Magnesium in PDB 6jlm: Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2)
Enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2)
All present enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2):
1.10.3.9;
Protein crystallography data
The structure of Xfel Structure of Cyanobacterial Photosystem II (Dark State, DATASET2), PDB code: 6jlm
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 /
2.35
|
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 (%)
|
15.3 /
20.9
|
Other elements in 6jlm:
The structure of Xfel Structure of Cyanobacterial Photosystem II (Dark 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 (Dark State, DATASET2)
(pdb code 6jlm). 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 (Dark State, DATASET2), PDB code: 6jlm:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 72 in 6jlm
Go back to
Magnesium Binding Sites List in 6jlm
Magnesium binding site 1 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II (Dark 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 (Dark State, DATASET2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg405
b:34.8
occ:1.00
|
MG
|
A:CLA405
|
0.0
|
34.8
|
1.0
|
ND
|
A:CLA405
|
2.0
|
36.1
|
1.0
|
NB
|
A:CLA405
|
2.0
|
34.6
|
1.0
|
NA
|
A:CLA405
|
2.1
|
36.0
|
1.0
|
NC
|
A:CLA405
|
2.1
|
30.6
|
1.0
|
NE2
|
A:HIS198
|
2.2
|
35.9
|
1.0
|
C4D
|
A:CLA405
|
3.0
|
37.4
|
1.0
|
C4A
|
A:CLA405
|
3.0
|
33.3
|
1.0
|
C1A
|
A:CLA405
|
3.0
|
40.0
|
1.0
|
C4B
|
A:CLA405
|
3.0
|
32.2
|
1.0
|
C1C
|
A:CLA405
|
3.0
|
42.0
|
1.0
|
CE1
|
A:HIS198
|
3.0
|
44.9
|
1.0
|
C1B
|
A:CLA405
|
3.1
|
36.3
|
1.0
|
C4C
|
A:CLA405
|
3.2
|
27.2
|
1.0
|
C1D
|
A:CLA405
|
3.3
|
35.8
|
1.0
|
CD2
|
A:HIS198
|
3.4
|
39.3
|
1.0
|
CHB
|
A:CLA405
|
3.4
|
35.2
|
1.0
|
CHC
|
A:CLA405
|
3.4
|
28.7
|
1.0
|
CHA
|
A:CLA405
|
3.4
|
30.6
|
1.0
|
CHD
|
A:CLA405
|
3.7
|
38.5
|
1.0
|
CE
|
A:MET183
|
3.9
|
29.1
|
1.0
|
ND1
|
A:HIS198
|
4.2
|
44.4
|
1.0
|
C3D
|
A:CLA405
|
4.3
|
24.6
|
1.0
|
CAB
|
D:CLA404
|
4.3
|
34.4
|
1.0
|
C3B
|
A:CLA405
|
4.4
|
29.1
|
1.0
|
C3A
|
A:CLA405
|
4.4
|
38.3
|
1.0
|
C2A
|
A:CLA405
|
4.4
|
33.1
|
1.0
|
C2B
|
A:CLA405
|
4.4
|
30.9
|
1.0
|
C2C
|
A:CLA405
|
4.4
|
37.7
|
1.0
|
CG
|
