Magnesium in PDB 5ws5: Native Xfel Structure of Photosystem II (Preflash Dark Dataset)
Enzymatic activity of Native Xfel Structure of Photosystem II (Preflash Dark Dataset)
All present enzymatic activity of Native Xfel Structure of Photosystem II (Preflash Dark Dataset):
1.10.3.9;
Protein crystallography data
The structure of Native Xfel Structure of Photosystem II (Preflash Dark Dataset), PDB code: 5ws5
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 (°)
|
124.700,
229.890,
285.500,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
13.3 /
17.1
|
Other elements in 5ws5:
The structure of Native Xfel Structure of Photosystem II (Preflash Dark Dataset) also contains other interesting chemical elements:
Magnesium Binding Sites:
Magnesium binding site 1 out
of 72 in 5ws5
Go back to
Magnesium Binding Sites List in 5ws5
Magnesium binding site 1 out
of 72 in the Native Xfel Structure of Photosystem II (Preflash Dark Dataset)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Native Xfel Structure of Photosystem II (Preflash Dark Dataset) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg404
b:50.8
occ:1.00
|
MG
|
A:CLA404
|
0.0
|
50.8
|
1.0
|
ND
|
A:CLA404
|
2.0
|
50.9
|
1.0
|
NB
|
A:CLA404
|
2.0
|
46.3
|
1.0
|
NA
|
A:CLA404
|
2.1
|
53.6
|
1.0
|
NC
|
A:CLA404
|
2.1
|
49.6
|
1.0
|
NE2
|
A:HIS198
|
2.2
|
46.7
|
1.0
|
C4D
|
A:CLA404
|
3.0
|
51.6
|
1.0
|
C4B
|
A:CLA404
|
3.0
|
48.6
|
1.0
|
C4A
|
A:CLA404
|
3.0
|
48.7
|
1.0
|
C1B
|
A:CLA404
|
3.0
|
46.2
|
1.0
|
C1C
|
A:CLA404
|
3.0
|
45.3
|
1.0
|
C1A
|
A:CLA404
|
3.1
|
48.7
|
1.0
|
CE1
|
A:HIS198
|
3.1
|
45.9
|
1.0
|
C4C
|
A:CLA404
|
3.1
|
44.3
|
1.0
|
C1D
|
A:CLA404
|
3.3
|
48.9
|
1.0
|
CD2
|
A:HIS198
|
3.3
|
45.6
|
1.0
|
CHB
|
A:CLA404
|
3.4
|
48.3
|
1.0
|
CHC
|
A:CLA404
|
3.4
|
49.5
|
1.0
|
CHA
|
A:CLA404
|
3.5
|
48.4
|
1.0
|
CHD
|
A:CLA404
|
3.7
|
48.9
|
1.0
|
CE
|
A:MET183
|
4.0
|
46.7
|
1.0
|
ND1
|
A:HIS198
|
4.3
|
46.2
|
1.0
|
C3D
|
A:CLA404
|
4.3
|
45.9
|
1.0
|
C3B
|
A:CLA404
|
4.3
|
44.9
|
1.0
|
C2B
|
A:CLA404
|
4.4
|
47.0
|
1.0
|
CAB
|
D:CLA405
|
4.4
|
50.9
|
1.0
|
CG
|
A:HIS198
|
4.4
|
47.4
|
1.0
|
C2A
|
A:CLA404
|
4.4
|
50.5
|
1.0
|
C3A
|
A:CLA404
|
4.4
