Magnesium in PDB 5ws6: Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset
Enzymatic activity of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset
All present enzymatic activity of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset:
1.10.3.9;
Protein crystallography data
The structure of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset, PDB code: 5ws6
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 (°)
|
124.960,
230.220,
286.020,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
12.9 /
17.5
|
Other elements in 5ws6:
The structure of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset also contains other interesting chemical elements:
Magnesium Binding Sites:
Magnesium binding site 1 out
of 72 in 5ws6
Go back to
Magnesium Binding Sites List in 5ws6
Magnesium binding site 1 out
of 72 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash 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 Two-Flash Dataset within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg404
b:41.6
occ:1.00
|
MG
|
A:CLA404
|
0.0
|
41.6
|
1.0
|
ND
|
A:CLA404
|
2.0
|
43.7
|
1.0
|
NB
|
A:CLA404
|
2.0
|
39.2
|
1.0
|
NA
|
A:CLA404
|
2.1
|
47.5
|
1.0
|
NC
|
A:CLA404
|
2.1
|
41.2
|
1.0
|
NE2
|
A:HIS198
|
2.2
|
39.0
|
1.0
|
C4D
|
A:CLA404
|
3.0
|
39.5
|
1.0
|
C4B
|
A:CLA404
|
3.0
|
39.9
|
1.0
|
C1B
|
A:CLA404
|
3.0
|
40.2
|
1.0
|
C1C
|
A:CLA404
|
3.0
|
38.1
|
1.0
|
C4A
|
A:CLA404
|
3.0
|
43.1
|
1.0
|
C1A
|
A:CLA404
|
3.1
|
42.7
|
1.0
|
CE1
|
A:HIS198
|
3.1
|
45.5
|
1.0
|
C4C
|
A:CLA404
|
3.2
|
39.4
|
1.0
|
C1D
|
A:CLA404
|
3.3
|
41.5
|
1.0
|
CD2
|
A:HIS198
|
3.3
|
36.2
|
1.0
|
CHB
|
A:CLA404
|
3.4
|
36.7
|
1.0
|
CHC
|
A:CLA404
|
3.4
|
43.9
|
1.0
|
CHA
|
A:CLA404
|
3.5
|
42.2
|
1.0
|
CHD
|
A:CLA404
|
3.7
|
37.4
|
1.0
|
CE
|
A:MET183
|
4.0
|
38.5
|
1.0
|
C3D
|
A:CLA404
|
4.3
|
36.4
|
1.0
|
ND1
|
A:HIS198
|
4.3
|
40.0
|
1.0
|
C3B
|
A:CLA404
|
4.3
|
43.3
|
1.0
|
C2B
|
A:CLA404
|
4.4
|
41.0
|
1.0
|
CG
|
A:HIS198
|
4.4
|
43.3
|
1.0
|
CAB
|
D:CLA402
|
4.4
|
38.9
|
1.0
|
C2C
|
A:CLA404
|
4.4
|
42.6
|
1.0
|
C2A
|
A:CLA404
|
4.4
|
45.7
|
1.0
|
C3A
|
A:CLA404
|
4.4
