Magnesium in PDB 4ub8: Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser
Enzymatic activity of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser
All present enzymatic activity of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser:
1.10.3.9;
Protein crystallography data
The structure of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser, PDB code: 4ub8
was solved by
M.Suga,
F.Akita,
K.Hirata,
G.Ueno,
H.Murakami,
Y.Nakajima,
T.Shimizu,
K.Yamashita,
M.Yamamoto,
H.Ago,
J.R.Shen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
61.90 /
1.95
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
123.807,
230.001,
288.502,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.8 /
22.5
|
Other elements in 4ub8:
The structure of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser also contains other interesting chemical elements:
Magnesium Binding Sites:
Magnesium binding site 1 out
of 72 in 4ub8
Go back to
Magnesium Binding Sites List in 4ub8
Magnesium binding site 1 out
of 72 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg405
b:18.8
occ:1.00
|
MG
|
A:CLA405
|
0.0
|
18.8
|
1.0
|
ND
|
A:CLA405
|
2.0
|
15.5
|
1.0
|
NB
|
A:CLA405
|
2.0
|
18.2
|
1.0
|
NC
|
A:CLA405
|
2.1
|
15.3
|
1.0
|
NA
|
A:CLA405
|
2.1
|
23.3
|
1.0
|
NE2
|
A:HIS198
|
2.2
|
18.3
|
1.0
|
C4D
|
A:CLA405
|
3.0
|
15.8
|
1.0
|
C4B
|
A:CLA405
|
3.0
|
15.3
|
1.0
|
C1B
|
A:CLA405
|
3.0
|
15.3
|
1.0
|
C1C
|
A:CLA405
|
3.1
|
15.3
|
1.0
|
C4A
|
A:CLA405
|
3.1
|
18.4
|
1.0
|
C1A
|
A:CLA405
|
3.1
|
15.6
|
1.0
|
C4C
|
A:CLA405
|
3.2
|
18.1
|
1.0
|
CE1
|
A:HIS198
|
3.2
|
15.9
|
1.0
|
C1D
|
A:CLA405
|
3.2
|
15.5
|
1.0
|
CD2
|
A:HIS198
|
3.3
|
16.1
|
1.0
|
CHC
|
A:CLA405
|
3.4
|
16.8
|
1.0
|
CHB
|
A:CLA405
|
3.4
|
15.6
|
1.0
|
CHA
|
A:CLA405
|
3.5
|
18.5
|
1.0
|
CHD
|
A:CLA405
|
3.6
|
15.5
|
1.0
|
CE
|
A:MET183
|
4.0
|
14.9
|
1.0
|
C3D
|
A:CLA405
|
4.3
|
16.3
|
1.0
|
ND1
|
A:HIS198
|
4.3
|
17.4
|
1.0
|
C3B
|
A:CLA405
|
4.3
|
15.2
|
1.0
|
CAB
|
D:CLA403
|
4.4
|
15.4
|
1.0
|
C2B
|
A:CLA405
|
4.4
|