|
53.6
|
1.0
|
C2C
|
A:CLA404
|
4.4
|
50.7
|
1.0
|
C3C
|
A:CLA404
|
4.4
|
48.8
|
1.0
|
C2D
|
A:CLA404
|
4.5
|
49.8
|
1.0
|
CBD
|
A:CLA404
|
4.9
|
51.6
|
1.0
|
|
Magnesium binding site 2 out
of 72 in 5ws5
Go back to
Magnesium Binding Sites List in 5ws5
Magnesium binding site 2 out
of 72 in the Native Xfel Structure of Photosystem II (Preflash Dark Dataset)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Native Xfel Structure of Photosystem II (Preflash Dark Dataset) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg405
b:53.7
occ:1.00
|
MG
|
A:CLA405
|
0.0
|
53.7
|
1.0
|
ND
|
A:CLA405
|
2.0
|
51.7
|
1.0
|
NB
|
A:CLA405
|
2.0
|
48.6
|
1.0
|
NC
|
A:CLA405
|
2.1
|
53.2
|
1.0
|
NA
|
A:CLA405
|
2.1
|
54.2
|
1.0
|
O
|
A:HOH586
|
2.2
|
46.4
|
1.0
|
C4D
|
A:CLA405
|
3.0
|
49.4
|
1.0
|
C1C
|
A:CLA405
|
3.0
|
49.2
|
1.0
|
C1B
|
A:CLA405
|
3.0
|
54.0
|
1.0
|
C4A
|
A:CLA405
|
3.0
|
51.6
|
1.0
|
C4B
|
A:CLA405
|
3.0
|
51.4
|
1.0
|
C1A
|
A:CLA405
|
3.1
|
47.0
|
1.0
|
C4C
|
A:CLA405
|
3.1
|
44.7
|
1.0
|
C1D
|
A:CLA405
|
3.3
|
49.9
|
1.0
|
CHB
|
A:CLA405
|
3.4
|
48.8
|
1.0
|
CHC
|
A:CLA405
|
3.4
|
51.4
|
1.0
|
CHA
|
A:CLA405
|
3.5
|
47.4
|
1.0
|
CHD
|
A:CLA405
|
3.7
|
47.2
|
1.0
|
CBB
|
A:PHO407
|
4.0
|
50.3
|
1.0
|
O
|
A:HOH604
|
4.1
|
47.2
|
1.0
|
C3D
|
A:CLA405
|
4.3
|
45.2
|
1.0
|
C3B
|
A:CLA405
|
4.4
|
49.8
|
1.0
|
C2B
|
A:CLA405
|
4.4
|
49.3
|
1.0
|
C2C
|
A:CLA405
|
4.4
|
52.1
|
1.0
|
C3A
|
A:CLA405
|
4.4
|
51.7
|
1.0
|
C2A
|
A:CLA405
|
4.4
|
53.9
|
1.0
|
C3C
|
A:CLA405
|
4.4
|
52.7
|
1.0
|
C2D
|
A:CLA405
|
4.5
|
48.0
|
1.0
|
CG2
|
A:THR179
|
4.5
|
46.1
|
1.0
|
OG1
|
A:THR179
|
4.7
|
49.6
|
1.0
|
CBA
|
A:CLA405
|
4.7
|
50.6
|
1.0
|
C19
|
A:PHO407
|
4.8
|
50.1
|
1.0
|
CBD
|
A:CLA405
|
4.9
|
52.6
|
1.0
|
|
Magnesium binding site 3 out
of 72 in 5ws5
Go back to
Magnesium Binding Sites List in 5ws5
Magnesium binding site 3 out
of 72 in the Native Xfel Structure of Photosystem II (Preflash Dark Dataset)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Native Xfel Structure of Photosystem II (Preflash Dark Dataset) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg406
b:53.5
occ:1.00
|
MG
|
A:CLA406
|
0.0
|
53.5
|
1.0
|