|
40.9
|
1.0
|
C3C
|
A:CLA404
|
4.5
|
44.6
|
1.0
|
C2D
|
A:CLA404
|
4.5
|
40.0
|
1.0
|
CBD
|
A:CLA404
|
4.9
|
48.0
|
1.0
|
|
Magnesium binding site 2 out
of 72 in 5ws6
Go back to
Magnesium Binding Sites List in 5ws6
Magnesium binding site 2 out
of 72 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash 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 Two-Flash Dataset within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg405
b:47.4
occ:1.00
|
MG
|
A:CLA405
|
0.0
|
47.4
|
1.0
|
ND
|
A:CLA405
|
2.0
|
39.5
|
1.0
|
NB
|
A:CLA405
|
2.0
|
40.3
|
1.0
|
NC
|
A:CLA405
|
2.1
|
46.8
|
1.0
|
NA
|
A:CLA405
|
2.1
|
46.9
|
1.0
|
O
|
A:HOH590
|
2.2
|
41.4
|
1.0
|
C4D
|
A:CLA405
|
3.0
|
41.0
|
1.0
|
C1C
|
A:CLA405
|
3.0
|
41.5
|
1.0
|
C1B
|
A:CLA405
|
3.0
|
47.0
|
1.0
|
C4B
|
A:CLA405
|
3.0
|
43.8
|
1.0
|
C4A
|
A:CLA405
|
3.1
|
50.3
|
1.0
|
C1A
|
A:CLA405
|
3.1
|
38.7
|
1.0
|
C4C
|
A:CLA405
|
3.1
|
37.7
|
1.0
|
C1D
|
A:CLA405
|
3.3
|
42.8
|
1.0
|
CHC
|
A:CLA405
|
3.4
|
41.1
|
1.0
|
CHB
|
A:CLA405
|
3.4
|
47.2
|
1.0
|
CHA
|
A:CLA405
|
3.4
|
42.5
|
1.0
|
CHD
|
A:CLA405
|
3.7
|
40.0
|
1.0
|
CBB
|
A:PHO407
|
3.9
|
47.9
|
1.0
|
O
|
A:HOH583
|
4.1
|
41.1
|
1.0
|
C3D
|
A:CLA405
|
4.2
|
37.8
|
1.0
|
C3B
|
A:CLA405
|
4.3
|
43.7
|
1.0
|
C2B
|
A:CLA405
|
4.4
|
47.8
|
1.0
|
C2C
|
A:CLA405
|
4.4
|
44.5
|
1.0
|
C3C
|
A:CLA405
|
4.4
|
46.3
|
1.0
|
C2A
|
A:CLA405
|
4.4
|
45.6
|
1.0
|
C3A
|
A:CLA405
|
4.4
|
46.7
|
1.0
|
CG2
|
A:THR179
|
4.5
|
35.4
|
1.0
|
C2D
|
A:CLA405
|
4.5
|
42.3
|
1.0
|
C19
|
A:PHO407
|
4.7
|
43.8
|
1.0
|
OG1
|
A:THR179
|
4.7
|
44.6
|
1.0
|
CBA
|
A:CLA405
|
4.7
|
43.0
|
1.0
|
CBD
|
A:CLA405
|
4.9
|
47.7
|
1.0
|
|
Magnesium binding site 3 out
of 72 in 5ws6
Go back to
Magnesium Binding Sites List in 5ws6
Magnesium binding site 3 out
of 72 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash 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 Two-Flash Dataset within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg406
b:44.7
occ:1.00
|
MG
|
A:CLA406
|
0.0
|
44.7
|
1.0
|
ND
|
A:CLA406
|
2.0
|
43.9
|
1.0
|
NB
|
A:CLA406
|
2.0
|
41.6
|
1.0
|
NC
|
A:CLA406
