Magnesium in PDB 6jlp: Xfel Structure of Cyanobacterial Photosystem II (3F State, DATASET2)
Enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II (3F State, DATASET2)
All present enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II (3F State, DATASET2):
1.10.3.9;
Protein crystallography data
The structure of Xfel Structure of Cyanobacterial Photosystem II (3F State, DATASET2), PDB code: 6jlp
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)
|
19.99 /
2.50
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
122.040,
228.840,
286.980,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15.1 /
21.1
|
Other elements in 6jlp:
The structure of Xfel Structure of Cyanobacterial Photosystem II (3F State, DATASET2) also contains other interesting chemical elements:
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
30;
Page 4, Binding sites: 31 -
40;
Page 5, Binding sites: 41 -
50;
Page 6, Binding sites: 51 -
60;
Page 7, Binding sites: 61 -
70;
Page 8, Binding sites: 71 -
72;
Binding sites:
The binding sites of Magnesium atom in the Xfel Structure of Cyanobacterial Photosystem II (3F State, DATASET2)
(pdb code 6jlp). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 72 binding sites of Magnesium where determined in the
Xfel Structure of Cyanobacterial Photosystem II (3F State, DATASET2), PDB code: 6jlp:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 72 in 6jlp
Go back to
Magnesium Binding Sites List in 6jlp
Magnesium binding site 1 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II (3F State, DATASET2)
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 (3F State, DATASET2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg404
b:43.5
occ:1.00
|
MG
|
A:CLA404
|
0.0
|
43.5
|
1.0
|
ND
|
A:CLA404
|
2.0
|
34.5
|
1.0
|
NB
|
A:CLA404
|
2.0
|
41.3
|
1.0
|
NA
|
A:CLA404
|
2.1
|
40.4
|
1.0
|
NC
|
A:CLA404
|
2.1
|
38.1
|
1.0
|
NE2
|
A:HIS198
|
2.2
|
48.6
|
1.0
|
C4D
|
A:CLA404
|
3.0
|
36.7
|
1.0
|
CE1
|
A:HIS198
|
3.0
|
43.2
|
1.0
|
C1C
|
A:CLA404
|
3.0
|
36.8
|
1.0
|
C4B
|
A:CLA404
|
3.0
|
34.4
|
1.0
|
C1A
|
A:CLA404
|
3.0
|
36.6
|
1.0
|
C4A
|
A:CLA404
|
3.0
|
42.6
|
1.0
|
C1B
|
A:CLA404
|
3.1
|
41.0
|
1.0
|
C4C
|
A:CLA404
|
3.2
|
34.3
|
1.0
|
C1D
|
A:CLA404
|
3.3
|
34.5
|
1.0
|
