|
1.0
|
CD2
|
A:HIS198
|
3.3
|
44.4
|
1.0
|
CHB
|
A:CLA404
|
3.4
|
39.8
|
1.0
|
CHC
|
A:CLA404
|
3.4
|
41.9
|
1.0
|
CHA
|
A:CLA404
|
3.5
|
42.4
|
1.0
|
CHD
|
A:CLA404
|
3.7
|
40.8
|
1.0
|
CE
|
A:MET183
|
4.1
|
34.1
|
1.0
|
ND1
|
A:HIS198
|
4.2
|
42.9
|
1.0
|
C3D
|
A:CLA404
|
4.3
|
42.0
|
1.0
|
C2C
|
A:CLA404
|
4.4
|
40.4
|
1.0
|
C2B
|
A:CLA404
|
4.4
|
41.6
|
1.0
|
CAB
|
D:CLA404
|
4.4
|
40.9
|
1.0
|
CG
|
A:HIS198
|
4.4
|
44.6
|
1.0
|
C2A
|
A:CLA404
|
4.4
|
43.9
|
1.0
|
C3A
|
A:CLA404
|
4.4
|
43.8
|
1.0
|
C3B
|
A:CLA404
|
4.4
|
41.1
|
1.0
|
C3C
|
A:CLA404
|
4.4
|
39.5
|
1.0
|
C2D
|
A:CLA404
|
4.5
|
43.4
|
1.0
|
CBD
|
A:CLA404
|
5.0
|
46.7
|
1.0
|
|
Magnesium binding site 2 out
of 72 in 8irc
Go back to
Magnesium Binding Sites List in 8irc
Magnesium binding site 2 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg405
b:44.9
occ:1.00
|
MG
|
A:CLA405
|
0.0
|
44.9
|
1.0
|
ND
|
A:CLA405
|
2.0
|
41.3
|
1.0
|
NB
|
A:CLA405
|
2.0
|
43.7
|
1.0
|
NC
|
A:CLA405
|
2.1
|
42.6
|
1.0
|
NA
|
A:CLA405
|
2.1
|
41.8
|
1.0
|
O
|
A:HOH595
|
2.2
|
40.6
|
1.0
|
C4D
|
A:CLA405
|
3.0
|
37.0
|
1.0
|
C4A
|
A:CLA405
|
3.0
|
46.8
|
1.0
|
C1C
|
A:CLA405
|
3.0
|
42.9
|
1.0
|
C1B
|
A:CLA405
|
3.0
|
42.8
|
1.0
|
C4B
|
A:CLA405
|
3.1
|
42.8
|
1.0
|
C1A
|
A:CLA405
|
3.1
|
41.5
|
1.0
|
C4C
|
A:CLA405
|
3.1
|
39.1
|
1.0
|
C1D
|
A:CLA405
|
3.2
|
38.5
|
1.0
|
CHB
|
A:CLA405
|
3.4
|
40.4
|
1.0
|
CHC
|
A:CLA405
|
3.4
|
45.2
|
1.0
|
CHA
|
A:CLA405
|
3.5
|
42.5
|
1.0
|
CHD
|
A:CLA405
|
3.7
|
37.8
|
1.0
|
CBB
|
A:PHO407
|
4.0
|
45.1
|
1.0
|
O
|
A:HOH601
|
4.2
|
40.9
|
1.0
|
C3D
|
A:CLA405
|
4.3
|
38.8
|
1.0
|
C3B
|
A:CLA405
|
4.4
|
44.4
|
1.0
|
C2B
|
A:CLA405
|
4.4
|
39.5
|
1.0
|
C2C
|
A:CLA405
|
4.4
|
46.6
|
1.0
|
C3A
|
A:CLA405
|
4.4
|
46.9
|
1.0
|
C3C
|
A:CLA405
|
4.4
|
41.2
|
1.0
|
C2A
|
A:CLA405
|
4.4
|
42.0
|
1.0
|
C2D
|
A:CLA405
|
4.5
|
44.1
|
1.0
|
CG2
|
A:THR179
|
4.5
|
35.8
|
1.0
|
OG1
|
A:THR179
|
4.7
|
41.6
|
1.0
|
C19
|
A:PHO407
|
4.8
|
42.3
|
1.0
|
CBA