20.2
|
1.0
|
CG
|
A:HIS198
|
4.4
|
16.3
|
1.0
|
C2C
|
A:CLA405
|
4.4
|
15.2
|
1.0
|
C3A
|
A:CLA405
|
4.4
|
16.9
|
1.0
|
C2D
|
A:CLA405
|
4.4
|
18.9
|
1.0
|
C2A
|
A:CLA405
|
4.5
|
16.1
|
1.0
|
C3C
|
A:CLA405
|
4.5
|
15.7
|
1.0
|
CBD
|
A:CLA405
|
5.0
|
15.7
|
1.0
|
|
Magnesium binding site 2 out
of 72 in 4ub8
Go back to
Magnesium Binding Sites List in 4ub8
Magnesium binding site 2 out
of 72 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg406
b:17.9
occ:1.00
|
MG
|
A:CLA406
|
0.0
|
17.9
|
1.0
|
NB
|
A:CLA406
|
2.0
|
16.9
|
1.0
|
ND
|
A:CLA406
|
2.0
|
17.6
|
1.0
|
NC
|
A:CLA406
|
2.1
|
18.0
|
1.0
|
NA
|
A:CLA406
|
2.1
|
20.2
|
1.0
|
O
|
A:HOH612
|
2.2
|
20.7
|
1.0
|
C4D
|
A:CLA406
|
3.0
|
16.5
|
1.0
|
C4B
|
A:CLA406
|
3.0
|
16.8
|
1.0
|
C1C
|
A:CLA406
|
3.0
|
21.3
|
1.0
|
C1B
|
A:CLA406
|
3.0
|
17.2
|
1.0
|
C4A
|
A:CLA406
|
3.1
|
17.2
|
1.0
|
C1A
|
A:CLA406
|
3.1
|
17.0
|
1.0
|
C4C
|
A:CLA406
|
3.1
|
16.7
|
1.0
|
C1D
|
A:CLA406
|
3.3
|
16.1
|
1.0
|
CHC
|
A:CLA406
|
3.4
|
16.5
|
1.0
|
CHB
|
A:CLA406
|
3.4
|
22.1
|
1.0
|
CHA
|
A:CLA406
|
3.4
|
16.8
|
1.0
|
CHD
|
A:CLA406
|
3.7
|
15.9
|
1.0
|
CBB
|
A:PHO408
|
3.9
|
26.8
|
1.0
|
O
|
A:HOH512
|
4.2
|
16.8
|
1.0
|
C3D
|
A:CLA406
|
4.3
|
16.4
|
1.0
|
C3B
|
A:CLA406
|
4.3
|
17.5
|
1.0
|
C2C
|
A:CLA406
|
4.4
|
17.5
|
1.0
|
C2B
|
A:CLA406
|
4.4
|
17.3
|
1.0
|
C2A
|
A:CLA406
|
4.4
|
17.3
|
1.0
|
C3A
|
A:CLA406
|
4.4
|
20.0
|
1.0
|
C3C
|
A:CLA406
|
4.4
|
22.5
|
1.0
|
C2D
|
A:CLA406
|
4.5
|
16.1
|
1.0
|
CG2
|
D:ILE178
|
4.6
|
16.2
|
1.0
|
CE1
|
A:PHE206
|
4.8
|
19.8
|
1.0
|
C20
|
A:PHO408
|
4.9
|
17.4
|
1.0
|
CBA
|
A:CLA406
|
4.9
|
17.1
|
1.0
|
CBD
|
A:CLA406
|
4.9
|
16.9
|
1.0
|
CG1
|
D:ILE178
|
4.9
|
18.6
|
1.0
|
|
Magnesium binding site 3 out
of 72 in 4ub8
Go back to
Magnesium Binding Sites List in 4ub8
Magnesium binding site 3 out
of 72 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg409
b:22.9
occ:1.00
|
MG
|
A:CLA409
|
0.0
|
22.9
|
1.0
|
ND
|
A:CLA409
|
2.0
|
27.8
|
1.0
|
NB
|
A:CLA409
|
2.0
|
20.7
|
1.0
|
NA
|
A:CLA409