CD2
|
A:HIS198
|
3.4
|
44.7
|
1.0
|
CHC
|
A:CLA404
|
3.4
|
34.3
|
1.0
|
CHB
|
A:CLA404
|
3.4
|
34.8
|
1.0
|
CHA
|
A:CLA404
|
3.4
|
34.8
|
1.0
|
CHD
|
A:CLA404
|
3.7
|
39.2
|
1.0
|
CE
|
A:MET183
|
3.9
|
37.5
|
1.0
|
ND1
|
A:HIS198
|
4.2
|
46.7
|
1.0
|
C3D
|
A:CLA404
|
4.3
|
37.0
|
1.0
|
CAB
|
D:CLA406
|
4.3
|
43.9
|
1.0
|
C3B
|
A:CLA404
|
4.3
|
36.0
|
1.0
|
C2C
|
A:CLA404
|
4.4
|
46.6
|
1.0
|
C2B
|
A:CLA404
|
4.4
|
34.6
|
1.0
|
C2A
|
A:CLA404
|
4.4
|
36.7
|
1.0
|
CG
|
A:HIS198
|
4.4
|
47.9
|
1.0
|
C3A
|
A:CLA404
|
4.4
|
35.0
|
1.0
|
C3C
|
A:CLA404
|
4.4
|
34.2
|
1.0
|
C2D
|
A:CLA404
|
4.5
|
40.4
|
1.0
|
CBD
|
A:CLA404
|
4.9
|
47.8
|
1.0
|
|
Magnesium binding site 2 out
of 72 in 6jlp
Go back to
Magnesium Binding Sites List in 6jlp
Magnesium binding site 2 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II (3F State, DATASET2)
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 (3F State, DATASET2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg405
b:38.2
occ:1.00
|
MG
|
A:CLA405
|
0.0
|
38.2
|
1.0
|
ND
|
A:CLA405
|
2.0
|
34.3
|
1.0
|
NB
|
A:CLA405
|
2.0
|
39.2
|
1.0
|
NC
|
A:CLA405
|
2.1
|
42.7
|
1.0
|
NA
|
A:CLA405
|
2.1
|
38.1
|
1.0
|
O
|
A:HOH624
|
2.2
|
38.9
|
1.0
|
C4D
|
A:CLA405
|
3.0
|
34.3
|
1.0
|
C1C
|
A:CLA405
|
3.0
|
41.4
|
1.0
|
C4B
|
A:CLA405
|
3.0
|
37.5
|
1.0
|
C4A
|
A:CLA405
|
3.0
|
45.2
|
1.0
|
C1B
|
A:CLA405
|
3.0
|
38.9
|
1.0
|
C1A
|
A:CLA405
|
3.0
|
35.7
|
1.0
|
C4C
|
A:CLA405
|
3.1
|
39.8
|
1.0
|
C1D
|
A:CLA405
|
3.3
|
43.7
|
1.0
|
CHB
|
A:CLA405
|
3.4
|
33.5
|
1.0
|
CHC
|
A:CLA405
|
3.4
|
37.9
|
1.0
|
CHA
|
A:CLA405
|
3.4
|
38.8
|
1.0
|
CHD
|
A:CLA405
|
3.7
|
32.7
|
1.0
|
CBB
|
D:PHO402
|
3.9
|
46.3
|
1.0
|
O
|
A:HOH591
|
4.2
|
42.4
|
1.0
|
C3D
|
A:CLA405
|
4.2
|
35.0
|
1.0
|
C3B
|
A:CLA405
|
4.3
|
39.7
|
1.0
|
C2B
|
A:CLA405
|
4.4
|
41.1
|
1.0
|
CG2
|
A:THR179
|
4.4
|
32.3
|
1.0
|
C2C
|
A:CLA405
|
4.4
|
38.2
|
1.0
|
C2A
|
A:CLA405
|
4.4
|
44.1
|
1.0
|
C3A
|
A:CLA405
|
4.4
|
43.5
|
1.0
|
C3C
|
A:CLA405
|
4.4
|
38.3
|
1.0
|
C2D
|
A:CLA405
|
4.5
|
40.1
|
1.0
|
OG1
|
A:THR179
|
4.7
|
38.2
|
1.0
|
C19
|
D:PHO402
|
4.7
|
32.3
|
1.0
|
CBA
|
A:CLA405
|
4.8
|
38.1
|
1.0
|
CBD
|
A:CLA405
|
4.9
|
33.8
|
1.0
|
|
Magnesium binding site 3 out
of 72 in 6jlp
Go back to
