Magnesium in PDB 8ir5: Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions
Enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions
All present enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions:
1.10.3.9;
Protein crystallography data
The structure of Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions, PDB code: 8ir5
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 /
2.15
|
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 (%)
|
14.5 /
17.5
|
Other elements in 8ir5:
The structure of Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions also contains other interesting chemical elements:
Magnesium Binding Sites:
Magnesium binding site 1 out
of 72 in 8ir5
Go back to
Magnesium Binding Sites List in 8ir5
Magnesium binding site 1 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions
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 Under Dark Conditions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg404
b:41.9
occ:1.00
|
MG
|
A:CLA404
|
0.0
|
41.9
|
1.0
|
ND
|
A:CLA404
|
2.0
|
45.5
|
1.0
|
NB
|
A:CLA404
|
2.1
|
40.5
|
1.0
|
NC
|
A:CLA404
|
2.1
|
45.9
|
1.0
|
NA
|
A:CLA404
|
2.1
|
46.1
|
1.0
|
NE2
|
A:HIS198
|
2.2
|
45.9
|
1.0
|
C4D
|
A:CLA404
|
3.0
|
42.4
|
1.0
|
C1C
|
A:CLA404
|
3.0
|
41.9
|
1.0
|
C1B
|
A:CLA404
|
3.0
|
42.1
|
1.0
|
C4A
|
A:CLA404
|
3.0
|
44.5
|
1.0
|
CE1
|
A:HIS198
|
3.1
|
43.8
|
1.0
|
C1A
|
A:CLA404
|
3.1
|
40.6
|
1.0
|
C4B
|
A:CLA404
|
3.1
|
41.6
|
1.0
|
C4C
|
A:CLA404
|
3.1
|
40.7
|
1.0
|
C1D
|
A:CLA404
|
3.2
|
38.6
|
1.0
|
CD2
|
A:HIS198
|
3.3
|
43.3
|
1.0
|
CHB
|
A:CLA404
|
3.4
|
41.8
|
1.0
|
CHC
|
A:CLA404
|
3.4
|
41.3
|
1.0
|
CHA
|
A:CLA404
|
3.5
|
42.5
|
1.0
|
CHD
|
A:CLA404
|
3.6
|
41.0
|
1.0
|
CE
|
A:MET183
|
4.1
|
37.6
|
1.0
|
ND1
|
A:HIS198
|
4.2
|
43.7
|
1.0
|
C3D
|
A:CLA404
|
4.3
|
44.2
|
1.0
|
C2B
|
A:CLA404
|
4.4
|
39.7
|
1.0
|
C2C
|
A:CLA404
|
4.4
|
42.1
|
1.0
|
CG
|
A:HIS198
|
4.4
|
48.7
|
1.0
|
C3A
|
A:CLA404
|
4.4
|
47.3
|
1.0
|
C2A
|
A:CLA404
|
4.4
|
46.8
|
1.0
|
C3C
|
A:CLA404
|
4.4
|
41.4
|
1.0
|
C3B
|
A:CLA404
|
4.4
|
41.6
|
1.0
|
CAB
|
D:CLA402
|