|
2.1
|
27.2
|
1.0
|
NC
|
A:CLA409
|
2.1
|
27.6
|
1.0
|
NE2
|
A:HIS118
|
2.2
|
24.6
|
1.0
|
C4D
|
A:CLA409
|
3.0
|
25.6
|
1.0
|
C4A
|
A:CLA409
|
3.0
|
20.7
|
1.0
|
C4B
|
A:CLA409
|
3.0
|
30.3
|
1.0
|
C1B
|
A:CLA409
|
3.0
|
23.4
|
1.0
|
C1A
|
A:CLA409
|
3.1
|
21.6
|
1.0
|
C1C
|
A:CLA409
|
3.1
|
23.1
|
1.0
|
CE1
|
A:HIS118
|
3.1
|
27.7
|
1.0
|
C4C
|
A:CLA409
|
3.1
|
24.9
|
1.0
|
C1D
|
A:CLA409
|
3.2
|
23.6
|
1.0
|
CD2
|
A:HIS118
|
3.3
|
22.1
|
1.0
|
CHB
|
A:CLA409
|
3.4
|
23.5
|
1.0
|
CHC
|
A:CLA409
|
3.4
|
27.6
|
1.0
|
CHA
|
A:CLA409
|
3.5
|
23.4
|
1.0
|
CHD
|
A:CLA409
|
3.7
|
19.8
|
1.0
|
ND1
|
A:HIS118
|
4.2
|
19.8
|
1.0
|
C3D
|
A:CLA409
|
4.3
|
24.5
|
1.0
|
C3B
|
A:CLA409
|
4.3
|
24.2
|
1.0
|
C3A
|
A:CLA409
|
4.4
|
26.3
|
1.0
|
CG
|
A:HIS118
|
4.4
|
27.8
|
1.0
|
C2B
|
A:CLA409
|
4.4
|
30.9
|
1.0
|
C2A
|
A:CLA409
|
4.4
|
20.0
|
1.0
|
C2C
|
A:CLA409
|
4.4
|
24.9
|
1.0
|
C3C
|
A:CLA409
|
4.4
|
20.0
|
1.0
|
CG1
|
I:VAL8
|
4.5
|
24.9
|
1.0
|
C2D
|
A:CLA409
|
4.5
|
22.5
|
1.0
|
CG2
|
I:VAL12
|
4.5
|
22.1
|
1.0
|
CBD
|
A:CLA409
|
4.9
|
25.2
|
1.0
|
CMA
|
A:CLA409
|
5.0
|
25.5
|
1.0
|
|
Magnesium binding site 4 out
of 72 in 4ub8
Go back to
Magnesium Binding Sites List in 4ub8
Magnesium binding site 4 out
of 72 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg602
b:34.5
occ:1.00
|
MG
|
B:CLA602
|
0.0
|
34.5
|
1.0
|
ND
|
B:CLA602
|
2.0
|
33.9
|
1.0
|
NB
|
B:CLA602
|
2.0
|
41.9
|
1.0
|
NC
|
B:CLA602
|
2.1
|
36.4
|
1.0
|
NA
|
B:CLA602
|
2.1
|
38.7
|
1.0
|
O
|
B:HOH884
|
2.2
|
32.5
|
1.0
|
C4D
|
B:CLA602
|
3.0
|
37.4
|
1.0
|
C1C
|
B:CLA602
|
3.0
|
33.8
|
1.0
|
C4B
|
B:CLA602
|
3.0
|
35.5
|
1.0
|
C1B
|
B:CLA602
|
3.0
|
38.6
|
1.0
|
C4A
|
B:CLA602
|
3.0
|
45.4
|
1.0
|
C1A
|
B:CLA602
|
3.1
|
42.8
|
1.0
|
C4C
|
B:CLA602
|
3.1
|
34.2
|
1.0
|
C1D
|
B:CLA602
|
3.3
|
29.2
|
1.0
|
C10
|
B:CLA602
|
3.3
|
60.6
|
1.0
|
CHC
|
B:CLA602
|
3.4
|
32.6
|
1.0
|
CHB
|
B:CLA602
|
3.4
|
27.1
|
1.0
|
CHA
|
B:CLA602
|
3.5
|
39.7
|
1.0
|
CHD
|
B:CLA602
|
3.7
|
28.1
|
1.0
|
C8
|
B:CLA602
|
4.1
|
53.4