|
A:CLA405
|
4.8
|
44.0
|
1.0
|
CBD
|
A:CLA405
|
4.9
|
41.8
|
1.0
|
|
Magnesium binding site 3 out
of 72 in 8irc
Go back to
Magnesium Binding Sites List in 8irc
Magnesium binding site 3 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg406
b:47.8
occ:1.00
|
MG
|
A:CLA406
|
0.0
|
47.8
|
1.0
|
ND
|
A:CLA406
|
2.0
|
45.9
|
1.0
|
NC
|
A:CLA406
|
2.1
|
44.4
|
1.0
|
NB
|
A:CLA406
|
2.1
|
45.4
|
1.0
|
NA
|
A:CLA406
|
2.1
|
45.3
|
1.0
|
O
|
A:HOH614
|
2.2
|
44.2
|
1.0
|
C4D
|
A:CLA406
|
3.0
|
44.4
|
1.0
|
C1C
|
A:CLA406
|
3.0
|
43.5
|
1.0
|
C4B
|
A:CLA406
|
3.0
|
45.7
|
1.0
|
C4A
|
A:CLA406
|
3.0
|
46.7
|
1.0
|
C1B
|
A:CLA406
|
3.1
|
42.5
|
1.0
|
C1A
|
A:CLA406
|
3.1
|
43.9
|
1.0
|
C4C
|
A:CLA406
|
3.1
|
41.5
|
1.0
|
C1D
|
A:CLA406
|
3.2
|
39.6
|
1.0
|
CHC
|
A:CLA406
|
3.4
|
41.4
|
1.0
|
CHB
|
A:CLA406
|
3.4
|
45.5
|
1.0
|
CHA
|
A:CLA406
|
3.4
|
45.7
|
1.0
|
CHD
|
A:CLA406
|
3.7
|
44.1
|
1.0
|
CBB
|
A:PHO416
|
4.0
|
42.2
|
1.0
|
O
|
A:HOH610
|
4.2
|
44.5
|
1.0
|
C3D
|
A:CLA406
|
4.2
|
41.3
|
1.0
|
C2C
|
A:CLA406
|
4.4
|
44.1
|
1.0
|
C3B
|
A:CLA406
|
4.4
|
45.4
|
1.0
|
C2B
|
A:CLA406
|
4.4
|
46.5
|
1.0
|
C2A
|
A:CLA406
|
4.4
|
47.2
|
1.0
|
C3C
|
A:CLA406
|
4.4
|
43.8
|
1.0
|
C3A
|
A:CLA406
|
4.4
|
46.6
|
1.0
|
C2D
|
A:CLA406
|
4.5
|
46.6
|
1.0
|
C20
|
A:PHO416
|
4.7
|
44.2
|
1.0
|
CG2
|
D:ILE178
|
4.7
|
45.1
|
1.0
|
CBA
|
A:CLA406
|
4.8
|
53.2
|
1.0
|
CBD
|
A:CLA406
|
4.9
|
48.8
|
1.0
|
|
Magnesium binding site 4 out
of 72 in 8irc
Go back to
Magnesium Binding Sites List in 8irc
Magnesium binding site 4 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg408
b:48.9
occ:1.00
|
MG
|
A:CLA408
|
0.0
|
48.9
|
1.0
|
ND
|
A:CLA408
|
2.0
|
46.7
|
1.0
|
NB
|
A:CLA408
|
2.0
|
51.1
|
1.0
|
NA
|
A:CLA408
|
2.1
|
53.1
|
1.0
|
NC
|
A:CLA408
|
2.1
|
50.6
|
1.0
|
NE2
|
A:HIS118
|
2.2
|
48.4
|
1.0
|
C4D
|
A:CLA408
|
3.0
|
48.2
|
1.0
|
C4A
|
A:CLA408
|
3.0
|
50.1
|
1.0
|
C4B
|
A:CLA408
|
3.0
|
48.5
|
1.0
|
C1C
|
A:CLA408
|
3.0
|
47.1
|
1.0
|
CE1
|