4.4
|
40.5
|
1.0
|
C2D
|
A:CLA404
|
4.5
|
43.4
|
1.0
|
CBD
|
A:CLA404
|
5.0
|
47.9
|
1.0
|
|
Magnesium binding site 2 out
of 72 in 8ir5
Go back to
Magnesium Binding Sites List in 8ir5
Magnesium binding site 2 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions
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 Under Dark Conditions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg405
b:44.4
occ:1.00
|
MG
|
A:CLA405
|
0.0
|
44.4
|
1.0
|
ND
|
A:CLA405
|
2.0
|
43.5
|
1.0
|
NB
|
A:CLA405
|
2.1
|
47.4
|
1.0
|
NC
|
A:CLA405
|
2.1
|
42.9
|
1.0
|
NA
|
A:CLA405
|
2.1
|
42.0
|
1.0
|
O
|
A:HOH583
|
2.2
|
40.9
|
1.0
|
C4D
|
A:CLA405
|
3.0
|
38.7
|
1.0
|
C1C
|
A:CLA405
|
3.0
|
46.0
|
1.0
|
C4A
|
A:CLA405
|
3.0
|
44.5
|
1.0
|
C1B
|
A:CLA405
|
3.0
|
44.8
|
1.0
|
C4B
|
A:CLA405
|
3.1
|
44.3
|
1.0
|
C1A
|
A:CLA405
|
3.1
|
43.5
|
1.0
|
C4C
|
A:CLA405
|
3.1
|
41.3
|
1.0
|
C1D
|
A:CLA405
|
3.2
|
39.6
|
1.0
|
CHB
|
A:CLA405
|
3.4
|
41.5
|
1.0
|
CHC
|
A:CLA405
|
3.4
|
46.5
|
1.0
|
CHA
|
A:CLA405
|
3.5
|
39.8
|
1.0
|
CHD
|
A:CLA405
|
3.6
|
40.8
|
1.0
|
CBB
|
A:PHO407
|
4.0
|
46.1
|
1.0
|
O
|
A:HOH586
|
4.2
|
41.6
|
1.0
|
C3D
|
A:CLA405
|
4.2
|
37.2
|
1.0
|
C2B
|
A:CLA405
|
4.4
|
42.7
|
1.0
|
C2C
|
A:CLA405
|
4.4
|
45.8
|
1.0
|
C3B
|
A:CLA405
|
4.4
|
45.1
|
1.0
|
C3C
|
A:CLA405
|
4.4
|
42.9
|
1.0
|
C3A
|
A:CLA405
|
4.4
|
47.2
|
1.0
|
C2A
|
A:CLA405
|
4.4
|
40.5
|
1.0
|
C2D
|
A:CLA405
|
4.5
|
44.8
|
1.0
|
CG2
|
A:THR179
|
4.6
|
38.7
|
1.0
|
OG1
|
A:THR179
|
4.7
|
45.2
|
1.0
|
CBA
|
A:CLA405
|
4.8
|
43.2
|
1.0
|
C19
|
A:PHO407
|
4.8
|
45.3
|
1.0
|
CBD
|
A:CLA405
|
4.9
|
43.3
|
1.0
|
|
Magnesium binding site 3 out
of 72 in 8ir5
Go back to
Magnesium Binding Sites List in 8ir5
Magnesium binding site 3 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions
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 Under Dark Conditions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg406
b:48.1
occ:1.00
|
MG
|
A:CLA406
|
0.0
|
48.1
|
1.0
|
ND
|
A:CLA406
|
2.0
|
47.2
|
1.0
|
NB
|
A:CLA406
|
2.0
|
46.6
|
1.0
|
NC
|
A:CLA406
|
2.1
|
44.2
|
1.0
|
NA
|