|
2.1
|
43.2
|
1.0
|
NA
|
A:CLA406
|
2.1
|
46.2
|
1.0
|
O
|
A:HOH611
|
2.2
|
42.9
|
1.0
|
C4D
|
A:CLA406
|
3.0
|
36.7
|
1.0
|
C1C
|
A:CLA406
|
3.0
|
43.9
|
1.0
|
C4A
|
A:CLA406
|
3.0
|
47.9
|
1.0
|
C1B
|
A:CLA406
|
3.0
|
45.3
|
1.0
|
C4B
|
A:CLA406
|
3.0
|
38.6
|
1.0
|
C1A
|
A:CLA406
|
3.1
|
45.1
|
1.0
|
C4C
|
A:CLA406
|
3.1
|
36.9
|
1.0
|
C1D
|
A:CLA406
|
3.3
|
37.5
|
1.0
|
CHB
|
A:CLA406
|
3.4
|
49.3
|
1.0
|
CHC
|
A:CLA406
|
3.4
|
47.6
|
1.0
|
CHA
|
A:CLA406
|
3.5
|
43.4
|
1.0
|
CHD
|
A:CLA406
|
3.7
|
46.5
|
1.0
|
CBB
|
A:PHO408
|
3.8
|
56.4
|
1.0
|
C3D
|
A:CLA406
|
4.3
|
39.5
|
1.0
|
O
|
D:HOH599
|
4.3
|
46.9
|
1.0
|
C3B
|
A:CLA406
|
4.3
|
44.0
|
1.0
|
C2B
|
A:CLA406
|
4.4
|
42.6
|
1.0
|
C2C
|
A:CLA406
|
4.4
|
42.7
|
1.0
|
C3A
|
A:CLA406
|
4.4
|
53.4
|
1.0
|
C2A
|
A:CLA406
|
4.4
|
47.6
|
1.0
|
C3C
|
A:CLA406
|
4.4
|
43.3
|
1.0
|
C2D
|
A:CLA406
|
4.5
|
42.2
|
1.0
|
C20
|
A:PHO408
|
4.7
|
45.2
|
1.0
|
CG2
|
D:ILE178
|
4.7
|
47.0
|
1.0
|
CBA
|
A:CLA406
|
4.7
|
50.0
|
1.0
|
CE1
|
A:PHE206
|
4.9
|
43.4
|
1.0
|
CBD
|
A:CLA406
|
4.9
|
46.7
|
1.0
|
|
Magnesium binding site 4 out
of 72 in 5ws6
Go back to
Magnesium Binding Sites List in 5ws6
Magnesium binding site 4 out
of 72 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash 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 Two-Flash Dataset within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg409
b:50.5
occ:1.00
|
MG
|
A:CLA409
|
0.0
|
50.5
|
1.0
|
ND
|
A:CLA409
|
2.0
|
50.8
|
1.0
|
NB
|
A:CLA409
|
2.0
|
50.5
|
1.0
|
NC
|
A:CLA409
|
2.1
|
54.8
|
1.0
|
NA
|
A:CLA409
|
2.1
|
53.3
|
1.0
|
NE2
|
A:HIS118
|
2.2
|
47.5
|
1.0
|
C4D
|
A:CLA409
|
3.0
|
53.8
|
1.0
|
C1C
|
A:CLA409
|
3.0
|
47.7
|
1.0
|
C4B
|
A:CLA409
|
3.0
|
47.9
|
1.0
|
C4A
|
A:CLA409
|
3.0
|
45.7
|
1.0
|
C1B
|
A:CLA409
|
3.0
|
46.1
|
1.0
|
C1A
|
A:CLA409
|
3.1
|
61.0
|
1.0
|
CE1
|
A:HIS118
|
3.1
|
53.7
|
1.0
|
C4C
|
A:CLA409
|
3.1
|
49.2
|
1.0
|
C1D
|
A:CLA409
|
3.3
|
49.3
|
1.0
|
CD2
|
A:HIS118
|
3.3
|
51.1
|
1.0
|
CHC
|
A:CLA409
|
3.4
|
51.0
|
1.0
|
CHB
|
A:CLA409
|
3.4
|
42.4
|
1.0
|
CHA
|
A:CLA409
|
3.4
|
52.9
|
1.0
|
CHD
|
A:CLA409
|
3.7