Magnesium Binding Sites List in 6jlp
Magnesium binding site 3 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II (3F State, DATASET2)
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 (3F State, DATASET2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg406
b:42.9
occ:1.00
|
MG
|
A:CLA406
|
0.0
|
42.9
|
1.0
|
NB
|
A:CLA406
|
2.0
|
43.4
|
1.0
|
ND
|
A:CLA406
|
2.0
|
43.1
|
1.0
|
NC
|
A:CLA406
|
2.1
|
40.1
|
1.0
|
NA
|
A:CLA406
|
2.1
|
44.1
|
1.0
|
O
|
A:HOH630
|
2.2
|
47.2
|
1.0
|
C4D
|
A:CLA406
|
3.0
|
42.5
|
1.0
|
C1C
|
A:CLA406
|
3.0
|
36.8
|
1.0
|
C4A
|
A:CLA406
|
3.0
|
39.0
|
1.0
|
C1B
|
A:CLA406
|
3.0
|
38.8
|
1.0
|
C4B
|
A:CLA406
|
3.0
|
38.0
|
1.0
|
C1A
|
A:CLA406
|
3.1
|
46.8
|
1.0
|
C4C
|
A:CLA406
|
3.1
|
38.2
|
1.0
|
C1D
|
A:CLA406
|
3.2
|
39.7
|
1.0
|
CHB
|
A:CLA406
|
3.4
|
42.8
|
1.0
|
CHC
|
A:CLA406
|
3.4
|
42.1
|
1.0
|
CHA
|
A:CLA406
|
3.5
|
46.2
|
1.0
|
CHD
|
A:CLA406
|
3.7
|
41.3
|
1.0
|
CBB
|
D:PHO403
|
3.8
|
46.0
|
0.5
|
CBB
|
D:PHO403
|
3.8
|
46.0
|
0.5
|
C3D
|
A:CLA406
|
4.3
|
42.9
|
1.0
|
O
|
A:HOH539
|
4.3
|
48.3
|
1.0
|
C2C
|
A:CLA406
|
4.4
|
36.1
|
1.0
|
C3B
|
A:CLA406
|
4.4
|
38.6
|
1.0
|
C2B
|
A:CLA406
|
4.4
|
39.1
|
1.0
|
C3A
|
A:CLA406
|
4.4
|
44.9
|
1.0
|
C2A
|
A:CLA406
|
4.4
|
46.9
|
1.0
|
C3C
|
A:CLA406
|
4.4
|
35.8
|
1.0
|
C2D
|
A:CLA406
|
4.5
|
40.0
|
1.0
|
CG2
|
D:ILE178
|
4.6
|
36.5
|
1.0
|
C20
|
D:PHO403
|
4.6
|
43.4
|
0.5
|
C20
|
D:PHO403
|
4.7
|
41.8
|
0.5
|
CG1
|
D:ILE178
|
4.8
|
42.5
|
1.0
|
CBA
|
A:CLA406
|
4.9
|
45.4
|
1.0
|
CBD
|
A:CLA406
|
4.9
|
48.5
|
1.0
|
CE1
|
A:PHE206
|
5.0
|
43.4
|
1.0
|
|
Magnesium binding site 4 out
of 72 in 6jlp
Go back to
Magnesium Binding Sites List in 6jlp
Magnesium binding site 4 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II (3F State, DATASET2)
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 (3F State, DATASET2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg407
b:47.6
occ:1.00
|
MG
|
A:CLA407
|
0.0
|
47.6
|
1.0
|
ND
|
A:CLA407
|
2.0
|
51.6
|
1.0
|
NB
|
A:CLA407
|
2.0
|
52.9
|
1.0
|
NA
|
A:CLA407
|
2.1
|
58.6
|
1.0
|
NC
|
A:CLA407
|
2.1
|
61.4
|
1.0
|
NE2
|
A:HIS118
|
2.2
|
38.4
|
1.0
|
C4D
|
A:CLA407
|
3.0
|
57.1
|
1.0
|
C4A
|
A:CLA407
|
3.0
|
62.6
|
1.0
|
CE1
|
A:HIS118
|
3.0
|
42.4
|
1.0
|
C1C