A:CLA406
|
2.1
|
46.4
|
1.0
|
O
|
A:HOH627
|
2.2
|
45.8
|
1.0
|
C4D
|
A:CLA406
|
3.0
|
47.8
|
1.0
|
C1C
|
A:CLA406
|
3.0
|
45.8
|
1.0
|
C4B
|
A:CLA406
|
3.0
|
46.8
|
1.0
|
C1B
|
A:CLA406
|
3.0
|
44.1
|
1.0
|
C4A
|
A:CLA406
|
3.0
|
46.6
|
1.0
|
C1A
|
A:CLA406
|
3.1
|
45.5
|
1.0
|
C4C
|
A:CLA406
|
3.1
|
43.0
|
1.0
|
C1D
|
A:CLA406
|
3.2
|
43.1
|
1.0
|
CHC
|
A:CLA406
|
3.4
|
47.9
|
1.0
|
CHB
|
A:CLA406
|
3.4
|
47.7
|
1.0
|
CHA
|
A:CLA406
|
3.4
|
50.1
|
1.0
|
CHD
|
A:CLA406
|
3.7
|
42.4
|
1.0
|
CBB
|
A:PHO416
|
4.0
|
45.3
|
1.0
|
O
|
A:HOH623
|
4.1
|
45.8
|
1.0
|
C3D
|
A:CLA406
|
4.2
|
43.2
|
1.0
|
C3B
|
A:CLA406
|
4.4
|
45.2
|
1.0
|
C2B
|
A:CLA406
|
4.4
|
48.1
|
1.0
|
C2C
|
A:CLA406
|
4.4
|
44.0
|
1.0
|
C3A
|
A:CLA406
|
4.4
|
51.1
|
1.0
|
C2A
|
A:CLA406
|
4.4
|
49.0
|
1.0
|
C3C
|
A:CLA406
|
4.4
|
45.9
|
1.0
|
C2D
|
A:CLA406
|
4.5
|
48.4
|
1.0
|
CG2
|
D:ILE178
|
4.7
|
42.5
|
1.0
|
C20
|
A:PHO416
|
4.8
|
44.9
|
1.0
|
CBA
|
A:CLA406
|
4.8
|
51.2
|
1.0
|
CBD
|
A:CLA406
|
4.9
|
49.7
|
1.0
|
CE2
|
A:PHE206
|
5.0
|
45.9
|
1.0
|
|
Magnesium binding site 4 out
of 72 in 8ir5
Go back to
Magnesium Binding Sites List in 8ir5
Magnesium binding site 4 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions
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 Under Dark Conditions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg408
b:51.1
occ:1.00
|
MG
|
A:CLA408
|
0.0
|
51.1
|
1.0
|
ND
|
A:CLA408
|
2.0
|
50.2
|
1.0
|
NB
|
A:CLA408
|
2.0
|
50.6
|
1.0
|
NA
|
A:CLA408
|
2.1
|
53.3
|
1.0
|
NC
|
A:CLA408
|
2.1
|
50.9
|
1.0
|
NE2
|
A:HIS118
|
2.2
|
51.3
|
1.0
|
C4D
|
A:CLA408
|
3.0
|
50.1
|
1.0
|
C4A
|
A:CLA408
|
3.0
|
51.5
|
1.0
|
CE1
|
A:HIS118
|
3.0
|
48.7
|
1.0
|
C4B
|
A:CLA408
|
3.0
|
52.4
|
1.0
|
C1C
|
A:CLA408
|
3.0
|
51.1
|
1.0
|
C1B
|
A:CLA408
|
3.1
|
53.6
|
1.0
|
C1A
|
A:CLA408
|
3.1
|
53.5
|
1.0
|
C4C
|
A:CLA408
|
3.1
|
46.0
|
1.0
|
C1D
|
A:CLA408
|
3.2
|
49.5
|
1.0
|
CD2
|
A:HIS118
|
3.3
|
50.0
|
1.0
|
CHB
|
A:CLA408
|
3.4
|
50.0
|
1.0
|
CHC
|
A:CLA408
|
3.4
|
53.3
|
1.0
|
CHA
|
A:CLA408
|
3.5
|
48.4
|
1.0
|
CHD
|
A:CLA408
|
3.7
|
49.0