|
1.0
|
C3D
|
B:CLA602
|
4.3
|
37.3
|
1.0
|
O
|
B:TRP185
|
4.3
|
37.9
|
1.0
|
C12
|
B:CLA602
|
4.3
|
35.6
|
1.0
|
CE2
|
B:PHE190
|
4.3
|
31.0
|
1.0
|
C3B
|
B:CLA602
|
4.3
|
32.9
|
1.0
|
C2B
|
B:CLA602
|
4.4
|
32.1
|
1.0
|
C2C
|
B:CLA602
|
4.4
|
25.5
|
1.0
|
C3A
|
B:CLA602
|
4.4
|
33.2
|
1.0
|
C2A
|
B:CLA602
|
4.4
|
29.6
|
1.0
|
C3C
|
B:CLA602
|
4.4
|
34.6
|
1.0
|
C11
|
B:CLA602
|
4.4
|
54.7
|
1.0
|
C2D
|
B:CLA602
|
4.5
|
39.1
|
1.0
|
CBB
|
B:CLA603
|
4.6
|
31.8
|
1.0
|
CZ
|
B:PHE190
|
4.6
|
28.8
|
1.0
|
O
|
B:HOH885
|
4.8
|
27.4
|
1.0
|
CBD
|
B:CLA602
|
4.9
|
47.5
|
1.0
|
|
Magnesium binding site 5 out
of 72 in 4ub8
Go back to
Magnesium Binding Sites List in 4ub8
Magnesium binding site 5 out
of 72 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg603
b:27.0
occ:1.00
|
MG
|
B:CLA603
|
0.0
|
27.0
|
1.0
|
ND
|
B:CLA603
|
2.0
|
21.4
|
1.0
|
NB
|
B:CLA603
|
2.0
|
26.8
|
1.0
|
NC
|
B:CLA603
|
2.1
|
28.5
|
1.0
|
NA
|
B:CLA603
|
2.1
|
28.1
|
1.0
|
ND1
|
B:HIS201
|
2.2
|
31.1
|
1.0
|
CE1
|
B:HIS201
|
3.0
|
28.0
|
1.0
|
C4D
|
B:CLA603
|
3.0
|
27.0
|
1.0
|
C1C
|
B:CLA603
|
3.0
|
23.1
|
1.0
|
C4A
|
B:CLA603
|
3.0
|
27.4
|
1.0
|
C1B
|
B:CLA603
|
3.0
|
32.0
|
1.0
|
C4B
|
B:CLA603
|
3.0
|
28.5
|
1.0
|
C1A
|
B:CLA603
|
3.1
|
28.0
|
1.0
|
C4C
|
B:CLA603
|
3.1
|
23.1
|
1.0
|
C1D
|
B:CLA603
|
3.2
|
21.6
|
1.0
|
CG
|
B:HIS201
|
3.3
|
32.8
|
1.0
|
CHB
|
B:CLA603
|
3.4
|
30.8
|
1.0
|
CHC
|
B:CLA603
|
3.4
|
29.8
|
1.0
|
CHA
|
B:CLA603
|
3.5
|
20.7
|
1.0
|
CHD
|
B:CLA603
|
3.7
|
23.6
|
1.0
|
CB
|
B:HIS201
|
3.8
|
31.4
|
1.0
|
CZ
|
H:PHE41
|
3.9
|
35.1
|
1.0
|
NE2
|
B:HIS201
|
4.2
|
33.3
|
1.0
|
C3D
|
B:CLA603
|
4.3
|
22.6
|
1.0
|
C3B
|
B:CLA603
|
4.4
|
25.8
|
1.0
|
CD2
|
B:HIS201
|
4.4
|
23.5
|
1.0
|
C2C
|
B:CLA603
|
4.4
|
23.4
|
1.0
|
C2B
|
B:CLA603
|
4.4
|
31.2
|
1.0
|
CE2
|
H:PHE41
|
4.4
|
35.0
|
1.0
|
C3A
|
B:CLA603
|
4.4
|
21.4
|
1.0
|
C2A
|
B:CLA603
|
4.4
|
24.4
|
1.0
|
CA
|
B:HIS201
|
4.4
|
29.7
|
1.0
|
C3C
|
B:CLA603
|
4.4
|
27.8
|
1.0
|
C2D
|
B:CLA603
|
4.5
|
20.8
|
1.0
|
CE1
|