A:HIS118
|
3.0
|
48.9
|
1.0
|
C1A
|
A:CLA408
|
3.1
|
50.7
|
1.0
|
C1B
|
A:CLA408
|
3.1
|
51.7
|
1.0
|
C4C
|
A:CLA408
|
3.2
|
42.7
|
1.0
|
C1D
|
A:CLA408
|
3.3
|
47.7
|
1.0
|
CD2
|
A:HIS118
|
3.3
|
50.5
|
1.0
|
CHB
|
A:CLA408
|
3.4
|
50.0
|
1.0
|
CHC
|
A:CLA408
|
3.4
|
56.6
|
1.0
|
CHA
|
A:CLA408
|
3.4
|
47.1
|
1.0
|
CHD
|
A:CLA408
|
3.7
|
48.1
|
1.0
|
ND1
|
A:HIS118
|
4.2
|
45.4
|
1.0
|
C3D
|
A:CLA408
|
4.2
|
43.2
|
1.0
|
C3B
|
A:CLA408
|
4.3
|
48.3
|
1.0
|
C3A
|
A:CLA408
|
4.4
|
53.9
|
1.0
|
C2B
|
A:CLA408
|
4.4
|
47.3
|
1.0
|
C2C
|
A:CLA408
|
4.4
|
47.7
|
1.0
|
CG
|
A:HIS118
|
4.4
|
46.4
|
1.0
|
C2A
|
A:CLA408
|
4.4
|
50.7
|
1.0
|
C3C
|
A:CLA408
|
4.5
|
50.4
|
1.0
|
C2D
|
A:CLA408
|
4.5
|
46.0
|
1.0
|
CG2
|
I:VAL12
|
4.5
|
52.2
|
1.0
|
CG1
|
I:VAL8
|
4.5
|
51.2
|
1.0
|
CBD
|
A:CLA408
|
4.9
|
47.7
|
1.0
|
CMA
|
A:CLA408
|
5.0
|
49.7
|
1.0
|
|
Magnesium binding site 5 out
of 72 in 8irc
Go back to
Magnesium Binding Sites List in 8irc
Magnesium binding site 5 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg601
b:72.1
occ:1.00
|
MG
|
B:CLA601
|
0.0
|
72.1
|
1.0
|
NB
|
B:CLA601
|
2.0
|
68.4
|
1.0
|
ND
|
B:CLA601
|
2.0
|
76.3
|
1.0
|
NC
|
B:CLA601
|
2.1
|
61.4
|
1.0
|
NA
|
B:CLA601
|
2.1
|
74.9
|
1.0
|
O
|
B:HOH757
|
2.2
|
67.2
|
1.0
|
C1C
|
B:CLA601
|
3.0
|
59.9
|
1.0
|
C4D
|
B:CLA601
|
3.0
|
74.5
|
1.0
|
C4B
|
B:CLA601
|
3.0
|
63.2
|
1.0
|
C4A
|
B:CLA601
|
3.0
|
72.9
|
1.0
|
C1B
|
B:CLA601
|
3.1
|
63.1
|
1.0
|
C1A
|
B:CLA601
|
3.1
|
76.4
|
1.0
|
C4C
|
B:CLA601
|
3.1
|
59.8
|
1.0
|
C1D
|
B:CLA601
|
3.3
|
72.6
|
1.0
|
CHC
|
B:CLA601
|
3.4
|
57.2
|
1.0
|
CHB
|
B:CLA601
|
3.4
|
68.1
|
1.0
|
CHA
|
B:CLA601
|
3.5
|
73.8
|
1.0
|
CHD
|
B:CLA601
|
3.7
|
69.0
|
1.0
|
C10
|
B:CLA601
|
3.9
|
79.8
|
1.0
|
C12
|
B:CLA601
|
4.0
|
80.0
|
1.0
|
C3D
|
B:CLA601
|
4.3
|
79.8
|
1.0
|
O
|
B:TRP185
|
4.3
|
66.2
|
1.0
|
C3B
|
B:CLA601
|
4.4
|
62.4
|
1.0
|
C2C
|
B:CLA601
|
4.4
|
62.7
|
1.0
|
C2B
|
B:CLA601
|
4.4
|
62.6
|
1.0
|
C3A
|
B:CLA601
|
4.4