|
1.0
|
ND1
|
A:HIS118
|
4.2
|
46.7
|
1.0
|
C3D
|
A:CLA408
|
4.2
|
49.0
|
1.0
|
C3B
|
A:CLA408
|
4.3
|
49.0
|
1.0
|
C3A
|
A:CLA408
|
4.4
|
55.7
|
1.0
|
C2B
|
A:CLA408
|
4.4
|
50.8
|
1.0
|
CG
|
A:HIS118
|
4.4
|
47.0
|
1.0
|
C2C
|
A:CLA408
|
4.4
|
51.8
|
1.0
|
C2A
|
A:CLA408
|
4.4
|
51.6
|
1.0
|
C3C
|
A:CLA408
|
4.4
|
54.4
|
1.0
|
C2D
|
A:CLA408
|
4.5
|
48.8
|
1.0
|
CG2
|
I:VAL12
|
4.5
|
53.4
|
1.0
|
CG1
|
I:VAL8
|
4.5
|
51.5
|
1.0
|
CBD
|
A:CLA408
|
4.9
|
49.1
|
1.0
|
CMA
|
A:CLA408
|
5.0
|
52.7
|
1.0
|
|
Magnesium binding site 5 out
of 72 in 8ir5
Go back to
Magnesium Binding Sites List in 8ir5
Magnesium binding site 5 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions
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 Under Dark Conditions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg601
b:70.2
occ:1.00
|
MG
|
B:CLA601
|
0.0
|
70.2
|
1.0
|
ND
|
B:CLA601
|
2.0
|
73.9
|
1.0
|
NB
|
B:CLA601
|
2.0
|
67.1
|
1.0
|
NC
|
B:CLA601
|
2.1
|
64.9
|
1.0
|
NA
|
B:CLA601
|
2.1
|
75.2
|
1.0
|
O
|
B:HOH745
|
2.2
|
70.2
|
1.0
|
C4D
|
B:CLA601
|
3.0
|
73.0
|
1.0
|
C1C
|
B:CLA601
|
3.0
|
62.5
|
1.0
|
C4B
|
B:CLA601
|
3.0
|
64.9
|
1.0
|
C4A
|
B:CLA601
|
3.0
|
73.1
|
1.0
|
C1B
|
B:CLA601
|
3.1
|
64.7
|
1.0
|
C1A
|
B:CLA601
|
3.1
|
77.9
|
1.0
|
C4C
|
B:CLA601
|
3.1
|
62.5
|
1.0
|
C1D
|
B:CLA601
|
3.3
|
72.4
|
1.0
|
CHC
|
B:CLA601
|
3.4
|
58.1
|
1.0
|
CHB
|
B:CLA601
|
3.4
|
68.0
|
1.0
|
CHA
|
B:CLA601
|
3.5
|
74.1
|
1.0
|
CHD
|
B:CLA601
|
3.7
|
67.7
|
1.0
|
C10
|
B:CLA601
|
3.9
|
81.6
|
1.0
|
C12
|
B:CLA601
|
4.0
|
76.7
|
1.0
|
C3D
|
B:CLA601
|
4.3
|
78.9
|
1.0
|
O
|
B:TRP185
|
4.3
|
67.8
|
1.0
|
C3B
|
B:CLA601
|
4.3
|
63.0
|
1.0
|
C2C
|
B:CLA601
|
4.4
|
63.0
|
1.0
|
C2B
|
B:CLA601
|
4.4
|
64.4
|
1.0
|
C3A
|
B:CLA601
|
4.4
|
78.0
|
1.0
|
C2A
|
B:CLA601
|
4.4
|
82.8
|
1.0
|
C3C
|
B:CLA601
|
4.4
|
61.6
|
1.0
|
CE2
|
B:PHE190
|
4.5
|
62.2
|
1.0
|
C2D
|
B:CLA601
|
4.5
|
76.5
|
1.0
|
C11
|
B:CLA601
|
4.5
|
83.9
|
1.0
|
CBB
|
B:CLA602
|
4.6
|
64.7
|
1.0
|
C8
|
B:CLA601
|
4.8
|
83.0
|
1.0
|
CZ
|
B:PHE190
|
4.8
|
58.7
|
1.0
|
CBD
|
B:CLA601
|
4.9