|
47.5
|
1.0
|
ND1
|
A:HIS118
|
4.2
|
44.0
|
1.0
|
C3D
|
A:CLA409
|
4.2
|
54.2
|
1.0
|
C3B
|
A:CLA409
|
4.3
|
46.1
|
1.0
|
CG
|
A:HIS118
|
4.4
|
45.6
|
1.0
|
C2C
|
A:CLA409
|
4.4
|
52.6
|
1.0
|
C2B
|
A:CLA409
|
4.4
|
42.8
|
1.0
|
C3A
|
A:CLA409
|
4.4
|
53.2
|
1.0
|
C2A
|
A:CLA409
|
4.4
|
49.0
|
1.0
|
C3C
|
A:CLA409
|
4.4
|
50.9
|
1.0
|
CG1
|
I:VAL8
|
4.5
|
54.6
|
1.0
|
C2D
|
A:CLA409
|
4.5
|
49.2
|
1.0
|
CG2
|
I:VAL12
|
4.5
|
44.7
|
1.0
|
CBD
|
A:CLA409
|
4.9
|
51.5
|
1.0
|
CMA
|
A:CLA409
|
5.0
|
42.7
|
1.0
|
|
Magnesium binding site 5 out
of 72 in 5ws6
Go back to
Magnesium Binding Sites List in 5ws6
Magnesium binding site 5 out
of 72 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash 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 Two-Flash Dataset within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg601
b:86.3
occ:1.00
|
MG
|
B:CLA601
|
0.0
|
86.3
|
1.0
|
ND
|
B:CLA601
|
2.0
|
73.5
|
1.0
|
NB
|
B:CLA601
|
2.0
|
63.9
|
1.0
|
NC
|
B:CLA601
|
2.1
|
70.0
|
1.0
|
NA
|
B:CLA601
|
2.1
|
75.2
|
1.0
|
O
|
B:HOH756
|
2.2
|
67.2
|
1.0
|
C4D
|
B:CLA601
|
3.0
|
69.5
|
1.0
|
C1C
|
B:CLA601
|
3.0
|
63.0
|
1.0
|
C4B
|
B:CLA601
|
3.0
|
68.1
|
1.0
|
C4A
|
B:CLA601
|
3.0
|
73.1
|
1.0
|
C1B
|
B:CLA601
|
3.0
|
56.0
|
1.0
|
C1A
|
B:CLA601
|
3.1
|
79.3
|
1.0
|
C4C
|
B:CLA601
|
3.1
|
63.9
|
1.0
|
C1D
|
B:CLA601
|
3.3
|
73.3
|
1.0
|
CHC
|
B:CLA601
|
3.4
|
64.3
|
1.0
|
CHB
|
B:CLA601
|
3.4
|
61.4
|
1.0
|
CHA
|
B:CLA601
|
3.5
|
72.2
|
1.0
|
CHD
|
B:CLA601
|
3.7
|
65.2
|
1.0
|
C10
|
B:CLA601
|
3.8
|
85.9
|
1.0
|
C12
|
B:CLA601
|
4.1
|
92.0
|
1.0
|
C3D
|
B:CLA601
|
4.3
|
72.6
|
1.0
|
O
|
B:TRP185
|
4.3
|
64.9
|
1.0
|
C3B
|
B:CLA601
|
4.4
|
60.8
|
1.0
|
C2C
|
B:CLA601
|
4.4
|
63.1
|
1.0
|
C2B
|
B:CLA601
|
4.4
|
55.5
|
1.0
|
C3A
|
B:CLA601
|
4.4
|
74.2
|
1.0
|
C2A
|
B:CLA601
|
4.4
|
79.5
|
1.0
|
C3C
|
B:CLA601
|
4.4
|
66.2
|
1.0
|
CE2
|
B:PHE190
|
4.5
|
57.0
|
1.0
|
C11
|
B:CLA601
|
4.5
|
87.4
|
1.0
|
C2D
|
B:CLA601
|
4.5
|
78.4
|
1.0
|
O
|
B:HOH729
|
4.6
|
95.2
|
1.0
|
CZ
|
B:PHE190
|
4.8
|
53.3
|
1.0
|
C8
|
B:CLA601
|
4.8
|
90.0
|
1.0
|
C7
|
B:CLA601
|
4.9
|
94.2
|
1.0