ND
|
A:CLA406
|
2.0
|
53.8
|
1.0
|
NB
|
A:CLA406
|
2.0
|
48.9
|
1.0
|
NC
|
A:CLA406
|
2.1
|
54.9
|
1.0
|
NA
|
A:CLA406
|
2.1
|
52.2
|
1.0
|
O
|
A:HOH619
|
2.2
|
50.9
|
1.0
|
C4D
|
A:CLA406
|
3.0
|
49.0
|
1.0
|
C1C
|
A:CLA406
|
3.0
|
48.4
|
1.0
|
C4B
|
A:CLA406
|
3.0
|
49.7
|
1.0
|
C4A
|
A:CLA406
|
3.0
|
52.6
|
1.0
|
C1B
|
A:CLA406
|
3.0
|
52.8
|
1.0
|
C1A
|
A:CLA406
|
3.0
|
52.4
|
1.0
|
C4C
|
A:CLA406
|
3.1
|
50.0
|
1.0
|
C1D
|
A:CLA406
|
3.2
|
49.0
|
1.0
|
CHC
|
A:CLA406
|
3.4
|
49.7
|
1.0
|
CHB
|
A:CLA406
|
3.4
|
54.3
|
1.0
|
CHA
|
A:CLA406
|
3.4
|
51.6
|
1.0
|
CHD
|
A:CLA406
|
3.7
|
54.9
|
1.0
|
CBB
|
A:PHO353
|
3.9
|
59.6
|
1.0
|
O
|
D:HOH604
|
4.2
|
55.8
|
1.0
|
C3D
|
A:CLA406
|
4.2
|
49.5
|
1.0
|
C3B
|
A:CLA406
|
4.3
|
53.2
|
1.0
|
C2C
|
A:CLA406
|
4.4
|
50.9
|
1.0
|
C2B
|
A:CLA406
|
4.4
|
50.1
|
1.0
|
C2A
|
A:CLA406
|
4.4
|
56.3
|
1.0
|
C3A
|
A:CLA406
|
4.4
|
56.1
|
1.0
|
C3C
|
A:CLA406
|
4.4
|
51.1
|
1.0
|
C2D
|
A:CLA406
|
4.5
|
50.7
|
1.0
|
CG2
|
D:ILE178
|
4.7
|
48.8
|
1.0
|
CBA
|
A:CLA406
|
4.8
|
57.0
|
1.0
|
C20
|
A:PHO353
|
4.8
|
51.3
|
1.0
|
CE1
|
A:PHE206
|
4.9
|
48.9
|
1.0
|
CBD
|
A:CLA406
|
4.9
|
56.8
|
1.0
|
|
Magnesium binding site 4 out
of 72 in 5ws5
Go back to
Magnesium Binding Sites List in 5ws5
Magnesium binding site 4 out
of 72 in the Native Xfel Structure of Photosystem II (Preflash Dark Dataset)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Native Xfel Structure of Photosystem II (Preflash Dark Dataset) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg408
b:55.4
occ:1.00
|
MG
|
A:CLA408
|
0.0
|
55.4
|
1.0
|
ND
|
A:CLA408
|
2.0
|
56.5
|
1.0
|
NB
|
A:CLA408
|
2.0
|
57.0
|
1.0
|
NC
|
A:CLA408
|
2.1
|
55.2
|
1.0
|
NA
|
A:CLA408
|
2.1
|
58.2
|
1.0
|
NE2
|
A:HIS118
|
2.2
|
49.9
|
1.0
|
C4D
|
A:CLA408
|
3.0
|
58.5
|
1.0
|
C1C
|
A:CLA408
|
3.0
|
54.5
|
1.0
|
C4B
|
A:CLA408
|
3.0
|
54.1
|
1.0
|
C4A
|
A:CLA408
|
3.0
|
59.3
|
1.0
|
C1B
|
A:CLA408
|
3.0
|
57.1
|
1.0
|
C1A
|
A:CLA408
|
3.1
|
65.3
|
1.0
|
CE1
|
A:HIS118
|
3.1
|
56.3
|
1.0
|
C4C
|
A:CLA408
|
3.1
|
59.4
|
1.0
|
CD2
|
A:HIS118
|
3.3
|
57.0
|
1.0
|
C1D
|
A:CLA408
|
3.3
|
58.5
|
1.0
|
CHC
|
A:CLA408
|
3.4
|
59.4
|
1.0
|
CHB
|
A:CLA408