A:HIS198
|
4.4
|
43.1
|
1.0
|
C3C
|
A:CLA405
|
4.5
|
28.5
|
1.0
|
C2D
|
A:CLA405
|
4.5
|
31.8
|
1.0
|
CBD
|
A:CLA405
|
4.9
|
39.4
|
1.0
|
CMA
|
A:CLA405
|
5.0
|
27.7
|
1.0
|
|
Magnesium binding site 2 out
of 72 in 6jlm
Go back to
Magnesium Binding Sites List in 6jlm
Magnesium binding site 2 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II (Dark 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 (Dark State, DATASET2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg406
b:35.8
occ:1.00
|
MG
|
A:CLA406
|
0.0
|
35.8
|
1.0
|
ND
|
A:CLA406
|
2.0
|
32.6
|
1.0
|
NB
|
A:CLA406
|
2.0
|
33.3
|
1.0
|
NC
|
A:CLA406
|
2.1
|
41.6
|
1.0
|
NA
|
A:CLA406
|
2.1
|
37.7
|
1.0
|
O
|
A:HOH625
|
2.2
|
33.0
|
1.0
|
C4D
|
A:CLA406
|
3.0
|
29.7
|
1.0
|
C1C
|
A:CLA406
|
3.0
|
31.9
|
1.0
|
C4B
|
A:CLA406
|
3.0
|
53.0
|
1.0
|
C1B
|
A:CLA406
|
3.0
|
36.1
|
1.0
|
C4A
|
A:CLA406
|
3.0
|
42.0
|
1.0
|
C1A
|
A:CLA406
|
3.1
|
32.6
|
1.0
|
C4C
|
A:CLA406
|
3.1
|
32.5
|
1.0
|
C1D
|
A:CLA406
|
3.2
|
35.6
|
1.0
|
CHB
|
A:CLA406
|
3.4
|
28.2
|
1.0
|
CHC
|
A:CLA406
|
3.4
|
48.9
|
1.0
|
CHA
|
A:CLA406
|
3.5
|
33.3
|
1.0
|
CHD
|
A:CLA406
|
3.7
|
30.4
|
1.0
|
CBB
|
A:PHO408
|
3.9
|
47.8
|
1.0
|
O
|
A:HOH617
|
4.1
|
36.4
|
1.0
|
C3D
|
A:CLA406
|
4.2
|
31.0
|
1.0
|
C3B
|
A:CLA406
|
4.3
|
39.7
|
1.0
|
C2B
|
A:CLA406
|
4.3
|
34.3
|
1.0
|
C2C
|
A:CLA406
|
4.4
|
41.4
|
1.0
|
CG2
|
A:THR179
|
4.4
|
28.4
|
1.0
|
C2A
|
A:CLA406
|
4.4
|
39.3
|
1.0
|
C3A
|
A:CLA406
|
4.4
|
41.0
|
1.0
|
C3C
|
A:CLA406
|
4.4
|
29.4
|
1.0
|
C2D
|
A:CLA406
|
4.5
|
34.0
|
1.0
|
OG1
|
A:THR179
|
4.6
|
27.2
|
1.0
|
C19
|
A:PHO408
|
4.6
|
36.3
|
1.0
|
CBA
|
A:CLA406
|
4.7
|
34.0
|
1.0
|
CBD
|
A:CLA406
|
4.9
|
31.9
|
1.0
|
CB
|
A:THR179
|
5.0
|
36.8
|
1.0
|
|
Magnesium binding site 3 out
of 72 in 6jlm
Go back to
Magnesium Binding Sites List in 6jlm
Magnesium binding site 3 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II (Dark 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 (Dark State, DATASET2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg407
b:41.1
occ:1.00
|
MG
|
A:CLA407
|
0.0
|
41.1
|
1.0
|
ND
|
A:CLA407
|
2.0
|
39.4
|
1.0
|
NB
|
A:CLA407
|
2.0
|
42.2
|
1.0
|
NC
|
A:CLA407