|
CBD
|
B:CLA601
|
4.9
|
76.7
|
1.0
|
|
Magnesium binding site 6 out
of 72 in 5ws6
Go back to
Magnesium Binding Sites List in 5ws6
Magnesium binding site 6 out
of 72 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash 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 Two-Flash Dataset within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg602
b:53.5
occ:1.00
|
MG
|
B:CLA602
|
0.0
|
53.5
|
1.0
|
ND
|
B:CLA602
|
2.0
|
54.9
|
1.0
|
NB
|
B:CLA602
|
2.0
|
52.5
|
1.0
|
NC
|
B:CLA602
|
2.1
|
54.8
|
1.0
|
NA
|
B:CLA602
|
2.1
|
56.5
|
1.0
|
ND1
|
B:HIS201
|
2.2
|
60.3
|
1.0
|
C4D
|
B:CLA602
|
3.0
|
50.3
|
1.0
|
CE1
|
B:HIS201
|
3.0
|
61.4
|
1.0
|
C1C
|
B:CLA602
|
3.0
|
63.9
|
1.0
|
C1B
|
B:CLA602
|
3.0
|
54.3
|
1.0
|
C4B
|
B:CLA602
|
3.0
|
55.3
|
1.0
|
C4A
|
B:CLA602
|
3.0
|
58.1
|
1.0
|
C1A
|
B:CLA602
|
3.1
|
55.1
|
1.0
|
C4C
|
B:CLA602
|
3.2
|
51.8
|
1.0
|
C1D
|
B:CLA602
|
3.3
|
51.7
|
1.0
|
CG
|
B:HIS201
|
3.3
|
55.2
|
1.0
|
CHB
|
B:CLA602
|
3.4
|
49.1
|
1.0
|
CHC
|
B:CLA602
|
3.4
|
57.3
|
1.0
|
CHA
|
B:CLA602
|
3.5
|
52.6
|
1.0
|
CHD
|
B:CLA602
|
3.7
|
52.2
|
1.0
|
CB
|
B:HIS201
|
3.8
|
53.6
|
1.0
|
CZ
|
H:PHE41
|
3.9
|
69.9
|
1.0
|
NE2
|
B:HIS201
|
4.2
|
54.8
|
1.0
|
C3D
|
B:CLA602
|
4.3
|
52.5
|
1.0
|
C3B
|
B:CLA602
|
4.3
|
60.0
|
1.0
|
C2B
|
B:CLA602
|
4.4
|
57.4
|
1.0
|
CE2
|
H:PHE41
|
4.4
|
71.2
|
1.0
|
CD2
|
B:HIS201
|
4.4
|
53.6
|
1.0
|
C2C
|
B:CLA602
|
4.4
|
56.0
|
1.0
|
CA
|
B:HIS201
|
4.4
|
53.1
|
1.0
|
C3A
|
B:CLA602
|
4.4
|
53.6
|
1.0
|
C2A
|
B:CLA602
|
4.4
|
55.8
|
1.0
|
C3C
|
B:CLA602
|
4.4
|
52.1
|
1.0
|
C2D
|
B:CLA602
|
4.5
|
47.2
|
1.0
|
CE1
|
B:PHE190
|
4.8
|
53.9
|
1.0
|
CBD
|
B:CLA602
|
4.9
|
56.1
|
1.0
|
CE1
|
H:PHE41
|
5.0
|
68.5
|
1.0
|
|
Magnesium binding site 7 out
of 72 in 5ws6
Go back to
Magnesium Binding Sites List in 5ws6
Magnesium binding site 7 out
of 72 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash 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 Two-Flash Dataset within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg603
b:53.9
occ:1.00
|
MG
|
B:CLA603
|
0.0
|
53.9
|
1.0
|
NB
|
B:CLA603
|
2.0
|
48.5