|
79.6
|
1.0
|
C7
|
B:CLA601
|
5.0
|
90.3
|
1.0
|
|
Magnesium binding site 6 out
of 72 in 8ir5
Go back to
Magnesium Binding Sites List in 8ir5
Magnesium binding site 6 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions
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 Under Dark Conditions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg602
b:54.6
occ:1.00
|
MG
|
B:CLA602
|
0.0
|
54.6
|
1.0
|
ND
|
B:CLA602
|
2.0
|
55.6
|
1.0
|
NB
|
B:CLA602
|
2.0
|
58.6
|
1.0
|
NA
|
B:CLA602
|
2.1
|
61.5
|
1.0
|
NC
|
B:CLA602
|
2.1
|
60.2
|
1.0
|
ND1
|
B:HIS201
|
2.2
|
58.6
|
1.0
|
C4D
|
B:CLA602
|
3.0
|
54.8
|
1.0
|
C4B
|
B:CLA602
|
3.0
|
59.9
|
1.0
|
C4A
|
B:CLA602
|
3.0
|
58.7
|
1.0
|
C1B
|
B:CLA602
|
3.0
|
61.3
|
1.0
|
CE1
|
B:HIS201
|
3.0
|
52.0
|
1.0
|
C1C
|
B:CLA602
|
3.1
|
58.3
|
1.0
|
C1A
|
B:CLA602
|
3.1
|
52.1
|
1.0
|
C4C
|
B:CLA602
|
3.2
|
56.7
|
1.0
|
C1D
|
B:CLA602
|
3.3
|
55.4
|
1.0
|
CG
|
B:HIS201
|
3.3
|
52.6
|
1.0
|
CHB
|
B:CLA602
|
3.4
|
55.3
|
1.0
|
CHC
|
B:CLA602
|
3.4
|
57.0
|
1.0
|
CHA
|
B:CLA602
|
3.5
|
53.3
|
1.0
|
CHD
|
B:CLA602
|
3.7
|
52.1
|
1.0
|
CB
|
B:HIS201
|
3.7
|
52.5
|
1.0
|
CZ
|
H:PHE41
|
4.0
|
62.4
|
1.0
|
NE2
|
B:HIS201
|
4.2
|
51.3
|
1.0
|
C3D
|
B:CLA602
|
4.3
|
55.4
|
1.0
|
C3B
|
B:CLA602
|
4.4
|
64.2
|
1.0
|
CD2
|
B:HIS201
|
4.4
|
49.4
|
1.0
|
C2B
|
B:CLA602
|
4.4
|
60.5
|
1.0
|
CA
|
B:HIS201
|
4.4
|
55.7
|
1.0
|
C3A
|
B:CLA602
|
4.4
|
61.7
|
1.0
|
C2A
|
B:CLA602
|
4.4
|
54.2
|
1.0
|
C2C
|
B:CLA602
|
4.4
|
58.8
|
1.0
|
CE2
|
H:PHE41
|
4.4
|
61.2
|
1.0
|
C3C
|
B:CLA602
|
4.5
|
56.8
|
1.0
|
C2D
|
B:CLA602
|
4.5
|
49.6
|
1.0
|
CBD
|
B:CLA602
|
4.9
|
54.6
|
1.0
|
CMA
|
B:CLA602
|
4.9
|
53.7
|
1.0
|
CE1
|
B:PHE190
|
5.0
|
59.0
|
1.0
|
|
Magnesium binding site 7 out
of 72 in 8ir5
Go back to
Magnesium Binding Sites List in 8ir5
Magnesium binding site 7 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions
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 Under Dark Conditions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg603
b:51.0
occ:1.00
|
MG
|
B:CLA603
|
0.0
|
51.0
|
1.0
|
NB
|