|
3.4
|
53.1
|
1.0
|
CHA
|
A:CLA408
|
3.4
|
60.6
|
1.0
|
CHD
|
A:CLA408
|
3.7
|
56.6
|
1.0
|
ND1
|
A:HIS118
|
4.2
|
49.0
|
1.0
|
C3D
|
A:CLA408
|
4.3
|
55.5
|
1.0
|
C3B
|
A:CLA408
|
4.3
|
60.7
|
1.0
|
C2C
|
A:CLA408
|
4.4
|
62.2
|
1.0
|
CG
|
A:HIS118
|
4.4
|
51.2
|
1.0
|
C2B
|
A:CLA408
|
4.4
|
55.0
|
1.0
|
C3A
|
A:CLA408
|
4.4
|
62.8
|
1.0
|
C2A
|
A:CLA408
|
4.4
|
58.5
|
1.0
|
C3C
|
A:CLA408
|
4.4
|
52.7
|
1.0
|
CG2
|
I:VAL12
|
4.4
|
56.3
|
1.0
|
CG1
|
I:VAL8
|
4.4
|
58.7
|
1.0
|
C2D
|
A:CLA408
|
4.5
|
57.2
|
1.0
|
CBD
|
A:CLA408
|
4.9
|
55.9
|
1.0
|
CMA
|
A:CLA408
|
4.9
|
51.4
|
1.0
|
|
Magnesium binding site 5 out
of 72 in 5ws5
Go back to
Magnesium Binding Sites List in 5ws5
Magnesium binding site 5 out
of 72 in the Native Xfel Structure of Photosystem II (Preflash Dark Dataset)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Native Xfel Structure of Photosystem II (Preflash Dark Dataset) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg601
b:89.3
occ:1.00
|
MG
|
B:CLA601
|
0.0
|
89.3
|
1.0
|
ND
|
B:CLA601
|
2.0
|
78.5
|
1.0
|
NB
|
B:CLA601
|
2.0
|
73.2
|
1.0
|
NC
|
B:CLA601
|
2.1
|
76.0
|
1.0
|
NA
|
B:CLA601
|
2.1
|
82.0
|
1.0
|
O
|
B:HOH748
|
2.2
|
72.2
|
1.0
|
C4D
|
B:CLA601
|
3.0
|
72.3
|
1.0
|
C1C
|
B:CLA601
|
3.0
|
74.6
|
1.0
|
C4B
|
B:CLA601
|
3.0
|
74.3
|
1.0
|
C4A
|
B:CLA601
|
3.0
|
83.7
|
1.0
|
C1B
|
B:CLA601
|
3.1
|
69.2
|
1.0
|
C1A
|
B:CLA601
|
3.1
|
83.7
|
1.0
|
C4C
|
B:CLA601
|
3.1
|
72.7
|
1.0
|
C1D
|
B:CLA601
|
3.3
|
82.4
|
1.0
|
CHC
|
B:CLA601
|
3.4
|
73.0
|
1.0
|
CHB
|
B:CLA601
|
3.4
|
69.2
|
1.0
|
CHA
|
B:CLA601
|
3.5
|
76.0
|
1.0
|
C10
|
B:CLA601
|
3.7
|
81.9
|
1.0
|
CHD
|
B:CLA601
|
3.7
|
76.5
|
1.0
|
C12
|
B:CLA601
|
4.0
|
82.1
|
1.0
|
C3D
|
B:CLA601
|
4.3
|
75.5
|
1.0
|
O
|
B:TRP185
|
4.3
|
73.6
|
1.0
|
C2C
|
B:CLA601
|
4.3
|
72.8
|
1.0
|
C3B
|
B:CLA601
|
4.4
|
70.4
|
1.0
|
C2B
|
B:CLA601
|
4.4
|
72.8
|
1.0
|
CE2
|
B:PHE190
|
4.4
|
69.5
|
1.0
|
C3A
|
B:CLA601
|
4.4
|
82.1
|
1.0
|
C2A
|
B:CLA601
|
4.4
|
79.8
|
1.0
|
C11
|
B:CLA601
|
4.4
|
85.2
|
1.0
|
C3C
|
B:CLA601
|
4.4
|
76.8
|
1.0
|
C2D
|
B:CLA601
|
4.5
|
82.8
|
1.0
|
O
|
B:HOH741
|
4.6
|
89.1
|
1.0
|
CZ
|
B:PHE190
|
4.8
|
61.3