|
A:CLA407
|
3.0
|
56.9
|
1.0
|
C4B
|
A:CLA407
|
3.0
|
52.3
|
1.0
|
C1B
|
A:CLA407
|
3.1
|
52.8
|
1.0
|
C1A
|
A:CLA407
|
3.1
|
57.5
|
1.0
|
C4C
|
A:CLA407
|
3.2
|
47.0
|
1.0
|
C1D
|
A:CLA407
|
3.3
|
53.9
|
1.0
|
CD2
|
A:HIS118
|
3.3
|
55.0
|
1.0
|
CHB
|
A:CLA407
|
3.4
|
57.8
|
1.0
|
CHC
|
A:CLA407
|
3.4
|
56.7
|
1.0
|
CHA
|
A:CLA407
|
3.5
|
59.4
|
1.0
|
CHD
|
A:CLA407
|
3.7
|
50.1
|
1.0
|
ND1
|
A:HIS118
|
4.2
|
39.3
|
1.0
|
C3D
|
A:CLA407
|
4.3
|
55.2
|
1.0
|
CG1
|
I:VAL8
|
4.3
|
47.7
|
1.0
|
C3B
|
A:CLA407
|
4.4
|
46.1
|
1.0
|
CG
|
A:HIS118
|
4.4
|
48.0
|
1.0
|
C2C
|
A:CLA407
|
4.4
|
53.4
|
1.0
|
C2B
|
A:CLA407
|
4.4
|
47.7
|
1.0
|
C3A
|
A:CLA407
|
4.4
|
57.5
|
1.0
|
C2A
|
A:CLA407
|
4.4
|
56.1
|
1.0
|
CG2
|
I:VAL12
|
4.4
|
52.1
|
1.0
|
C3C
|
A:CLA407
|
4.4
|
49.0
|
1.0
|
C2D
|
A:CLA407
|
4.5
|
53.9
|
1.0
|
CBD
|
A:CLA407
|
4.9
|
53.0
|
1.0
|
|
Magnesium binding site 5 out
of 72 in 6jlp
Go back to
Magnesium Binding Sites List in 6jlp
Magnesium binding site 5 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II (3F State, DATASET2)
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 (3F State, DATASET2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg602
b:59.2
occ:1.00
|
MG
|
B:CLA602
|
0.0
|
59.2
|
1.0
|
ND
|
B:CLA602
|
2.0
|
54.9
|
1.0
|
NB
|
B:CLA602
|
2.0
|
67.9
|
1.0
|
NC
|
B:CLA602
|
2.1
|
64.0
|
1.0
|
NA
|
B:CLA602
|
2.1
|
79.3
|
1.0
|
O
|
B:HOH703
|
2.2
|
75.4
|
1.0
|
C4D
|
B:CLA602
|
3.0
|
70.0
|
1.0
|
C1C
|
B:CLA602
|
3.0
|
59.0
|
1.0
|
C4B
|
B:CLA602
|
3.0
|
63.7
|
1.0
|
C4A
|
B:CLA602
|
3.0
|
73.3
|
1.0
|
C1B
|
B:CLA602
|
3.1
|
66.1
|
1.0
|
C1A
|
B:CLA602
|
3.1
|
80.9
|
1.0
|
C4C
|
B:CLA602
|
3.2
|
63.1
|
1.0
|
C1D
|
B:CLA602
|
3.3
|
66.4
|
1.0
|
CHC
|
B:CLA602
|
3.4
|
58.8
|
1.0
|
CHB
|
B:CLA602
|
3.4
|
60.3
|
1.0
|
CHA
|
B:CLA602
|
3.5
|
74.4
|
1.0
|
CHD
|
B:CLA602
|
3.7
|
64.5
|
1.0
|
C10
|
B:CLA602
|
3.8
|
82.4
|
1.0
|
C12
|
B:CLA602
|
3.8
|
70.8
|
1.0
|
O
|
B:TRP185
|
4.1
|
60.6
|
1.0
|
C11
|
B:CLA602
|
4.2
|
78.3
|
1.0
|
C8
|
B:CLA602
|
4.3
|
92.8
|
1.0
|
C3D
|
B:CLA602
|
4.3
|
69.4
|
1.0
|
C3B
|
B:CLA602
|
4.3
|
55.5
|
1.0
|
CE2
|
B:PHE190
|
4.3
|
61.9
|
1.0
|
CBB
|
B:CLA603
|
4.4
|
68.6
|
1.0
|
C2C
|
B:CLA602
|
4.4
|
61.3
|
1.0
|
C2B
|
B:CLA602
|
4.4
|
58.7
|
1.0
|