B:CLA603
|
2.0
|
55.8
|
1.0
|
ND
|
B:CLA603
|
2.0
|
52.7
|
1.0
|
NC
|
B:CLA603
|
2.1
|
50.8
|
1.0
|
NA
|
B:CLA603
|
2.1
|
51.7
|
1.0
|
NE2
|
B:HIS202
|
2.2
|
50.4
|
1.0
|
C4D
|
B:CLA603
|
3.0
|
50.2
|
1.0
|
C1B
|
B:CLA603
|
3.0
|
50.9
|
1.0
|
C4B
|
B:CLA603
|
3.0
|
52.1
|
1.0
|
C1C
|
B:CLA603
|
3.0
|
57.1
|
1.0
|
C4A
|
B:CLA603
|
3.0
|
50.2
|
1.0
|
C1A
|
B:CLA603
|
3.1
|
49.0
|
1.0
|
CD2
|
B:HIS202
|
3.1
|
46.6
|
1.0
|
C4C
|
B:CLA603
|
3.1
|
52.2
|
1.0
|
CE1
|
B:HIS202
|
3.2
|
54.4
|
1.0
|
C1D
|
B:CLA603
|
3.3
|
52.7
|
1.0
|
CHB
|
B:CLA603
|
3.4
|
52.1
|
1.0
|
CHC
|
B:CLA603
|
3.4
|
47.9
|
1.0
|
CHA
|
B:CLA603
|
3.5
|
49.5
|
1.0
|
CHD
|
B:CLA603
|
3.7
|
50.7
|
1.0
|
CG
|
B:HIS202
|
4.3
|
56.7
|
1.0
|
C3D
|
B:CLA603
|
4.3
|
50.0
|
1.0
|
ND1
|
B:HIS202
|
4.3
|
47.9
|
1.0
|
C3B
|
B:CLA603
|
4.3
|
55.6
|
1.0
|
C2B
|
B:CLA603
|
4.3
|
51.9
|
1.0
|
C2C
|
B:CLA603
|
4.4
|
48.0
|
1.0
|
C2A
|
B:CLA603
|
4.4
|
50.6
|
1.0
|
C3A
|
B:CLA603
|
4.4
|
53.9
|
1.0
|
C3C
|
B:CLA603
|
4.4
|
51.0
|
1.0
|
C2D
|
B:CLA603
|
4.5
|
54.4
|
1.0
|
C6
|
B:CLA605
|
4.6
|
61.8
|
1.0
|
C7
|
B:CLA605
|
4.8
|
63.7
|
1.0
|
NE2
|
B:HIS201
|
4.8
|
51.3
|
1.0
|
C4
|
B:CLA605
|
4.9
|
55.6
|
1.0
|
CD2
|
B:HIS201
|
4.9
|
49.4
|
1.0
|
CBD
|
B:CLA603
|
4.9
|
53.5
|
1.0
|
CBA
|
B:CLA603
|
5.0
|
44.4
|
1.0
|
|
Magnesium binding site 8 out
of 72 in 8ir5
Go back to
Magnesium Binding Sites List in 8ir5
Magnesium binding site 8 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions
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 Under Dark Conditions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg604
b:42.5
occ:1.00
|
MG
|
B:CLA604
|
0.0
|
42.5
|
1.0
|
ND
|
B:CLA604
|
2.0
|
48.2
|
1.0
|
NB
|
B:CLA604
|
2.0
|
43.8
|
1.0
|
NC
|
B:CLA604
|
2.1
|
45.1
|
1.0
|
NA
|
B:CLA604
|
2.1
|
43.8
|
1.0
|
NE2
|
B:HIS455
|
2.2
|
44.6
|
1.0
|
C4D
|
B:CLA604
|
3.0
|
44.3
|
1.0
|
C4B
|
B:CLA604
|
3.0
|
46.2
|
1.0
|
C1B
|
B:CLA604
|
3.1
|
44.1
|
1.0
|
C1C
|
B:CLA604
|
3.1
|
43.2
|
1.0
|
C4A
|
B:CLA604
|
3.1
|
47.1
|
1.0
|
C1A
|
B:CLA604
|
3.1
|
45.7
|
1.0
|
CD2
|
B:HIS455
|
3.1
|
46.5
|
1.0