|
2.1
|
47.1
|
1.0
|
NA
|
A:CLA407
|
2.1
|
39.8
|
1.0
|
O
|
A:HOH637
|
2.2
|
44.7
|
1.0
|
C4D
|
A:CLA407
|
3.0
|
31.0
|
1.0
|
C1C
|
A:CLA407
|
3.0
|
28.2
|
1.0
|
C4A
|
A:CLA407
|
3.0
|
40.0
|
1.0
|
C1B
|
A:CLA407
|
3.0
|
36.9
|
1.0
|
C4B
|
A:CLA407
|
3.1
|
35.0
|
1.0
|
C1A
|
A:CLA407
|
3.1
|
34.4
|
1.0
|
C4C
|
A:CLA407
|
3.1
|
36.5
|
1.0
|
C1D
|
A:CLA407
|
3.2
|
37.5
|
1.0
|
CHB
|
A:CLA407
|
3.4
|
35.0
|
1.0
|
CHC
|
A:CLA407
|
3.4
|
39.3
|
1.0
|
CHA
|
A:CLA407
|
3.5
|
43.8
|
1.0
|
CHD
|
A:CLA407
|
3.7
|
39.5
|
1.0
|
CBB
|
D:PHO401
|
3.8
|
48.6
|
1.0
|
O
|
A:HOH610
|
4.2
|
37.1
|
1.0
|
C3D
|
A:CLA407
|
4.3
|
37.1
|
1.0
|
C2C
|
A:CLA407
|
4.4
|
34.8
|
1.0
|
C3B
|
A:CLA407
|
4.4
|
44.8
|
1.0
|
C2B
|
A:CLA407
|
4.4
|
37.1
|
1.0
|
C3A
|
A:CLA407
|
4.4
|
41.8
|
1.0
|
C2A
|
A:CLA407
|
4.4
|
41.5
|
1.0
|
C3C
|
A:CLA407
|
4.4
|
36.1
|
1.0
|
C2D
|
A:CLA407
|
4.5
|
42.0
|
1.0
|
CG2
|
D:ILE178
|
4.6
|
30.1
|
1.0
|
C20
|
D:PHO401
|
4.7
|
32.1
|
1.0
|
CE1
|
A:PHE206
|
4.8
|
43.1
|
1.0
|
CBA
|
A:CLA407
|
4.9
|
47.4
|
1.0
|
CBD
|
A:CLA407
|
4.9
|
44.6
|
1.0
|
CG1
|
D:ILE178
|
5.0
|
40.4
|
1.0
|
|
Magnesium binding site 4 out
of 72 in 6jlm
Go back to
Magnesium Binding Sites List in 6jlm
Magnesium binding site 4 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II (Dark 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 (Dark State, DATASET2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg409
b:41.3
occ:1.00
|
MG
|
A:CLA409
|
0.0
|
41.3
|
1.0
|
ND
|
A:CLA409
|
2.0
|
45.8
|
1.0
|
NB
|
A:CLA409
|
2.1
|
40.4
|
1.0
|
NC
|
A:CLA409
|
2.1
|
54.1
|
1.0
|
NA
|
A:CLA409
|
2.1
|
51.8
|
1.0
|
NE2
|
A:HIS118
|
2.2
|
35.7
|
1.0
|
C4D
|
A:CLA409
|
3.0
|
51.9
|
1.0
|
CE1
|
A:HIS118
|
3.0
|
45.6
|
1.0
|
C1C
|
A:CLA409
|
3.0
|
43.2
|
1.0
|
C4B
|
A:CLA409
|
3.0
|
48.0
|
1.0
|
C4A
|
A:CLA409
|
3.1
|
54.2
|
1.0
|
C1B
|
A:CLA409
|
3.1
|
45.1
|
1.0
|
C1A
|
A:CLA409
|
3.1
|
46.0
|
1.0
|
C4C
|
A:CLA409
|
3.2
|
46.8
|
1.0
|
C1D
|
A:CLA409
|
3.3
|
54.2
|
1.0
|
CD2
|
A:HIS118
|
3.3
|
47.2
|
1.0
|
CHC
|
A:CLA409
|
3.4
|
49.0
|
1.0
|
CHB
|
A:CLA409
|
3.4
|
42.1
|
1.0
|
CHA
|
A:CLA409
|
3.4
|
46.9
|
1.0
|
CHD
|
A:CLA409
|
3.7
|
49.8
|
1.0
|
ND1
|
A:HIS118
|