C3A
|
B:CLA602
|
4.4
|
83.5
|
1.0
|
C2A
|
B:CLA602
|
4.4
|
83.7
|
1.0
|
C3C
|
B:CLA602
|
4.4
|
59.2
|
1.0
|
C2D
|
B:CLA602
|
4.5
|
72.0
|
1.0
|
CZ
|
B:PHE190
|
4.5
|
63.9
|
1.0
|
O
|
B:HOH707
|
4.6
|
71.7
|
1.0
|
CBD
|
B:CLA602
|
4.9
|
74.9
|
1.0
|
CBA
|
B:CLA602
|
5.0
|
0.9
|
1.0
|
|
Magnesium binding site 6 out
of 72 in 6jlp
Go back to
Magnesium Binding Sites List in 6jlp
Magnesium binding site 6 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II (3F State, DATASET2)
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 (3F State, DATASET2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg603
b:62.4
occ:1.00
|
MG
|
B:CLA603
|
0.0
|
62.4
|
1.0
|
ND
|
B:CLA603
|
2.0
|
51.4
|
1.0
|
NB
|
B:CLA603
|
2.0
|
51.6
|
1.0
|
NC
|
B:CLA603
|
2.1
|
48.1
|
1.0
|
NA
|
B:CLA603
|
2.1
|
56.1
|
1.0
|
ND1
|
B:HIS201
|
2.2
|
61.9
|
1.0
|
CE1
|
B:HIS201
|
2.9
|
58.9
|
1.0
|
C4D
|
B:CLA603
|
3.0
|
50.5
|
1.0
|
C1C
|
B:CLA603
|
3.0
|
50.6
|
1.0
|
C4B
|
B:CLA603
|
3.0
|
57.8
|
1.0
|
C1B
|
B:CLA603
|
3.0
|
51.1
|
1.0
|
C4A
|
B:CLA603
|
3.0
|
56.4
|
1.0
|
C1A
|
B:CLA603
|
3.1
|
57.7
|
1.0
|
C4C
|
B:CLA603
|
3.1
|
49.3
|
1.0
|
C1D
|
B:CLA603
|
3.3
|
53.5
|
1.0
|
CG
|
B:HIS201
|
3.3
|
57.6
|
1.0
|
CHB
|
B:CLA603
|
3.4
|
47.1
|
1.0
|
CHC
|
B:CLA603
|
3.4
|
52.6
|
1.0
|
CHA
|
B:CLA603
|
3.5
|
54.9
|
1.0
|
CHD
|
B:CLA603
|
3.7
|
48.0
|
1.0
|
CZ
|
H:PHE41
|
3.8
|
54.3
|
1.0
|
CB
|
B:HIS201
|
3.8
|
53.1
|
1.0
|
NE2
|
B:HIS201
|
4.1
|
60.5
|
1.0
|
C3D
|
B:CLA603
|
4.3
|
43.5
|
1.0
|
CE2
|
H:PHE41
|
4.3
|
56.9
|
1.0
|
C3B
|
B:CLA603
|
4.3
|
52.9
|
1.0
|
CD2
|
B:HIS201
|
4.3
|
52.2
|
1.0
|
C2B
|
B:CLA603
|
4.4
|
57.7
|
1.0
|
C2C
|
B:CLA603
|
4.4
|
54.6
|
1.0
|
C3A
|
B:CLA603
|
4.4
|
57.4
|
1.0
|
C2A
|
B:CLA603
|
4.4
|
58.9
|
1.0
|
C3C
|
B:CLA603
|
4.4
|
52.2
|
1.0
|
CA
|
B:HIS201
|
4.4
|
57.8
|
1.0
|
C2D
|
B:CLA603
|
4.5
|
44.0
|
1.0
|
CE1
|
H:PHE41
|
4.9
|
57.1
|
1.0
|
CBD
|
B:CLA603
|
4.9
|
43.5
|
1.0
|
|
Magnesium binding site 7 out
of 72 in 6jlp
Go back to
Magnesium Binding Sites List in 6jlp
Magnesium binding site 7 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II (3F State, DATASET2)
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 (3F State, DATASET2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg604