|
1.0
|
C8
|
B:CLA601
|
4.9
|
81.1
|
1.0
|
CBD
|
B:CLA601
|
4.9
|
78.7
|
1.0
|
|
Magnesium binding site 6 out
of 72 in 5ws5
Go back to
Magnesium Binding Sites List in 5ws5
Magnesium binding site 6 out
of 72 in the Native Xfel Structure of Photosystem II (Preflash Dark Dataset)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Native Xfel Structure of Photosystem II (Preflash Dark Dataset) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg602
b:60.5
occ:1.00
|
MG
|
B:CLA602
|
0.0
|
60.5
|
1.0
|
ND
|
B:CLA602
|
2.0
|
59.4
|
1.0
|
NB
|
B:CLA602
|
2.0
|
57.5
|
1.0
|
NC
|
B:CLA602
|
2.1
|
62.2
|
1.0
|
NA
|
B:CLA602
|
2.1
|
61.9
|
1.0
|
ND1
|
B:HIS201
|
2.2
|
65.3
|
1.0
|
C4D
|
B:CLA602
|
3.0
|
59.6
|
1.0
|
C1C
|
B:CLA602
|
3.0
|
64.3
|
1.0
|
CE1
|
B:HIS201
|
3.0
|
64.6
|
1.0
|
C1B
|
B:CLA602
|
3.0
|
62.6
|
1.0
|
C4B
|
B:CLA602
|
3.0
|
60.9
|
1.0
|
C4A
|
B:CLA602
|
3.1
|
63.7
|
1.0
|
C1A
|
B:CLA602
|
3.1
|
60.5
|
1.0
|
C4C
|
B:CLA602
|
3.1
|
58.4
|
1.0
|
C1D
|
B:CLA602
|
3.3
|
60.0
|
1.0
|
CG
|
B:HIS201
|
3.3
|
60.4
|
1.0
|
CHC
|
B:CLA602
|
3.4
|
59.8
|
1.0
|
CHB
|
B:CLA602
|
3.4
|
55.3
|
1.0
|
CHA
|
B:CLA602
|
3.5
|
56.7
|
1.0
|
CHD
|
B:CLA602
|
3.7
|
58.7
|
1.0
|
CB
|
B:HIS201
|
3.8
|
60.4
|
1.0
|
CZ
|
H:PHE41
|
3.9
|
69.5
|
1.0
|
NE2
|
B:HIS201
|
4.2
|
61.1
|
1.0
|
C3D
|
B:CLA602
|
4.3
|
57.4
|
1.0
|
C3B
|
B:CLA602
|
4.3
|
64.4
|
1.0
|
C2B
|
B:CLA602
|
4.3
|
60.1
|
1.0
|
CD2
|
B:HIS201
|
4.4
|
59.1
|
1.0
|
C2C
|
B:CLA602
|
4.4
|
61.7
|
1.0
|
CA
|
B:HIS201
|
4.4
|
60.2
|
1.0
|
CE2
|
H:PHE41
|
4.4
|
72.2
|
1.0
|
C3A
|
B:CLA602
|
4.4
|
58.9
|
1.0
|
C2A
|
B:CLA602
|
4.4
|
56.4
|
1.0
|
C3C
|
B:CLA602
|
4.4
|
60.6
|
1.0
|
C2D
|
B:CLA602
|
4.5
|
58.0
|
1.0
|
CE1
|
B:PHE190
|
4.9
|
62.2
|
1.0
|
CE1
|
H:PHE41
|
4.9
|
71.9
|
1.0
|
CBD
|
B:CLA602
|
4.9
|
60.8
|
1.0
|
|
Magnesium binding site 7 out
of 72 in 5ws5
Go back to
Magnesium Binding Sites List in 5ws5
Magnesium binding site 7 out
of 72 in the Native Xfel Structure of Photosystem II (Preflash Dark Dataset)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Native Xfel Structure of Photosystem II (Preflash Dark Dataset) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg603