|
C4C
|
B:CLA604
|
3.2
|
42.1
|
1.0
|
CE1
|
B:HIS455
|
3.2
|
45.3
|
1.0
|
C1D
|
B:CLA604
|
3.2
|
41.6
|
1.0
|
CHB
|
B:CLA604
|
3.4
|
45.2
|
1.0
|
CHC
|
B:CLA604
|
3.4
|
41.6
|
1.0
|
CHA
|
B:CLA604
|
3.5
|
46.9
|
1.0
|
CHD
|
B:CLA604
|
3.7
|
47.0
|
1.0
|
C14
|
B:CLA612
|
4.2
|
55.7
|
1.0
|
C3D
|
B:CLA604
|
4.3
|
45.5
|
1.0
|
CG
|
B:HIS455
|
4.3
|
46.5
|
1.0
|
ND1
|
B:HIS455
|
4.3
|
45.9
|
1.0
|
C3B
|
B:CLA604
|
4.3
|
46.1
|
1.0
|
C2B
|
B:CLA604
|
4.4
|
46.2
|
1.0
|
C2C
|
B:CLA604
|
4.4
|
46.3
|
1.0
|
C3A
|
B:CLA604
|
4.5
|
47.6
|
1.0
|
C2D
|
B:CLA604
|
4.5
|
46.2
|
1.0
|
C2A
|
B:CLA604
|
4.5
|
46.4
|
1.0
|
C3C
|
B:CLA604
|
4.5
|
47.0
|
1.0
|
C15
|
B:CLA612
|
4.6
|
55.7
|
1.0
|
C13
|
B:CLA612
|
4.9
|
58.5
|
1.0
|
CBD
|
B:CLA604
|
5.0
|
48.1
|
1.0
|
CE2
|
B:PHE451
|
5.0
|
46.1
|
1.0
|
|
Magnesium binding site 9 out
of 72 in 8ir5
Go back to
Magnesium Binding Sites List in 8ir5
Magnesium binding site 9 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions
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 Under Dark Conditions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg605
b:47.3
occ:1.00
|
MG
|
B:CLA605
|
0.0
|
47.3
|
1.0
|
ND
|
B:CLA605
|
2.0
|
45.0
|
1.0
|
NB
|
B:CLA605
|
2.1
|
45.9
|
1.0
|
NC
|
B:CLA605
|
2.1
|
50.8
|
1.0
|
NA
|
B:CLA605
|
2.1
|
47.9
|
1.0
|
NE2
|
B:HIS100
|
2.2
|
49.0
|
1.0
|
C4D
|
B:CLA605
|
3.0
|
44.4
|
1.0
|
C4B
|
B:CLA605
|
3.0
|
47.2
|
1.0
|
C1C
|
B:CLA605
|
3.0
|
46.0
|
1.0
|
C1B
|
B:CLA605
|
3.1
|
50.0
|
1.0
|
C4A
|
B:CLA605
|
3.1
|
50.2
|
1.0
|
C1A
|
B:CLA605
|
3.1
|
46.5
|
1.0
|
CE1
|
B:HIS100
|
3.1
|
47.0
|
1.0
|
C4C
|
B:CLA605
|
3.2
|
46.8
|
1.0
|
CD2
|
B:HIS100
|
3.2
|
46.0
|
1.0
|
C1D
|
B:CLA605
|
3.3
|
45.6
|
1.0
|
CHB
|
B:CLA605
|
3.4
|
43.7
|
1.0
|
CHC
|
B:CLA605
|
3.4
|
45.8
|
1.0
|
CHA
|
B:CLA605
|
3.5
|
45.6
|
1.0
|
CHD
|
B:CLA605
|
3.7
|
43.4
|
1.0
|
C1
|
B:CLA604
|
4.0
|
56.3
|
1.0
|
C3D
|
B:CLA605
|
4.3
|
45.8
|
1.0
|
ND1
|
B:HIS100
|
4.3
|
47.3
|
1.0
|
C3B
|
B:CLA605
|
4.4
|
49.0
|
1.0
|
CG
|
B:HIS100
|
4.4
|
45.2
|
1.0
|
C2B
|
B:CLA605
|
4.4
|
50.1
|
1.0
|
C2C
|
B:CLA605
|
4.4