|
73.3
|
1.0
|
C2A
|
B:CLA601
|
4.4
|
80.2
|
1.0
|
C3C
|
B:CLA601
|
4.4
|
62.6
|
1.0
|
CE2
|
B:PHE190
|
4.5
|
63.6
|
1.0
|
C11
|
B:CLA601
|
4.5
|
79.7
|
1.0
|
C2D
|
B:CLA601
|
4.5
|
75.3
|
1.0
|
CBB
|
B:CLA602
|
4.6
|
64.7
|
1.0
|
C8
|
B:CLA601
|
4.7
|
82.6
|
1.0
|
CZ
|
B:PHE190
|
4.8
|
57.6
|
1.0
|
C7
|
B:CLA601
|
4.9
|
89.0
|
1.0
|
CBD
|
B:CLA601
|
4.9
|
78.3
|
1.0
|
|
Magnesium binding site 6 out
of 72 in 8irc
Go back to
Magnesium Binding Sites List in 8irc
Magnesium binding site 6 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg602
b:55.4
occ:1.00
|
MG
|
B:CLA602
|
0.0
|
55.4
|
1.0
|
ND
|
B:CLA602
|
2.0
|
55.4
|
1.0
|
NB
|
B:CLA602
|
2.0
|
59.5
|
1.0
|
NA
|
B:CLA602
|
2.1
|
59.5
|
1.0
|
NC
|
B:CLA602
|
2.1
|
60.1
|
1.0
|
ND1
|
B:HIS201
|
2.2
|
56.6
|
1.0
|
C4D
|
B:CLA602
|
3.0
|
52.1
|
1.0
|
C4B
|
B:CLA602
|
3.0
|
57.2
|
1.0
|
CE1
|
B:HIS201
|
3.0
|
55.9
|
1.0
|
C1B
|
B:CLA602
|
3.0
|
59.7
|
1.0
|
C4A
|
B:CLA602
|
3.0
|
59.7
|
1.0
|
C1C
|
B:CLA602
|
3.0
|
56.9
|
1.0
|
C1A
|
B:CLA602
|
3.1
|
54.0
|
1.0
|
C4C
|
B:CLA602
|
3.2
|
55.0
|
1.0
|
C1D
|
B:CLA602
|
3.3
|
55.8
|
1.0
|
CG
|
B:HIS201
|
3.3
|
52.3
|
1.0
|
CHB
|
B:CLA602
|
3.4
|
56.9
|
1.0
|
CHC
|
B:CLA602
|
3.4
|
53.1
|
1.0
|
CHA
|
B:CLA602
|
3.5
|
51.2
|
1.0
|
CHD
|
B:CLA602
|
3.7
|
51.8
|
1.0
|
CB
|
B:HIS201
|
3.7
|
53.8
|
1.0
|
CZ
|
H:PHE41
|
4.0
|
60.3
|
1.0
|
NE2
|
B:HIS201
|
4.2
|
50.4
|
1.0
|
C3D
|
B:CLA602
|
4.3
|
53.8
|
1.0
|
C3B
|
B:CLA602
|
4.3
|
59.6
|
1.0
|
C2B
|
B:CLA602
|
4.4
|
60.1
|
1.0
|
CD2
|
B:HIS201
|
4.4
|
51.0
|
1.0
|
C3A
|
B:CLA602
|
4.4
|
57.7
|
1.0
|
C2A
|
B:CLA602
|
4.4
|
54.1
|
1.0
|
CA
|
B:HIS201
|
4.4
|
54.1
|
1.0
|
C2C
|
B:CLA602
|
4.4
|
57.1
|
1.0
|
CE2
|
H:PHE41
|
4.4
|
57.1
|
1.0
|
C3C
|
B:CLA602
|
4.5
|
56.5
|
1.0
|
C2D
|
B:CLA602
|
4.5
|
48.7
|
1.0
|
CBD
|
B:CLA602
|
4.9
|
52.0
|
1.0
|
CMA
|
B:CLA602
|
5.0
|
55.6
|
1.0
|
|
Magnesium binding site 7 out
of 72 in 8irc
Go back to
Magnesium Binding Sites List in 8irc