H:PHE41
|
4.9
|
25.3
|
1.0
|
CBD
|
B:CLA603
|
5.0
|
22.8
|
1.0
|
CMA
|
B:CLA603
|
5.0
|
21.2
|
1.0
|
|
Magnesium binding site 6 out
of 72 in 4ub8
Go back to
Magnesium Binding Sites List in 4ub8
Magnesium binding site 6 out
of 72 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg604
b:26.1
occ:1.00
|
MG
|
B:CLA604
|
0.0
|
26.1
|
1.0
|
ND
|
B:CLA604
|
2.0
|
26.0
|
1.0
|
NB
|
B:CLA604
|
2.0
|
23.7
|
1.0
|
NA
|
B:CLA604
|
2.1
|
23.9
|
1.0
|
NC
|
B:CLA604
|
2.1
|
25.6
|
1.0
|
NE2
|
B:HIS202
|
2.2
|
23.5
|
1.0
|
C4D
|
B:CLA604
|
3.0
|
24.9
|
1.0
|
C4B
|
B:CLA604
|
3.0
|
21.5
|
1.0
|
C1B
|
B:CLA604
|
3.0
|
23.5
|
1.0
|
C1C
|
B:CLA604
|
3.0
|
27.4
|
1.0
|
C4A
|
B:CLA604
|
3.1
|
19.4
|
1.0
|
C1A
|
B:CLA604
|
3.1
|
25.1
|
1.0
|
CE1
|
B:HIS202
|
3.1
|
27.0
|
1.0
|
C4C
|
B:CLA604
|
3.2
|
29.7
|
1.0
|
CD2
|
B:HIS202
|
3.2
|
24.0
|
1.0
|
C1D
|
B:CLA604
|
3.3
|
23.8
|
1.0
|
CHC
|
B:CLA604
|
3.4
|
28.1
|
1.0
|
CHB
|
B:CLA604
|
3.4
|
19.6
|
1.0
|
CHA
|
B:CLA604
|
3.5
|
20.7
|
1.0
|
CHD
|
B:CLA604
|
3.7
|
25.0
|
1.0
|
ND1
|
B:HIS202
|
4.3
|
24.2
|
1.0
|
C3D
|
B:CLA604
|
4.3
|
27.2
|
1.0
|
C3B
|
B:CLA604
|
4.3
|
24.9
|
1.0
|
CG
|
B:HIS202
|
4.3
|
25.7
|
1.0
|
C2B
|
B:CLA604
|
4.4
|
27.7
|
1.0
|
C2A
|
B:CLA604
|
4.4
|
26.4
|
1.0
|
C2C
|
B:CLA604
|
4.4
|
27.4
|
1.0
|
C3A
|
B:CLA604
|
4.4
|
23.9
|
1.0
|
C3C
|
B:CLA604
|
4.5
|
29.4
|
1.0
|
C2D
|
B:CLA604
|
4.5
|
24.0
|
1.0
|
C5
|
B:CLA606
|
4.6
|
25.3
|
1.0
|
C4
|
B:CLA606
|
4.7
|
29.0
|
1.0
|
C7
|
B:CLA606
|
4.7
|
26.4
|
1.0
|
C6
|
B:CLA606
|
4.7
|
24.8
|
1.0
|
NE2
|
B:HIS201
|
4.8
|
33.3
|
1.0
|
CD2
|
B:HIS201
|
4.9
|
23.5
|
1.0
|
CBA
|
B:CLA604
|
4.9
|
25.5
|
1.0
|
CBD
|
B:CLA604
|
4.9
|
32.0
|
1.0
|
C3
|
B:CLA606
|
5.0
|
33.2
|
1.0
|
C9
|
B:CLA606
|
5.0
|
33.7
|
1.0
|
|
Magnesium binding site 7 out
of 72 in 4ub8
Go back to
Magnesium Binding Sites List in 4ub8
Magnesium binding site 7 out
of 72 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg605
b:18.9
occ:1.00
|
MG
|
B:CLA605
|
0.0
|
18.9
|
1.0
|
ND
|
B:CLA605
|
2.0
|
16.4
|
1.0