|
50.1
|
1.0
|
C3A
|
B:CLA605
|
4.4
|
44.0
|
1.0
|
C2A
|
B:CLA605
|
4.4
|
45.5
|
1.0
|
C3C
|
B:CLA605
|
4.5
|
47.0
|
1.0
|
C2D
|
B:CLA605
|
4.5
|
46.4
|
1.0
|
C2
|
B:CLA604
|
4.6
|
58.2
|
1.0
|
CBD
|
B:CLA605
|
4.9
|
47.0
|
1.0
|
C4
|
B:CLA606
|
5.0
|
49.4
|
1.0
|
|
Magnesium binding site 10 out
of 72 in 8ir5
Go back to
Magnesium Binding Sites List in 8ir5
Magnesium binding site 10 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions
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 Under Dark Conditions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg606
b:57.1
occ:1.00
|
MG
|
B:CLA606
|
0.0
|
57.1
|
1.0
|
ND
|
B:CLA606
|
2.0
|
59.3
|
1.0
|
NB
|
B:CLA606
|
2.0
|
51.3
|
1.0
|
NC
|
B:CLA606
|
2.1
|
61.9
|
1.0
|
NA
|
B:CLA606
|
2.1
|
55.5
|
1.0
|
ND1
|
B:HIS157
|
2.2
|
49.7
|
1.0
|
CE1
|
B:HIS157
|
2.9
|
55.9
|
1.0
|
C4D
|
B:CLA606
|
3.0
|
58.0
|
1.0
|
C1B
|
B:CLA606
|
3.0
|
55.0
|
1.0
|
C1C
|
B:CLA606
|
3.0
|
58.5
|
1.0
|
C4B
|
B:CLA606
|
3.1
|
52.2
|
1.0
|
C4A
|
B:CLA606
|
3.1
|
52.8
|
1.0
|
C1A
|
B:CLA606
|
3.1
|
54.0
|
1.0
|
C4C
|
B:CLA606
|
3.1
|
52.9
|
1.0
|
C1D
|
B:CLA606
|
3.3
|
62.9
|
1.0
|
CHB
|
B:CLA606
|
3.4
|
49.3
|
1.0
|
CHC
|
B:CLA606
|
3.4
|
54.2
|
1.0
|
CG
|
B:HIS157
|
3.4
|
53.5
|
1.0
|
CHA
|
B:CLA606
|
3.5
|
54.9
|
1.0
|
CHD
|
B:CLA606
|
3.7
|
59.7
|
1.0
|
CB
|
B:HIS157
|
4.0
|
56.1
|
1.0
|
C16
|
B:UNL626
|
4.0
|
67.2
|
1.0
|
NE2
|
B:HIS157
|
4.1
|
49.9
|
1.0
|
C3D
|
B:CLA606
|
4.3
|
62.2
|
1.0
|
C15
|
B:UNL626
|
4.4
|
73.9
|
1.0
|
C2B
|
B:CLA606
|
4.4
|
54.6
|
1.0
|
C3B
|
B:CLA606
|
4.4
|
51.3
|
1.0
|
C2C
|
B:CLA606
|
4.4
|
60.0
|
1.0
|
CD2
|
B:HIS157
|
4.4
|
49.6
|
1.0
|
C3C
|
B:CLA606
|
4.4
|
55.8
|
1.0
|
C3A
|
B:CLA606
|
4.4
|
49.7
|
1.0
|
C2A
|
B:CLA606
|
4.4
|
52.4
|
1.0
|
C2D
|
B:CLA606
|
4.5
|
65.2
|
1.0
|
C14
|
B:UNL626
|
4.7
|
81.4
|
1.0
|
CBD
|
B:CLA606
|
4.9
|
61.6
|
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,
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ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-023-06987-5
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