b:55.5
occ:1.00
|
MG
|
B:CLA603
|
0.0
|
55.5
|
1.0
|
ND
|
B:CLA603
|
2.0
|
57.6
|
1.0
|
NB
|
B:CLA603
|
2.0
|
58.6
|
1.0
|
NC
|
B:CLA603
|
2.1
|
56.8
|
1.0
|
NA
|
B:CLA603
|
2.1
|
57.6
|
1.0
|
NE2
|
B:HIS202
|
2.2
|
55.5
|
1.0
|
C4D
|
B:CLA603
|
3.0
|
58.7
|
1.0
|
C1B
|
B:CLA603
|
3.0
|
57.7
|
1.0
|
C4B
|
B:CLA603
|
3.0
|
57.7
|
1.0
|
C1C
|
B:CLA603
|
3.0
|
59.3
|
1.0
|
C4A
|
B:CLA603
|
3.0
|
62.0
|
1.0
|
CD2
|
B:HIS202
|
3.0
|
55.2
|
1.0
|
C1A
|
B:CLA603
|
3.1
|
57.4
|
1.0
|
C4C
|
B:CLA603
|
3.1
|
54.6
|
1.0
|
C1D
|
B:CLA603
|
3.2
|
59.2
|
1.0
|
CE1
|
B:HIS202
|
3.3
|
62.1
|
1.0
|
CHB
|
B:CLA603
|
3.4
|
57.0
|
1.0
|
CHC
|
B:CLA603
|
3.4
|
53.1
|
1.0
|
CHA
|
B:CLA603
|
3.5
|
56.4
|
1.0
|
CHD
|
B:CLA603
|
3.7
|
59.2
|
1.0
|
CG
|
B:HIS202
|
4.2
|
55.7
|
1.0
|
C3D
|
B:CLA603
|
4.3
|
54.2
|
1.0
|
C6
|
B:CLA605
|
4.3
|
64.0
|
1.0
|
ND1
|
B:HIS202
|
4.3
|
58.3
|
1.0
|
C3B
|
B:CLA603
|
4.3
|
58.0
|
1.0
|
C2B
|
B:CLA603
|
4.4
|
61.3
|
1.0
|
C2C
|
B:CLA603
|
4.4
|
55.6
|
1.0
|
C2A
|
B:CLA603
|
4.4
|
55.0
|
1.0
|
C3A
|
B:CLA603
|
4.4
|
56.1
|
1.0
|
C3C
|
B:CLA603
|
4.4
|
59.5
|
1.0
|
C2D
|
B:CLA603
|
4.5
|
62.3
|
1.0
|
C9
|
B:CLA605
|
4.5
|
58.6
|
1.0
|
NE2
|
B:HIS201
|
4.8
|
61.1
|
1.0
|
C4
|
B:CLA605
|
4.8
|
65.2
|
1.0
|
CD2
|
B:HIS201
|
4.9
|
59.1
|
1.0
|
CE2
|
B:PHE153
|
4.9
|
60.1
|
1.0
|
CBD
|
B:CLA603
|
4.9
|
64.5
|
1.0
|
CBA
|
B:CLA603
|
5.0
|
52.8
|
1.0
|
|
Magnesium binding site 8 out
of 72 in 5ws5
Go back to
Magnesium Binding Sites List in 5ws5
Magnesium binding site 8 out
of 72 in the Native Xfel Structure of Photosystem II (Preflash Dark Dataset)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Native Xfel Structure of Photosystem II (Preflash Dark Dataset) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg604
b:50.6
occ:1.00
|
MG
|
B:CLA604
|
0.0
|
50.6
|
1.0
|
ND
|
B:CLA604
|
2.0
|
51.5
|
1.0
|
NB
|
B:CLA604
|
2.0
|
48.0
|
1.0
|
NC
|
B:CLA604
|
2.1
|
52.0
|
1.0
|
NA
|
B:CLA604
|
2.1
|
52.3
|
1.0
|
NE2
|
B:HIS455
|
2.2
|
51.9
|
1.0
|
C4D
|
B:CLA604
|
3.0
|
50.8
|
1.0
|
C4B
|
B:CLA604
|
3.0
|
50.5
|
1.0
|
C1B
|
B:CLA604
|
3.0
|
50.3
|
1.0
|
C1C
|
B:CLA604
|
3.0
|
48.6
|
1.0
|
C4A
|
B:CLA604
|
3.1