|
NB
|
B:CLA605
|
2.0
|
21.1
|
1.0
|
NC
|
B:CLA605
|
2.1
|
21.8
|
1.0
|
NA
|
B:CLA605
|
2.1
|
28.5
|
1.0
|
NE2
|
B:HIS455
|
2.2
|
25.2
|
1.0
|
C4D
|
B:CLA605
|
3.0
|
19.1
|
1.0
|
C4B
|
B:CLA605
|
3.0
|
23.0
|
1.0
|
C1B
|
B:CLA605
|
3.0
|
18.4
|
1.0
|
C4A
|
B:CLA605
|
3.1
|
17.9
|
1.0
|
C1C
|
B:CLA605
|
3.1
|
17.2
|
1.0
|
C1A
|
B:CLA605
|
3.1
|
16.0
|
1.0
|
C4C
|
B:CLA605
|
3.1
|
15.7
|
1.0
|
CD2
|
B:HIS455
|
3.2
|
17.7
|
1.0
|
CE1
|
B:HIS455
|
3.2
|
19.4
|
1.0
|
C1D
|
B:CLA605
|
3.2
|
16.2
|
1.0
|
CHB
|
B:CLA605
|
3.4
|
17.4
|
1.0
|
CHC
|
B:CLA605
|
3.4
|
20.6
|
1.0
|
CHA
|
B:CLA605
|
3.5
|
19.4
|
1.0
|
CHD
|
B:CLA605
|
3.7
|
16.2
|
1.0
|
C3D
|
B:CLA605
|
4.2
|
16.6
|
1.0
|
ND1
|
B:HIS455
|
4.3
|
24.1
|
1.0
|
CG
|
B:HIS455
|
4.3
|
28.9
|
1.0
|
C3B
|
B:CLA605
|
4.3
|
18.3
|
1.0
|
C2B
|
B:CLA605
|
4.4
|
22.2
|
1.0
|
C2C
|
B:CLA605
|
4.4
|
18.6
|
1.0
|
C3A
|
B:CLA605
|
4.4
|
19.6
|
1.0
|
C3C
|
B:CLA605
|
4.5
|
20.6
|
1.0
|
C14
|
B:CLA613
|
4.5
|
33.1
|
1.0
|
C2D
|
B:CLA605
|
4.5
|
19.8
|
1.0
|
C2A
|
B:CLA605
|
4.5
|
20.8
|
1.0
|
C15
|
B:CLA613
|
4.9
|
20.4
|
1.0
|
CBD
|
B:CLA605
|
5.0
|
24.0
|
1.0
|
C13
|
B:CLA613
|
5.0
|
25.3
|
1.0
|
|
Magnesium binding site 8 out
of 72 in 4ub8
Go back to
Magnesium Binding Sites List in 4ub8
Magnesium binding site 8 out
of 72 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg606
b:22.9
occ:1.00
|
MG
|
B:CLA606
|
0.0
|
22.9
|
1.0
|
ND
|
B:CLA606
|
2.0
|
16.6
|
1.0
|
NB
|
B:CLA606
|
2.0
|
17.7
|
1.0
|
NC
|
B:CLA606
|
2.1
|
23.1
|
1.0
|
NA
|
B:CLA606
|
2.1
|
22.0
|
1.0
|
NE2
|
B:HIS100
|
2.2
|
16.9
|
1.0
|
C4D
|
B:CLA606
|
3.0
|
16.7
|
1.0
|
C4B
|
B:CLA606
|
3.0
|
28.0
|
1.0
|
C1C
|
B:CLA606
|
3.0
|
22.2
|
1.0
|
C4A
|
B:CLA606
|
3.1
|
17.6
|
1.0
|
C1B
|
B:CLA606
|
3.1
|
26.4
|
1.0
|
C1A
|
B:CLA606
|
3.1
|
17.7
|
1.0
|
CE1
|
B:HIS100
|
3.1
|
21.1
|
1.0
|
C4C
|
B:CLA606
|
3.2
|
21.1
|
1.0
|
C1D
|
B:CLA606
|
3.3
|
26.3
|
1.0
|
CD2
|
B:HIS100
|
3.3
|
17.8
|
1.0
|
CHB
|
B:CLA606
|
3.4
|
18.3
|
1.0
|
CHC
|
B:CLA606
|
3.4
|
17.8
|
1.0
|
CHA
|