|
1.0
|
ND
|
B:CLA603
|
2.0
|
53.2
|
1.0
|
NC
|
B:CLA603
|
2.1
|
48.4
|
1.0
|
NA
|
B:CLA603
|
2.1
|
49.9
|
1.0
|
NE2
|
B:HIS202
|
2.2
|
48.0
|
1.0
|
C4D
|
B:CLA603
|
3.0
|
52.2
|
1.0
|
C1B
|
B:CLA603
|
3.0
|
50.7
|
1.0
|
C4B
|
B:CLA603
|
3.0
|
51.4
|
1.0
|
C4A
|
B:CLA603
|
3.0
|
48.9
|
1.0
|
C1C
|
B:CLA603
|
3.1
|
52.0
|
1.0
|
C1A
|
B:CLA603
|
3.1
|
48.0
|
1.0
|
CD2
|
B:HIS202
|
3.1
|
47.1
|
1.0
|
C4C
|
B:CLA603
|
3.1
|
44.7
|
1.0
|
CE1
|
B:HIS202
|
3.2
|
57.0
|
1.0
|
C1D
|
B:CLA603
|
3.3
|
53.7
|
1.0
|
CHB
|
B:CLA603
|
3.4
|
46.8
|
1.0
|
CHC
|
B:CLA603
|
3.4
|
50.8
|
1.0
|
CHA
|
B:CLA603
|
3.5
|
51.8
|
1.0
|
CHD
|
B:CLA603
|
3.7
|
53.5
|
1.0
|
C3D
|
B:CLA603
|
4.3
|
54.1
|
1.0
|
CG
|
B:HIS202
|
4.3
|
49.9
|
1.0
|
ND1
|
B:HIS202
|
4.3
|
45.8
|
1.0
|
C6
|
B:CLA605
|
4.3
|
66.3
|
1.0
|
C3B
|
B:CLA603
|
4.3
|
51.0
|
1.0
|
C2B
|
B:CLA603
|
4.3
|
52.1
|
1.0
|
C2C
|
B:CLA603
|
4.4
|
53.0
|
1.0
|
C2A
|
B:CLA603
|
4.4
|
44.2
|
1.0
|
C3A
|
B:CLA603
|
4.4
|
48.4
|
1.0
|
C3C
|
B:CLA603
|
4.4
|
49.6
|
1.0
|
C2D
|
B:CLA603
|
4.5
|
54.8
|
1.0
|
NE2
|
B:HIS201
|
4.8
|
54.8
|
1.0
|
C4
|
B:CLA605
|
4.9
|
68.2
|
1.0
|
C9
|
B:CLA605
|
4.9
|
59.6
|
1.0
|
CBA
|
B:CLA603
|
4.9
|
44.5
|
1.0
|
CD2
|
B:HIS201
|
4.9
|
53.6
|
1.0
|
CBD
|
B:CLA603
|
4.9
|
59.9
|
1.0
|
C7
|
B:CLA605
|
5.0
|
62.8
|
1.0
|
|
Magnesium binding site 8 out
of 72 in 5ws6
Go back to
Magnesium Binding Sites List in 5ws6
Magnesium binding site 8 out
of 72 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash 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 Two-Flash Dataset within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg604
b:43.4
occ:1.00
|
MG
|
B:CLA604
|
0.0
|
43.4
|
1.0
|
ND
|
B:CLA604
|
2.0
|
43.4
|
1.0
|
NB
|
B:CLA604
|
2.0
|
44.4
|
1.0
|
NC
|
B:CLA604
|
2.1
|
46.4
|
1.0
|
NA
|
B:CLA604
|
2.1
|
43.5
|
1.0
|
NE2
|
B:HIS455
|
2.2
|
46.1
|
1.0
|
C4D
|
B:CLA604
|
3.0
|
44.7
|
1.0
|
C4B
|
B:CLA604
|
3.0
|
42.4
|
1.0
|
C1B
|
B:CLA604
|
3.0
|
46.1
|
1.0
|
C1C
|
B:CLA604
|
3.0
|
43.0
|
1.0
|
C4A
|
B:CLA604
|
3.1
|
44.3
|
1.0
|
C1A
|
B:CLA604
|
3.1
|
38.2
|
1.0
|
C4C
|
B:CLA604
|
3.1
|
35.3
|
1.0