b:56.9
occ:1.00
|
MG
|
B:CLA604
|
0.0
|
56.9
|
1.0
|
ND
|
B:CLA604
|
2.0
|
52.6
|
1.0
|
NB
|
B:CLA604
|
2.0
|
53.7
|
1.0
|
NC
|
B:CLA604
|
2.1
|
48.4
|
1.0
|
NA
|
B:CLA604
|
2.1
|
57.1
|
1.0
|
NE2
|
B:HIS202
|
2.2
|
43.8
|
1.0
|
C4D
|
B:CLA604
|
3.0
|
49.0
|
1.0
|
C1B
|
B:CLA604
|
3.0
|
54.6
|
1.0
|
C4A
|
B:CLA604
|
3.0
|
52.3
|
1.0
|
C1C
|
B:CLA604
|
3.0
|
47.6
|
1.0
|
C4B
|
B:CLA604
|
3.0
|
52.3
|
1.0
|
C1A
|
B:CLA604
|
3.1
|
54.4
|
1.0
|
C4C
|
B:CLA604
|
3.1
|
46.6
|
1.0
|
CD2
|
B:HIS202
|
3.2
|
49.0
|
1.0
|
CE1
|
B:HIS202
|
3.2
|
48.4
|
1.0
|
C1D
|
B:CLA604
|
3.3
|
51.6
|
1.0
|
CHB
|
B:CLA604
|
3.4
|
57.0
|
1.0
|
CHC
|
B:CLA604
|
3.4
|
52.7
|
1.0
|
CHA
|
B:CLA604
|
3.5
|
50.5
|
1.0
|
CHD
|
B:CLA604
|
3.7
|
48.1
|
1.0
|
C3D
|
B:CLA604
|
4.3
|
56.3
|
1.0
|
ND1
|
B:HIS202
|
4.3
|
43.7
|
1.0
|
CG
|
B:HIS202
|
4.3
|
50.4
|
1.0
|
C2B
|
B:CLA604
|
4.4
|
52.8
|
1.0
|
C3B
|
B:CLA604
|
4.4
|
47.6
|
1.0
|
C2C
|
B:CLA604
|
4.4
|
49.6
|
1.0
|
C2A
|
B:CLA604
|
4.4
|
54.3
|
1.0
|
C3A
|
B:CLA604
|
4.4
|
55.2
|
1.0
|
C3C
|
B:CLA604
|
4.4
|
52.9
|
1.0
|
C2D
|
B:CLA604
|
4.5
|
52.7
|
1.0
|
C6
|
B:CLA606
|
4.5
|
55.3
|
1.0
|
C7
|
B:CLA606
|
4.6
|
59.3
|
1.0
|
C5
|
B:CLA606
|
4.6
|
53.6
|
1.0
|
C4
|
B:CLA606
|
4.8
|
47.8
|
1.0
|
NE2
|
B:HIS201
|
4.8
|
60.5
|
1.0
|
CBA
|
B:CLA604
|
4.9
|
39.0
|
1.0
|
CD2
|
B:HIS201
|
4.9
|
52.2
|
1.0
|
C3
|
B:CLA606
|
5.0
|
54.1
|
1.0
|
CBD
|
B:CLA604
|
5.0
|
50.9
|
1.0
|
|
Magnesium binding site 8 out
of 72 in 6jlp
Go back to
Magnesium Binding Sites List in 6jlp
Magnesium binding site 8 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II (3F State, DATASET2)
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 (3F State, DATASET2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg605
b:45.2
occ:1.00
|
MG
|
B:CLA605
|
0.0
|
45.2
|
1.0
|
ND
|
B:CLA605
|
2.0
|
36.9
|
1.0
|
NB
|
B:CLA605
|
2.0
|
40.5
|
1.0
|
NC
|
B:CLA605
|
2.1
|
44.0
|
1.0
|
NA
|
B:CLA605
|
2.1
|
36.6
|
1.0
|
NE2
|
B:HIS455
|
2.2
|
49.8
|
1.0
|
C4D
|
B:CLA605
|
3.0
|
42.5
|
1.0
|
C1B
|
B:CLA605
|
3.0
|
41.1
|
1.0
|
C4B
|
B:CLA605
|
3.0
|
38.2
|
1.0
|
C4A
|
B:CLA605
|
3.1
|
37.1
|
1.0
|
C1C
|
B:CLA605
|
3.1
|
44.0
|
1.0
|
C1A
|
B:CLA605
|
3.1
|
40.0
|
1.0
|
CD2
|
B:HIS455
|
3.1
|
40.3
|
1.0
|
C4C
|
B:CLA605