4.2
|
33.9
|
1.0
|
C3D
|
A:CLA409
|
4.2
|
55.8
|
1.0
|
CG1
|
I:VAL8
|
4.3
|
37.7
|
1.0
|
C3B
|
A:CLA409
|
4.4
|
45.3
|
1.0
|
C2C
|
A:CLA409
|
4.4
|
48.6
|
1.0
|
CG
|
A:HIS118
|
4.4
|
47.1
|
1.0
|
C2B
|
A:CLA409
|
4.4
|
43.1
|
1.0
|
C3A
|
A:CLA409
|
4.4
|
56.7
|
1.0
|
C2A
|
A:CLA409
|
4.4
|
47.0
|
1.0
|
C3C
|
A:CLA409
|
4.5
|
47.3
|
1.0
|
C2D
|
A:CLA409
|
4.5
|
50.3
|
1.0
|
CG2
|
I:VAL12
|
4.5
|
52.0
|
1.0
|
CBD
|
A:CLA409
|
4.9
|
43.0
|
1.0
|
|
Magnesium binding site 5 out
of 72 in 6jlm
Go back to
Magnesium Binding Sites List in 6jlm
Magnesium binding site 5 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II (Dark 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 (Dark State, DATASET2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg602
b:60.6
occ:1.00
|
MG
|
B:CLA602
|
0.0
|
60.6
|
1.0
|
NB
|
B:CLA602
|
2.0
|
60.3
|
1.0
|
ND
|
B:CLA602
|
2.0
|
51.4
|
1.0
|
NC
|
B:CLA602
|
2.1
|
55.7
|
1.0
|
NA
|
B:CLA602
|
2.1
|
78.1
|
1.0
|
O
|
B:HOH729
|
2.2
|
68.4
|
1.0
|
C1C
|
B:CLA602
|
3.0
|
60.8
|
1.0
|
C4D
|
B:CLA602
|
3.0
|
61.5
|
1.0
|
C4B
|
B:CLA602
|
3.0
|
65.8
|
1.0
|
C4A
|
B:CLA602
|
3.0
|
67.8
|
1.0
|
C1B
|
B:CLA602
|
3.0
|
53.5
|
1.0
|
C1A
|
B:CLA602
|
3.1
|
71.0
|
1.0
|
C4C
|
B:CLA602
|
3.1
|
48.1
|
1.0
|
C1D
|
B:CLA602
|
3.3
|
58.3
|
1.0
|
CHC
|
B:CLA602
|
3.4
|
54.3
|
1.0
|
CHB
|
B:CLA602
|
3.4
|
51.1
|
1.0
|
CHA
|
B:CLA602
|
3.5
|
60.5
|
1.0
|
CHD
|
B:CLA602
|
3.7
|
60.8
|
1.0
|
C10
|
B:CLA602
|
3.8
|
69.0
|
1.0
|
C12
|
B:CLA602
|
4.1
|
62.8
|
1.0
|
C8
|
B:CLA602
|
4.1
|
79.3
|
1.0
|
O
|
B:TRP185
|
4.1
|
62.3
|
1.0
|
C3D
|
B:CLA602
|
4.3
|
62.4
|
1.0
|
C11
|
B:CLA602
|
4.3
|
67.5
|
1.0
|
CE2
|
B:PHE190
|
4.3
|
52.9
|
1.0
|
C3B
|
B:CLA602
|
4.3
|
58.6
|
1.0
|
C2C
|
B:CLA602
|
4.3
|
58.8
|
1.0
|
C2B
|
B:CLA602
|
4.4
|
52.1
|
1.0
|
C3A
|
B:CLA602
|
4.4
|
69.1
|
1.0
|
C2A
|
B:CLA602
|
4.4
|
68.4
|
1.0
|
CBB
|
B:CLA603
|
4.4
|
67.0
|
1.0
|
C3C
|
B:CLA602
|
4.4
|
43.4
|
1.0
|
C2D
|
B:CLA602
|
4.5
|
62.7
|
1.0
|
CZ
|
B:PHE190
|
4.6
|
46.2
|
1.0
|
C9
|
B:CLA602
|
4.7
|
75.2
|
1.0
|
O
|
B:HOH726
|
4.8
|
88.8
|
1.0
|
CBD
|
B:CLA602
|
4.9
|
61.0
|
1.0
|
CBA
|
B:CLA602
|
5.0
|
95.1
|
1.0
|
|
Magnesium binding site 6 out