|
48.9
|
1.0
|
C1A
|
B:CLA604
|
3.1
|
49.7
|
1.0
|
CE1
|
B:HIS455
|
3.1
|
54.8
|
1.0
|
C4C
|
B:CLA604
|
3.1
|
44.7
|
1.0
|
CD2
|
B:HIS455
|
3.2
|
51.7
|
1.0
|
C1D
|
B:CLA604
|
3.2
|
54.7
|
1.0
|
CHB
|
B:CLA604
|
3.4
|
56.2
|
1.0
|
CHC
|
B:CLA604
|
3.4
|
48.2
|
1.0
|
CHA
|
B:CLA604
|
3.5
|
53.1
|
1.0
|
CHD
|
B:CLA604
|
3.7
|
52.0
|
1.0
|
C14
|
B:CLA612
|
4.2
|
52.8
|
1.0
|
C3D
|
B:CLA604
|
4.2
|
52.9
|
1.0
|
ND1
|
B:HIS455
|
4.3
|
52.0
|
1.0
|
CG
|
B:HIS455
|
4.3
|
55.6
|
1.0
|
C3B
|
B:CLA604
|
4.3
|
50.0
|
1.0
|
C2B
|
B:CLA604
|
4.4
|
51.6
|
1.0
|
C2C
|
B:CLA604
|
4.4
|
47.5
|
1.0
|
C3C
|
B:CLA604
|
4.4
|
52.1
|
1.0
|
C3A
|
B:CLA604
|
4.4
|
55.3
|
1.0
|
C2D
|
B:CLA604
|
4.5
|
52.6
|
1.0
|
C2A
|
B:CLA604
|
4.5
|
50.7
|
1.0
|
C15
|
B:CLA612
|
4.5
|
56.6
|
1.0
|
C13
|
B:CLA612
|
4.7
|
57.8
|
1.0
|
CE1
|
B:PHE451
|
4.9
|
51.8
|
1.0
|
CBD
|
B:CLA604
|
4.9
|
53.4
|
1.0
|
|
Magnesium binding site 9 out
of 72 in 5ws5
Go back to
Magnesium Binding Sites List in 5ws5
Magnesium binding site 9 out
of 72 in the Native Xfel Structure of Photosystem II (Preflash Dark Dataset)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Native Xfel Structure of Photosystem II (Preflash Dark Dataset) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg605
b:54.6
occ:1.00
|
MG
|
B:CLA605
|
0.0
|
54.6
|
1.0
|
ND
|
B:CLA605
|
2.0
|
52.2
|
1.0
|
NB
|
B:CLA605
|
2.1
|
52.5
|
1.0
|
NC
|
B:CLA605
|
2.1
|
53.9
|
1.0
|
NA
|
B:CLA605
|
2.1
|
55.2
|
1.0
|
NE2
|
B:HIS100
|
2.2
|
53.9
|
1.0
|
C4D
|
B:CLA605
|
3.0
|
48.5
|
1.0
|
C1C
|
B:CLA605
|
3.0
|
50.3
|
1.0
|
C4B
|
B:CLA605
|
3.0
|
52.2
|
1.0
|
C1A
|
B:CLA605
|
3.1
|
50.2
|
1.0
|
C4A
|
B:CLA605
|
3.1
|
48.2
|
1.0
|
C1B
|
B:CLA605
|
3.1
|
52.3
|
1.0
|
CE1
|
B:HIS100
|
3.1
|
54.7
|
1.0
|
C4C
|
B:CLA605
|
3.2
|
50.9
|
1.0
|
C1D
|
B:CLA605
|
3.3
|
58.4
|
1.0
|
CD2
|
B:HIS100
|
3.3
|
49.2
|
1.0
|
CHC
|
B:CLA605
|
3.4
|
51.8
|
1.0
|
CHB
|
B:CLA605
|
3.4
|
52.6
|
1.0
|
CHA
|
B:CLA605
|
3.4
|
52.3
|
1.0
|
CHD
|
B:CLA605
|
3.7
|
50.5
|
1.0
|
C1
|
B:CLA604
|
4.0
|
58.9
|
1.0
|
ND1
|
B:HIS100
|
4.2
|
53.8
|
1.0
|
C3D
|
B:CLA605
|
4.2
|
53.1
|
1.0
|
C3B
|
B:CLA605
|
4.4
|
52.3
|
1.0
|
CG
|
B:HIS100
|
4.4
|
52.6