Magnesium binding site 7 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg603
b:50.7
occ:1.00
|
MG
|
B:CLA603
|
0.0
|
50.7
|
1.0
|
NB
|
B:CLA603
|
2.0
|
54.9
|
1.0
|
ND
|
B:CLA603
|
2.0
|
50.2
|
1.0
|
NC
|
B:CLA603
|
2.1
|
49.0
|
1.0
|
NA
|
B:CLA603
|
2.1
|
50.6
|
1.0
|
NE2
|
B:HIS202
|
2.2
|
48.9
|
1.0
|
C4D
|
B:CLA603
|
3.0
|
50.0
|
1.0
|
C1B
|
B:CLA603
|
3.0
|
54.3
|
1.0
|
C4B
|
B:CLA603
|
3.0
|
51.8
|
1.0
|
C1C
|
B:CLA603
|
3.0
|
54.4
|
1.0
|
C4A
|
B:CLA603
|
3.1
|
49.9
|
1.0
|
C1A
|
B:CLA603
|
3.1
|
49.6
|
1.0
|
CD2
|
B:HIS202
|
3.1
|
49.3
|
1.0
|
C4C
|
B:CLA603
|
3.1
|
51.1
|
1.0
|
CE1
|
B:HIS202
|
3.2
|
50.9
|
1.0
|
C1D
|
B:CLA603
|
3.3
|
51.9
|
1.0
|
CHB
|
B:CLA603
|
3.4
|
50.7
|
1.0
|
CHC
|
B:CLA603
|
3.4
|
46.6
|
1.0
|
CHA
|
B:CLA603
|
3.5
|
48.6
|
1.0
|
CHD
|
B:CLA603
|
3.7
|
49.2
|
1.0
|
C3D
|
B:CLA603
|
4.3
|
47.8
|
1.0
|
CG
|
B:HIS202
|
4.3
|
54.6
|
1.0
|
ND1
|
B:HIS202
|
4.3
|
48.8
|
1.0
|
C3B
|
B:CLA603
|
4.3
|
54.1
|
1.0
|
C2B
|
B:CLA603
|
4.3
|
48.5
|
1.0
|
C6
|
B:CLA605
|
4.3
|
59.9
|
1.0
|
C2C
|
B:CLA603
|
4.4
|
50.5
|
1.0
|
C2A
|
B:CLA603
|
4.4
|
52.8
|
1.0
|
C3A
|
B:CLA603
|
4.4
|
52.9
|
1.0
|
C3C
|
B:CLA603
|
4.4
|
52.2
|
1.0
|
C2D
|
B:CLA603
|
4.5
|
52.6
|
1.0
|
C9
|
B:CLA605
|
4.8
|
56.0
|
1.0
|
NE2
|
B:HIS201
|
4.8
|
50.4
|
1.0
|
C7
|
B:CLA605
|
4.9
|
56.9
|
1.0
|
CD2
|
B:HIS201
|
4.9
|
51.0
|
1.0
|
C4
|
B:CLA605
|
4.9
|
54.5
|
1.0
|
CBD
|
B:CLA603
|
5.0
|
52.2
|
1.0
|
CBA
|
B:CLA603
|
5.0
|
45.4
|
1.0
|
|
Magnesium binding site 8 out
of 72 in 8irc
Go back to
Magnesium Binding Sites List in 8irc
Magnesium binding site 8 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg604
b:42.9
occ:1.00
|
MG
|
B:CLA604
|
0.0
|
42.9
|
1.0
|
ND
|
B:CLA604
|
2.0
|
45.6
|
1.0
|
NB
|
B:CLA604
|
2.1
|
44.0
|
1.0
|
NC
|
B:CLA604
|
2.1
|
43.3
|
1.0
|
NA
|
B:CLA604
|
2.1
|
45.4
|
1.0
|
NE2
|
B:HIS455
|
2.2
|
44.0
|
1.0
|
C4D
|
B:CLA604
|
3.0
|
44.5
|
1.0
|
C1B
|
B:CLA604
|
3.1
|
42.6
|
1.0
|
C4B
|
B:CLA604
|
3.1
|
46.3
|
1.0
|