of 72 in 6jlm
Go back to
Magnesium Binding Sites List in 6jlm
Magnesium binding site 6 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II (Dark 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 (Dark State, DATASET2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg603
b:60.4
occ:1.00
|
MG
|
B:CLA603
|
0.0
|
60.4
|
1.0
|
ND
|
B:CLA603
|
2.0
|
51.5
|
1.0
|
NB
|
B:CLA603
|
2.0
|
55.9
|
1.0
|
NC
|
B:CLA603
|
2.1
|
46.8
|
1.0
|
NA
|
B:CLA603
|
2.1
|
43.4
|
1.0
|
ND1
|
B:HIS201
|
2.2
|
56.5
|
1.0
|
C4D
|
B:CLA603
|
3.0
|
52.7
|
1.0
|
CE1
|
B:HIS201
|
3.0
|
52.0
|
1.0
|
C4A
|
B:CLA603
|
3.0
|
49.8
|
1.0
|
C1C
|
B:CLA603
|
3.0
|
49.0
|
1.0
|
C1B
|
B:CLA603
|
3.0
|
53.2
|
1.0
|
C4B
|
B:CLA603
|
3.0
|
55.1
|
1.0
|
C1A
|
B:CLA603
|
3.1
|
52.8
|
1.0
|
C4C
|
B:CLA603
|
3.1
|
50.5
|
1.0
|
C1D
|
B:CLA603
|
3.3
|
51.6
|
1.0
|
CG
|
B:HIS201
|
3.3
|
51.9
|
1.0
|
CHB
|
B:CLA603
|
3.4
|
56.5
|
1.0
|
CHC
|
B:CLA603
|
3.4
|
50.5
|
1.0
|
CHA
|
B:CLA603
|
3.5
|
48.7
|
1.0
|
CHD
|
B:CLA603
|
3.7
|
57.3
|
1.0
|
CB
|
B:HIS201
|
3.8
|
46.4
|
1.0
|
CZ
|
H:PHE41
|
3.9
|
56.2
|
1.0
|
CE2
|
H:PHE41
|
4.2
|
49.5
|
1.0
|
NE2
|
B:HIS201
|
4.2
|
57.5
|
1.0
|
C3D
|
B:CLA603
|
4.3
|
40.2
|
1.0
|
C3B
|
B:CLA603
|
4.4
|
53.3
|
1.0
|
C2B
|
B:CLA603
|
4.4
|
54.9
|
1.0
|
CD2
|
B:HIS201
|
4.4
|
55.9
|
1.0
|
C2C
|
B:CLA603
|
4.4
|
49.4
|
1.0
|
C3A
|
B:CLA603
|
4.4
|
46.6
|
1.0
|
CA
|
B:HIS201
|
4.4
|
53.5
|
1.0
|
C2A
|
B:CLA603
|
4.4
|
48.7
|
1.0
|
C3C
|
B:CLA603
|
4.4
|
49.0
|
1.0
|
C2D
|
B:CLA603
|
4.5
|
38.3
|
1.0
|
CMA
|
B:CLA603
|
4.9
|
39.5
|
1.0
|
CBD
|
B:CLA603
|
4.9
|
38.1
|
1.0
|
CE1
|
B:PHE190
|
5.0
|
46.7
|
1.0
|
|
Magnesium binding site 7 out
of 72 in 6jlm
Go back to
Magnesium Binding Sites List in 6jlm
Magnesium binding site 7 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II (Dark 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 (Dark State, DATASET2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg604
b:49.2
occ:1.00
|
MG
|
B:CLA604
|
0.0
|
49.2
|
1.0
|
NB
|
B:CLA604
|
2.0
|
55.4
|
1.0
|
ND
|
B:CLA604
|
2.0
|
53.6
|
1.0
|
NC
|
B:CLA604
|
2.1
|
48.5
|
1.0
|
NA
|
B:CLA604
|
2.1
|
63.2
|
1.0
|
NE2
|
B:HIS202
|
2.2
|
49.1
|
1.0
|
C4D