|
1.0
|
C2C
|
B:CLA605
|
4.4
|
50.9
|
1.0
|
C2B
|
B:CLA605
|
4.4
|
52.3
|
1.0
|
C2A
|
B:CLA605
|
4.4
|
54.1
|
1.0
|
C3A
|
B:CLA605
|
4.4
|
53.8
|
1.0
|
C3C
|
B:CLA605
|
4.4
|
48.1
|
1.0
|
C2D
|
B:CLA605
|
4.5
|
47.7
|
1.0
|
C2
|
B:CLA604
|
4.5
|
66.7
|
1.0
|
CBD
|
B:CLA605
|
4.9
|
56.3
|
1.0
|
O1A
|
B:CLA604
|
5.0
|
58.0
|
1.0
|
C4
|
B:CLA606
|
5.0
|
60.3
|
1.0
|
CBA
|
B:CLA605
|
5.0
|
51.0
|
1.0
|
|
Magnesium binding site 10 out
of 72 in 5ws5
Go back to
Magnesium Binding Sites List in 5ws5
Magnesium binding site 10 out
of 72 in the Native Xfel Structure of Photosystem II (Preflash Dark Dataset)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Native Xfel Structure of Photosystem II (Preflash Dark Dataset) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg606
b:60.1
occ:1.00
|
MG
|
B:CLA606
|
0.0
|
60.1
|
1.0
|
ND
|
B:CLA606
|
2.0
|
59.9
|
1.0
|
NB
|
B:CLA606
|
2.0
|
57.0
|
1.0
|
NC
|
B:CLA606
|
2.1
|
58.2
|
1.0
|
NA
|
B:CLA606
|
2.1
|
58.1
|
1.0
|
ND1
|
B:HIS157
|
2.2
|
60.3
|
1.0
|
CE1
|
B:HIS157
|
2.8
|
61.8
|
1.0
|
C4D
|
B:CLA606
|
3.0
|
55.4
|
1.0
|
C4B
|
B:CLA606
|
3.0
|
53.4
|
1.0
|
C1C
|
B:CLA606
|
3.0
|
57.9
|
1.0
|
C1B
|
B:CLA606
|
3.0
|
57.1
|
1.0
|
C4A
|
B:CLA606
|
3.1
|
57.4
|
1.0
|
C1A
|
B:CLA606
|
3.1
|
56.6
|
1.0
|
C4C
|
B:CLA606
|
3.1
|
59.9
|
1.0
|
C1D
|
B:CLA606
|
3.2
|
58.9
|
1.0
|
CHC
|
B:CLA606
|
3.4
|
58.5
|
1.0
|
CHB
|
B:CLA606
|
3.4
|
54.5
|
1.0
|
CG
|
B:HIS157
|
3.4
|
56.4
|
1.0
|
CHA
|
B:CLA606
|
3.5
|
59.0
|
1.0
|
CHD
|
B:CLA606
|
3.7
|
65.9
|
1.0
|
C16
|
B:UNL627
|
3.9
|
76.8
|
1.0
|
C15
|
B:UNL627
|
4.0
|
81.5
|
1.0
|
CB
|
B:HIS157
|
4.0
|
54.0
|
1.0
|
NE2
|
B:HIS157
|
4.1
|
53.8
|
1.0
|
C3D
|
B:CLA606
|
4.2
|
60.5
|
1.0
|
C3B
|
B:CLA606
|
4.3
|
61.0
|
1.0
|
C2C
|
B:CLA606
|
4.4
|
56.5
|
1.0
|
C2B
|
B:CLA606
|
4.4
|
51.2
|
1.0
|
CD2
|
B:HIS157
|
4.4
|
50.8
|
1.0
|
C3C
|
B:CLA606
|
4.4
|
55.8
|
1.0
|
C2A
|
B:CLA606
|
4.4
|
58.5
|
1.0
|
C3A
|
B:CLA606
|
4.4
|
53.7
|
1.0
|
C2D
|
B:CLA606
|
4.5
|
58.7
|
1.0
|
C14
|
B:UNL627
|
4.6
|
87.2
|
1.0
|
CBD
|
B:CLA606
|
4.9
|
61.6
|
1.0
|
CD
|
B:PRO164
|
5.0
|
62.0
|
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 Sep 30 06:54:27 2024
|