C4A
|
B:CLA604
|
3.1
|
44.8
|
1.0
|
C1C
|
B:CLA604
|
3.1
|
42.8
|
1.0
|
C1A
|
B:CLA604
|
3.1
|
42.7
|
1.0
|
CD2
|
B:HIS455
|
3.1
|
46.0
|
1.0
|
C4C
|
B:CLA604
|
3.2
|
38.4
|
1.0
|
CE1
|
B:HIS455
|
3.2
|
45.9
|
1.0
|
C1D
|
B:CLA604
|
3.2
|
42.8
|
1.0
|
CHB
|
B:CLA604
|
3.4
|
44.5
|
1.0
|
CHC
|
B:CLA604
|
3.5
|
43.6
|
1.0
|
CHA
|
B:CLA604
|
3.5
|
44.1
|
1.0
|
CHD
|
B:CLA604
|
3.7
|
45.8
|
1.0
|
C14
|
B:CLA612
|
4.2
|
52.2
|
1.0
|
C3D
|
B:CLA604
|
4.3
|
42.8
|
1.0
|
ND1
|
B:HIS455
|
4.3
|
46.5
|
1.0
|
CG
|
B:HIS455
|
4.3
|
47.1
|
1.0
|
C3B
|
B:CLA604
|
4.4
|
48.4
|
1.0
|
C2B
|
B:CLA604
|
4.4
|
43.9
|
1.0
|
C2C
|
B:CLA604
|
4.4
|
42.8
|
1.0
|
C3A
|
B:CLA604
|
4.4
|
45.7
|
1.0
|
C2D
|
B:CLA604
|
4.5
|
45.6
|
1.0
|
C2A
|
B:CLA604
|
4.5
|
43.2
|
1.0
|
C3C
|
B:CLA604
|
4.5
|
45.5
|
1.0
|
C15
|
B:CLA612
|
4.6
|
55.9
|
1.0
|
C13
|
B:CLA612
|
4.8
|
56.1
|
1.0
|
CBD
|
B:CLA604
|
5.0
|
46.2
|
1.0
|
CE2
|
B:PHE451
|
5.0
|
43.5
|
1.0
|
|
Magnesium binding site 9 out
of 72 in 8irc
Go back to
Magnesium Binding Sites List in 8irc
Magnesium binding site 9 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg605
b:44.8
occ:1.00
|
MG
|
B:CLA605
|
0.0
|
44.8
|
1.0
|
ND
|
B:CLA605
|
2.0
|
44.6
|
1.0
|
NB
|
B:CLA605
|
2.0
|
45.6
|
1.0
|
NC
|
B:CLA605
|
2.1
|
48.9
|
1.0
|
NA
|
B:CLA605
|
2.1
|
46.8
|
1.0
|
NE2
|
B:HIS100
|
2.2
|
49.0
|
1.0
|
C4D
|
B:CLA605
|
3.0
|
42.5
|
1.0
|
C4B
|
B:CLA605
|
3.0
|
46.6
|
1.0
|
C1C
|
B:CLA605
|
3.0
|
45.2
|
1.0
|
C1B
|
B:CLA605
|
3.0
|
50.5
|
1.0
|
C4A
|
B:CLA605
|
3.1
|
48.3
|
1.0
|
C1A
|
B:CLA605
|
3.1
|
46.0
|
1.0
|
CE1
|
B:HIS100
|
3.1
|
49.4
|
1.0
|
C4C
|
B:CLA605
|
3.2
|
47.1
|
1.0
|
CD2
|
B:HIS100
|
3.2
|
47.0
|
1.0
|
C1D
|
B:CLA605
|
3.3
|
46.4
|
1.0
|
CHB
|
B:CLA605
|
3.4
|
40.5
|
1.0
|
CHC
|
B:CLA605
|
3.4
|
46.0
|
1.0
|
CHA
|
B:CLA605
|
3.5
|
46.1
|
1.0
|
CHD
|
B:CLA605
|
3.7
|
40.7
|
1.0
|
C1
|
B:CLA604
|
4.1
|
53.7
|
1.0
|
C3D
|
B:CLA605
|
4.3
|
47.0
|
1.0
|
ND1
|
B:HIS100
|
4.3
|
45.4
|
1.0
|
C3B
|