|
CE1
|
B:HIS455
|
3.2
|
54.7
|
1.0
|
CD2
|
B:HIS455
|
3.2
|
44.2
|
1.0
|
C1D
|
B:CLA604
|
3.2
|
46.7
|
1.0
|
CHB
|
B:CLA604
|
3.4
|
50.5
|
1.0
|
CHC
|
B:CLA604
|
3.4
|
39.6
|
1.0
|
CHA
|
B:CLA604
|
3.5
|
44.8
|
1.0
|
CHD
|
B:CLA604
|
3.7
|
45.2
|
1.0
|
C14
|
B:CLA612
|
4.2
|
51.4
|
1.0
|
C3D
|
B:CLA604
|
4.3
|
46.4
|
1.0
|
ND1
|
B:HIS455
|
4.3
|
43.9
|
1.0
|
C3B
|
B:CLA604
|
4.3
|
42.3
|
1.0
|
CG
|
B:HIS455
|
4.3
|
50.7
|
1.0
|
C2B
|
B:CLA604
|
4.4
|
39.6
|
1.0
|
C15
|
B:CLA612
|
4.4
|
57.5
|
1.0
|
C2C
|
B:CLA604
|
4.4
|
41.6
|
1.0
|
C3A
|
B:CLA604
|
4.4
|
49.9
|
1.0
|
C3C
|
B:CLA604
|
4.4
|
44.3
|
1.0
|
C2A
|
B:CLA604
|
4.4
|
46.6
|
1.0
|
C2D
|
B:CLA604
|
4.5
|
44.6
|
1.0
|
C13
|
B:CLA612
|
4.7
|
57.3
|
1.0
|
CBD
|
B:CLA604
|
5.0
|
47.0
|
1.0
|
CE1
|
B:PHE451
|
5.0
|
44.6
|
1.0
|
|
Magnesium binding site 9 out
of 72 in 5ws6
Go back to
Magnesium Binding Sites List in 5ws6
Magnesium binding site 9 out
of 72 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash 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 Two-Flash Dataset within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg605
b:49.0
occ:1.00
|
MG
|
B:CLA605
|
0.0
|
49.0
|
1.0
|
ND
|
B:CLA605
|
2.0
|
47.9
|
1.0
|
NB
|
B:CLA605
|
2.1
|
46.6
|
1.0
|
NC
|
B:CLA605
|
2.1
|
51.3
|
1.0
|
NA
|
B:CLA605
|
2.1
|
49.9
|
1.0
|
NE2
|
B:HIS100
|
2.2
|
48.7
|
1.0
|
C4D
|
B:CLA605
|
3.0
|
44.7
|
1.0
|
C1C
|
B:CLA605
|
3.0
|
41.8
|
1.0
|
C4A
|
B:CLA605
|
3.0
|
43.8
|
1.0
|
C4B
|
B:CLA605
|
3.1
|
47.3
|
1.0
|
C1A
|
B:CLA605
|
3.1
|
45.0
|
1.0
|
C1B
|
B:CLA605
|
3.1
|
48.5
|
1.0
|
CE1
|
B:HIS100
|
3.1
|
48.5
|
1.0
|
C4C
|
B:CLA605
|
3.1
|
48.9
|
1.0
|
CD2
|
B:HIS100
|
3.2
|
43.5
|
1.0
|
C1D
|
B:CLA605
|
3.3
|
53.1
|
1.0
|
CHC
|
B:CLA605
|
3.4
|
45.5
|
1.0
|
CHB
|
B:CLA605
|
3.4
|
39.8
|
1.0
|
CHA
|
B:CLA605
|
3.4
|
45.4
|
1.0
|
CHD
|
B:CLA605
|
3.7
|
44.8
|
1.0
|
C1
|
B:CLA604
|
4.0
|
58.0
|
1.0
|
C3D
|
B:CLA605
|
4.2
|
47.7
|
1.0
|
ND1
|
B:HIS100
|
4.3
|
50.6
|
1.0
|
CG
|
B:HIS100
|
4.4
|
45.1
|
1.0
|
C2C
|
B:CLA605
|
4.4
|
42.4
|
1.0
|
C3B
|
B:CLA605
|
4.4
|
49.6
|
1.0
|
C2B
|
B:CLA605
|
4.4
|
47.7
|
1.0
|