B:CLA606
|
3.5
|
20.6
|
1.0
|
CHD
|
B:CLA606
|
3.7
|
17.5
|
1.0
|
C2
|
B:CLA605
|
4.2
|
36.3
|
1.0
|
C3D
|
B:CLA606
|
4.3
|
16.1
|
1.0
|
ND1
|
B:HIS100
|
4.3
|
21.0
|
1.0
|
C1
|
B:CLA605
|
4.3
|
42.6
|
1.0
|
C3B
|
B:CLA606
|
4.4
|
26.2
|
1.0
|
CG
|
B:HIS100
|
4.4
|
18.4
|
1.0
|
C2B
|
B:CLA606
|
4.4
|
18.5
|
1.0
|
C2C
|
B:CLA606
|
4.4
|
19.7
|
1.0
|
C3A
|
B:CLA606
|
4.4
|
17.7
|
1.0
|
C2A
|
B:CLA606
|
4.4
|
18.0
|
1.0
|
C3C
|
B:CLA606
|
4.5
|
21.3
|
1.0
|
C2D
|
B:CLA606
|
4.5
|
16.0
|
1.0
|
CBD
|
B:CLA606
|
4.9
|
25.5
|
1.0
|
|
Magnesium binding site 9 out
of 72 in 4ub8
Go back to
Magnesium Binding Sites List in 4ub8
Magnesium binding site 9 out
of 72 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg607
b:23.1
occ:1.00
|
MG
|
B:CLA607
|
0.0
|
23.1
|
1.0
|
ND
|
B:CLA607
|
2.0
|
29.8
|
1.0
|
NB
|
B:CLA607
|
2.0
|
27.4
|
1.0
|
NC
|
B:CLA607
|
2.1
|
24.7
|
1.0
|
NA
|
B:CLA607
|
2.1
|
29.2
|
1.0
|
ND1
|
B:HIS157
|
2.2
|
26.1
|
1.0
|
CE1
|
B:HIS157
|
2.9
|
24.6
|
1.0
|
C4D
|
B:CLA607
|
3.0
|
30.4
|
1.0
|
C4B
|
B:CLA607
|
3.0
|
22.6
|
1.0
|
C1B
|
B:CLA607
|
3.0
|
22.8
|
1.0
|
C1C
|
B:CLA607
|
3.1
|
21.2
|
1.0
|
C4A
|
B:CLA607
|
3.1
|
20.7
|
1.0
|
C1A
|
B:CLA607
|
3.1
|
25.7
|
1.0
|
C4C
|
B:CLA607
|
3.2
|
21.7
|
1.0
|
C1D
|
B:CLA607
|
3.3
|
25.1
|
1.0
|
CHB
|
B:CLA607
|
3.4
|
27.1
|
1.0
|
CG
|
B:HIS157
|
3.4
|
28.8
|
1.0
|
CHC
|
B:CLA607
|
3.4
|
26.3
|
1.0
|
CHA
|
B:CLA607
|
3.5
|
24.2
|
1.0
|
CHD
|
B:CLA607
|
3.7
|
23.5
|
1.0
|
CB
|
B:HIS157
|
3.9
|
22.7
|
1.0
|
C15
|
B:UNL632
|
4.0
|
44.5
|
1.0
|
C16
|
B:UNL632
|
4.0
|
39.6
|
1.0
|
NE2
|
B:HIS157
|
4.2
|
24.3
|
1.0
|
C3D
|
B:CLA607
|
4.3
|
31.7
|
1.0
|
C3B
|
B:CLA607
|
4.3
|
25.9
|
1.0
|
C14
|
B:UNL632
|
4.3
|
42.8
|
1.0
|
C2B
|
B:CLA607
|
4.4
|
23.3
|
1.0
|
CD2
|
B:HIS157
|
4.4
|
24.4
|
1.0
|
C2C
|
B:CLA607
|
4.4
|
21.8
|
1.0
|
C3A
|
B:CLA607
|
4.4
|
19.0
|
1.0
|
C2A
|
B:CLA607
|
4.4
|
23.5
|
1.0
|
C3C
|
B:CLA607
|
4.5
|
22.1
|
1.0
|
C2D
|
B:CLA607
|
4.5
|
31.8
|
1.0
|
C13
|
B:UNL632
|
4.6
|
43.7
|
1.0
|
CBD
|
B:CLA607