B:CLA605
|
4.4
|
49.4
|
1.0
|
CG
|
B:HIS100
|
4.4
|
44.6
|
1.0
|
C2B
|
B:CLA605
|
4.4
|
48.3
|
1.0
|
C2C
|
B:CLA605
|
4.4
|
47.3
|
1.0
|
C2A
|
B:CLA605
|
4.4
|
44.9
|
1.0
|
C3A
|
B:CLA605
|
4.4
|
43.0
|
1.0
|
C3C
|
B:CLA605
|
4.5
|
45.5
|
1.0
|
C2D
|
B:CLA605
|
4.5
|
47.0
|
1.0
|
C2
|
B:CLA604
|
4.8
|
64.2
|
1.0
|
CBD
|
B:CLA605
|
4.9
|
43.4
|
1.0
|
O1A
|
B:CLA604
|
5.0
|
53.3
|
1.0
|
|
Magnesium binding site 10 out
of 72 in 8irc
Go back to
Magnesium Binding Sites List in 8irc
Magnesium binding site 10 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg606
b:54.7
occ:1.00
|
MG
|
B:CLA606
|
0.0
|
54.7
|
1.0
|
NB
|
B:CLA606
|
2.0
|
50.1
|
1.0
|
ND
|
B:CLA606
|
2.0
|
55.6
|
1.0
|
NC
|
B:CLA606
|
2.1
|
58.6
|
1.0
|
NA
|
B:CLA606
|
2.1
|
54.6
|
1.0
|
ND1
|
B:HIS157
|
2.2
|
52.8
|
1.0
|
CE1
|
B:HIS157
|
2.9
|
56.7
|
1.0
|
C4D
|
B:CLA606
|
3.0
|
55.9
|
1.0
|
C1B
|
B:CLA606
|
3.0
|
49.2
|
1.0
|
C1C
|
B:CLA606
|
3.1
|
58.8
|
1.0
|
C4B
|
B:CLA606
|
3.1
|
53.2
|
1.0
|
C4A
|
B:CLA606
|
3.1
|
55.4
|
1.0
|
C1A
|
B:CLA606
|
3.1
|
53.5
|
1.0
|
C4C
|
B:CLA606
|
3.1
|
52.2
|
1.0
|
C1D
|
B:CLA606
|
3.3
|
59.6
|
1.0
|
CHB
|
B:CLA606
|
3.4
|
49.0
|
1.0
|
CHC
|
B:CLA606
|
3.4
|
53.1
|
1.0
|
CG
|
B:HIS157
|
3.4
|
54.1
|
1.0
|
CHA
|
B:CLA606
|
3.5
|
53.8
|
1.0
|
CHD
|
B:CLA606
|
3.7
|
59.3
|
1.0
|
C16
|
B:UNL626
|
4.0
|
64.1
|
1.0
|
CB
|
B:HIS157
|
4.0
|
53.0
|
1.0
|
NE2
|
B:HIS157
|
4.1
|
52.8
|
1.0
|
C15
|
B:UNL626
|
4.2
|
70.3
|
1.0
|
C3D
|
B:CLA606
|
4.3
|
60.0
|
1.0
|
C3B
|
B:CLA606
|
4.4
|
47.6
|
1.0
|
C2B
|
B:CLA606
|
4.4
|
52.2
|
1.0
|
CD2
|
B:HIS157
|
4.4
|
49.9
|
1.0
|
C2C
|
B:CLA606
|
4.4
|
57.9
|
1.0
|
C3C
|
B:CLA606
|
4.4
|
54.7
|
1.0
|
C3A
|
B:CLA606
|
4.4
|
49.0
|
1.0
|
C2A
|
B:CLA606
|
4.5
|
50.3
|
1.0
|
C2D
|
B:CLA606
|
4.5
|
59.3
|
1.0
|
C14
|
B:UNL626
|
4.5
|
78.0
|
1.0
|
CBD
|
B:CLA606
|
5.0
|
58.9
|
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: Fri Oct 4 09:38:23 2024
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