C3A
|
B:CLA605
|
4.4
|
43.2
|
1.0
|
C2A
|
B:CLA605
|
4.4
|
45.0
|
1.0
|
C3C
|
B:CLA605
|
4.4
|
41.0
|
1.0
|
C2
|
B:CLA604
|
4.5
|
64.6
|
1.0
|
C2D
|
B:CLA605
|
4.5
|
46.3
|
1.0
|
CBD
|
B:CLA605
|
4.9
|
49.7
|
1.0
|
O1A
|
B:CLA604
|
4.9
|
51.6
|
1.0
|
|
Magnesium binding site 10 out
of 72 in 5ws6
Go back to
Magnesium Binding Sites List in 5ws6
Magnesium binding site 10 out
of 72 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash 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 Two-Flash Dataset within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg606
b:51.1
occ:1.00
|
MG
|
B:CLA606
|
0.0
|
51.1
|
1.0
|
ND
|
B:CLA606
|
2.0
|
49.1
|
1.0
|
NB
|
B:CLA606
|
2.0
|
46.4
|
1.0
|
NC
|
B:CLA606
|
2.1
|
56.7
|
1.0
|
NA
|
B:CLA606
|
2.1
|
51.8
|
1.0
|
ND1
|
B:HIS157
|
2.2
|
54.2
|
1.0
|
CE1
|
B:HIS157
|
2.8
|
56.7
|
1.0
|
C4D
|
B:CLA606
|
3.0
|
48.1
|
1.0
|
C1C
|
B:CLA606
|
3.0
|
49.1
|
1.0
|
C1B
|
B:CLA606
|
3.0
|
53.0
|
1.0
|
C4B
|
B:CLA606
|
3.0
|
48.4
|
1.0
|
C4A
|
B:CLA606
|
3.1
|
52.5
|
1.0
|
C1A
|
B:CLA606
|
3.1
|
49.7
|
1.0
|
C4C
|
B:CLA606
|
3.1
|
52.2
|
1.0
|
C1D
|
B:CLA606
|
3.3
|
48.7
|
1.0
|
CHB
|
B:CLA606
|
3.4
|
50.3
|
1.0
|
CHC
|
B:CLA606
|
3.4
|
50.5
|
1.0
|
CG
|
B:HIS157
|
3.4
|
52.0
|
1.0
|
CHA
|
B:CLA606
|
3.5
|
49.8
|
1.0
|
CHD
|
B:CLA606
|
3.7
|
54.2
|
1.0
|
C16
|
B:UNL629
|
4.0
|
57.8
|
1.0
|
NE2
|
B:HIS157
|
4.0
|
44.4
|
1.0
|
CB
|
B:HIS157
|
4.0
|
48.9
|
1.0
|
C15
|
B:UNL629
|
4.1
|
61.1
|
1.0
|
C3D
|
B:CLA606
|
4.3
|
52.2
|
1.0
|
C3B
|
B:CLA606
|
4.3
|
55.0
|
1.0
|
CD2
|
B:HIS157
|
4.3
|
41.8
|
1.0
|
C2B
|
B:CLA606
|
4.4
|
47.9
|
1.0
|
C2C
|
B:CLA606
|
4.4
|
49.8
|
1.0
|
C3C
|
B:CLA606
|
4.4
|
48.8
|
1.0
|
C3A
|
B:CLA606
|
4.4
|
49.9
|
1.0
|
C2A
|
B:CLA606
|
4.4
|
50.5
|
1.0
|
C2D
|
B:CLA606
|
4.5
|
47.1
|
1.0
|
C14
|
B:UNL629
|
4.7
|
70.5
|
1.0
|
CBD
|
B:CLA606
|
4.9
|
58.5
|
1.0
|
C17
|
B:UNL629
|
5.0
|
63.2
|
1.0
|
|
Reference:
M.Suga,
F.Akita,
M.Sugahara,
M.Kubo,
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ISSN: ESSN 1476-4687
PubMed: 28219079
DOI: 10.1038/NATURE21400
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