|
4.9
|
33.0
|
1.0
|
CD
|
B:PRO164
|
5.0
|
30.9
|
1.0
|
|
Magnesium binding site 10 out
of 72 in 4ub8
Go back to
Magnesium Binding Sites List in 4ub8
Magnesium binding site 10 out
of 72 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg608
b:22.1
occ:1.00
|
MG
|
B:CLA608
|
0.0
|
22.1
|
1.0
|
ND
|
B:CLA608
|
2.0
|
22.3
|
1.0
|
NB
|
B:CLA608
|
2.0
|
20.0
|
1.0
|
NC
|
B:CLA608
|
2.1
|
24.0
|
1.0
|
NA
|
B:CLA608
|
2.1
|
18.1
|
1.0
|
O
|
B:HOH880
|
2.2
|
15.6
|
1.0
|
C4D
|
B:CLA608
|
3.0
|
25.0
|
1.0
|
C1B
|
B:CLA608
|
3.0
|
18.9
|
1.0
|
C4B
|
B:CLA608
|
3.1
|
22.5
|
1.0
|
C4A
|
B:CLA608
|
3.1
|
14.0
|
1.0
|
C1C
|
B:CLA608
|
3.1
|
18.1
|
1.0
|
C1A
|
B:CLA608
|
3.1
|
20.1
|
1.0
|
C4C
|
B:CLA608
|
3.1
|
22.2
|
1.0
|
C1D
|
B:CLA608
|
3.2
|
26.3
|
1.0
|
CHB
|
B:CLA608
|
3.4
|
14.1
|
1.0
|
C12
|
B:LMG621
|
3.4
|
36.9
|
1.0
|
CHC
|
B:CLA608
|
3.5
|
14.5
|
1.0
|
CHA
|
B:CLA608
|
3.5
|
13.7
|
1.0
|
CHD
|
B:CLA608
|
3.6
|
21.3
|
1.0
|
C14
|
B:LMG621
|
4.2
|
30.0
|
1.0
|
C3D
|
B:CLA608
|
4.3
|
19.9
|
1.0
|
O
|
B:HOH723
|
4.3
|
18.1
|
1.0
|
C13
|
B:LMG621
|
4.4
|
29.9
|
1.0
|
C2B
|
B:CLA608
|
4.4
|
24.1
|
1.0
|
C3B
|
B:CLA608
|
4.4
|
22.1
|
1.0
|
C2C
|
B:CLA608
|
4.4
|
17.4
|
1.0
|
C3C
|
B:CLA608
|
4.4
|
15.0
|
1.0
|
C3A
|
B:CLA608
|
4.4
|
14.8
|
1.0
|
C2A
|
B:CLA608
|
4.5
|
14.3
|
1.0
|
C2D
|
B:CLA608
|
4.5
|
20.1
|
1.0
|
SD
|
B:MET37
|
4.5
|
20.5
|
1.0
|
C11
|
B:LMG621
|
4.5
|
31.8
|
1.0
|
O9
|
B:LMG621
|
4.6
|
49.9
|
1.0
|
CD2
|
B:PHE61
|
4.6
|
17.9
|
1.0
|
CE
|
B:MET37
|
4.7
|
17.7
|
1.0
|
CB
|
B:PHE61
|
4.8
|
21.8
|
1.0
|
CG
|
B:PHE61
|
4.9
|
17.5
|
1.0
|
C10
|
B:LMG621
|
4.9
|
41.6
|
1.0
|
CBA
|
B:CLA608
|
4.9
|
19.7
|
1.0
|
CBD
|
B:CLA608
|
5.0
|
18.7
|
1.0
|
|
Reference:
M.Suga,
F.Akita,
K.Hirata,
G.Ueno,
H.Murakami,
Y.Nakajima,
T.Shimizu,
K.Yamashita,
M.Yamamoto,
H.Ago,
J.R.Shen.
Native Structure of Photosystem II at 1.95A Nature 2014.
ISSN: ESSN 1476-4687
DOI: 10.1038/NATURE13991
Page generated: Tue Aug 20 04:35:07 2024
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