|
3.1
|
34.7
|
1.0
|
C1D
|
B:CLA605
|
3.2
|
42.2
|
1.0
|
CE1
|
B:HIS455
|
3.2
|
47.6
|
1.0
|
CHB
|
B:CLA605
|
3.4
|
33.3
|
1.0
|
CHC
|
B:CLA605
|
3.4
|
39.7
|
1.0
|
CHA
|
B:CLA605
|
3.5
|
40.6
|
1.0
|
CHD
|
B:CLA605
|
3.7
|
50.8
|
1.0
|
C14
|
B:CLA613
|
4.2
|
47.8
|
1.0
|
C3D
|
B:CLA605
|
4.2
|
36.2
|
1.0
|
CG
|
B:HIS455
|
4.3
|
50.4
|
1.0
|
ND1
|
B:HIS455
|
4.3
|
43.6
|
1.0
|
C3B
|
B:CLA605
|
4.4
|
38.0
|
1.0
|
C2B
|
B:CLA605
|
4.4
|
34.0
|
1.0
|
C2C
|
B:CLA605
|
4.4
|
43.1
|
1.0
|
C3C
|
B:CLA605
|
4.4
|
41.8
|
1.0
|
C3A
|
B:CLA605
|
4.4
|
37.3
|
1.0
|
C2D
|
B:CLA605
|
4.5
|
36.7
|
1.0
|
C2A
|
B:CLA605
|
4.5
|
38.8
|
1.0
|
C13
|
B:CLA613
|
4.7
|
42.6
|
1.0
|
C15
|
B:CLA613
|
4.8
|
40.3
|
1.0
|
CBD
|
B:CLA605
|
5.0
|
41.2
|
1.0
|
|
Magnesium binding site 9 out
of 72 in 6jlp
Go back to
Magnesium Binding Sites List in 6jlp
Magnesium binding site 9 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II (3F State, DATASET2)
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 (3F State, DATASET2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg606
b:44.4
occ:1.00
|
MG
|
B:CLA606
|
0.0
|
44.4
|
1.0
|
NB
|
B:CLA606
|
2.0
|
38.4
|
1.0
|
ND
|
B:CLA606
|
2.0
|
39.6
|
1.0
|
NC
|
B:CLA606
|
2.1
|
37.1
|
1.0
|
NA
|
B:CLA606
|
2.1
|
37.6
|
1.0
|
NE2
|
B:HIS100
|
2.2
|
51.2
|
1.0
|
C4D
|
B:CLA606
|
3.0
|
39.2
|
1.0
|
C1C
|
B:CLA606
|
3.0
|
45.2
|
1.0
|
C4B
|
B:CLA606
|
3.0
|
41.0
|
1.0
|
CE1
|
B:HIS100
|
3.0
|
50.5
|
1.0
|
C4A
|
B:CLA606
|
3.0
|
44.5
|
1.0
|
C1B
|
B:CLA606
|
3.1
|
39.1
|
1.0
|
C1A
|
B:CLA606
|
3.1
|
40.9
|
1.0
|
C4C
|
B:CLA606
|
3.1
|
39.4
|
1.0
|
C1D
|
B:CLA606
|
3.3
|
42.1
|
1.0
|
CD2
|
B:HIS100
|
3.3
|
52.9
|
1.0
|
CHC
|
B:CLA606
|
3.4
|
38.2
|
1.0
|
CHB
|
B:CLA606
|
3.4
|
43.5
|
1.0
|
CHA
|
B:CLA606
|
3.5
|
40.9
|
1.0
|
CHD
|
B:CLA606
|
3.7
|
40.8
|
1.0
|
C1
|
B:CLA605
|
4.0
|
55.8
|
1.0
|
C2
|
B:CLA605
|
4.1
|
65.7
|
1.0
|
ND1
|
B:HIS100
|
4.2
|
41.5
|
1.0
|
C3D
|
B:CLA606
|
4.3
|
40.9
|
1.0
|
C3B
|
B:CLA606
|
4.3
|
40.2
|
1.0
|
C2B
|
B:CLA606
|
4.4
|
38.8
|
1.0
|
C2C
|
B:CLA606
|
4.4
|
43.4
|
1.0
|
CG
|
B:HIS100
|
4.4
|
49.5
|
1.0
|
C2A
|
B:CLA606
|
4.4
|
39.1
|
1.0
|
C3A
|
B:CLA606
|
4.4
|
45.0
|
1.0
|
C3C
|
B:CLA606
|
4.4
|
42.9
|
1.0
|
C2D
|
B:CLA606
|
4.5
|
39.6
|
1.0
|
C4
|
B:CLA607
|
4.9
|
37.2
|
1.0
|
CBD
|
B:CLA606
|
4.9
|
40.8
|
1.0
|
|
Magnesium binding site 10 out
of 72 in 6jlp
Go back to
Magnesium Binding Sites List in 6jlp
Magnesium binding site 10 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II (3F State, DATASET2)
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 (3F State, DATASET2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg607
b:48.5
occ:1.00
|
MG
|
B:CLA607
|
0.0
|
48.5
|
1.0
|
ND
|
B:CLA607
|
2.0
|
56.8
|
1.0
|
NB
|
B:CLA607
|
2.0
|
41.3
|
1.0
|
NC
|
B:CLA607
|
2.1
|
43.3
|
1.0
|
NA
|
B:CLA607
|
2.1
|
58.5
|
1.0
|
ND1
|
B:HIS157
|
2.2
|
51.7
|
1.0
|
CE1
|
B:HIS157
|
2.8
|
54.9
|
1.0
|
C4D
|
B:CLA607
|
3.0
|
56.2
|
1.0
|
C4B
|
B:CLA607
|
3.0
|
41.8
|
1.0
|
C1C
|
B:CLA607
|
3.0
|
48.5
|
1.0
|
C1B
|
B:CLA607
|
3.0
|
54.5
|
1.0
|
C4A
|
B:CLA607
|
3.1
|
55.2
|
1.0
|
C1A
|
B:CLA607
|
3.1
|
52.3
|
1.0
|
C4C
|
B:CLA607
|
3.1
|
50.0
|
1.0
|
C1D
|
B:CLA607
|
3.3
|
60.1
|
1.0
|
CHB
|
B:CLA607
|
3.4
|
53.9
|
1.0
|
CHC
|
B:CLA607
|
3.4
|
48.6
|
1.0
|
CG
|
B:HIS157
|
3.5
|
49.2
|
1.0
|
CHA
|
B:CLA607
|
3.5
|
55.8
|
1.0
|
CHD
|
B:CLA607
|
3.7
|
57.3
|
1.0
|
C15
|
B:UNL631
|
4.0
|
61.3
|
1.0
|
C14
|
B:UNL631
|
4.0
|
68.1
|
1.0
|
C13
|
B:UNL631
|
4.0
|
75.2
|
1.0
|
CB
|
B:HIS157
|
4.1
|
53.5
|
1.0
|
NE2
|
B:HIS157
|
4.1
|
52.9
|
1.0
|
C3D
|
B:CLA607
|
4.3
|
55.4
|
1.0
|
C3B
|
B:CLA607
|
4.3
|
48.7
|
1.0
|
C2B
|
B:CLA607
|
4.4
|
44.2
|
1.0
|
C16
|
B:UNL631
|
4.4
|
61.4
|
1.0
|
C2C
|
B:CLA607
|
4.4
|
49.4
|
1.0
|
CD2
|
B:HIS157
|
4.4
|
49.7
|
1.0
|
C3C
|
B:CLA607
|
4.4
|
53.5
|
1.0
|
C3A
|
B:CLA607
|
4.4
|
43.3
|
1.0
|
C2A
|
B:CLA607
|
4.4
|
49.5
|
1.0
|
C2D
|
B:CLA607
|
4.5
|
57.9
|
1.0
|
CBD
|
B:CLA607
|
5.0
|
53.4
|
1.0
|
|
Reference:
M.Suga,
F.Akita,
K.Yamashita,
Y.Nakajima,
G.Ueno,
H.Li,
T.Yamane,
K.Hirata,
Y.Umena,
S.Yonekura,
L.J.Yu,
H.Murakami,
T.Nomura,
T.Kimura,
M.Kubo,
S.Baba,
T.Kumasaka,
K.Tono,
M.Yabashi,
H.Isobe,
K.Yamaguchi,
M.Yamamoto,
H.Ago,
J.R.Shen.
An Oxyl/Oxo Mechanism For Oxygen-Oxygen Coupling in Psii Revealed By An X-Ray Free-Electron Laser. Science V. 366 334 2019.
ISSN: ESSN 1095-9203
PubMed: 31624207
DOI: 10.1126/SCIENCE.AAX6998
Page generated: Tue Oct 1 05:03:58 2024
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