|
B:CLA604
|
3.0
|
51.8
|
1.0
|
C1B
|
B:CLA604
|
3.0
|
53.5
|
1.0
|
C4A
|
B:CLA604
|
3.0
|
47.7
|
1.0
|
C1C
|
B:CLA604
|
3.0
|
40.7
|
1.0
|
C4B
|
B:CLA604
|
3.0
|
46.5
|
1.0
|
C1A
|
B:CLA604
|
3.1
|
57.0
|
1.0
|
C4C
|
B:CLA604
|
3.1
|
46.3
|
1.0
|
CE1
|
B:HIS202
|
3.2
|
45.1
|
1.0
|
CD2
|
B:HIS202
|
3.2
|
48.6
|
1.0
|
C1D
|
B:CLA604
|
3.3
|
53.9
|
1.0
|
CHB
|
B:CLA604
|
3.4
|
57.3
|
1.0
|
CHC
|
B:CLA604
|
3.4
|
42.1
|
1.0
|
CHA
|
B:CLA604
|
3.5
|
42.7
|
1.0
|
CHD
|
B:CLA604
|
3.7
|
45.8
|
1.0
|
ND1
|
B:HIS202
|
4.3
|
46.3
|
1.0
|
C3D
|
B:CLA604
|
4.3
|
57.4
|
1.0
|
CG
|
B:HIS202
|
4.3
|
44.1
|
1.0
|
C3B
|
B:CLA604
|
4.4
|
42.8
|
1.0
|
C2B
|
B:CLA604
|
4.4
|
44.1
|
1.0
|
C2C
|
B:CLA604
|
4.4
|
40.7
|
1.0
|
C2A
|
B:CLA604
|
4.4
|
53.3
|
1.0
|
C3A
|
B:CLA604
|
4.4
|
56.5
|
1.0
|
C3C
|
B:CLA604
|
4.4
|
46.5
|
1.0
|
C2D
|
B:CLA604
|
4.5
|
41.3
|
1.0
|
C6
|
B:CLA606
|
4.5
|
49.3
|
1.0
|
C7
|
B:CLA606
|
4.7
|
55.9
|
1.0
|
C5
|
B:CLA606
|
4.7
|
53.4
|
1.0
|
C4
|
B:CLA606
|
4.8
|
39.0
|
1.0
|
NE2
|
B:HIS201
|
4.8
|
57.5
|
1.0
|
CD2
|
B:HIS201
|
4.9
|
55.9
|
1.0
|
CBA
|
B:CLA604
|
5.0
|
46.3
|
1.0
|
CBD
|
B:CLA604
|
5.0
|
49.0
|
1.0
|
|
Magnesium binding site 8 out
of 72 in 6jlm
Go back to
Magnesium Binding Sites List in 6jlm
Magnesium binding site 8 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II (Dark 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 (Dark State, DATASET2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg605
b:37.5
occ:1.00
|
MG
|
B:CLA605
|
0.0
|
37.5
|
1.0
|
ND
|
B:CLA605
|
2.0
|
38.1
|
1.0
|
NB
|
B:CLA605
|
2.0
|
37.2
|
1.0
|
NC
|
B:CLA605
|
2.1
|
39.9
|
1.0
|
NA
|
B:CLA605
|
2.1
|
32.0
|
1.0
|
NE2
|
B:HIS455
|
2.2
|
44.8
|
1.0
|
C4D
|
B:CLA605
|
3.0
|
40.7
|
1.0
|
C4B
|
B:CLA605
|
3.0
|
42.4
|
1.0
|
C4A
|
B:CLA605
|
3.1
|
38.1
|
1.0
|
C1B
|
B:CLA605
|
3.1
|
36.1
|
1.0
|
C1C
|
B:CLA605
|
3.1
|
42.2
|
1.0
|
C1A
|
B:CLA605
|
3.1
|
41.6
|
1.0
|
C4C
|
B:CLA605
|
3.2
|
28.5
|
1.0
|
CD2
|
B:HIS455
|
3.2
|
50.0
|
1.0
|
CE1
|
B:HIS455
|
3.2
|
51.2
|
1.0
|
C1D
|
B:CLA605
|
3.3
|
35.2
|
1.0
|
CHB
|
B:CLA605
|
3.4
|
32.2
|
1.0
|
CHC
|
B:CLA605
|
3.4
|
43.8
|
1.0
|
CHA
|
B:CLA605
|
3.5
|
35.2
|
1.0
|
CHD
|
B:CLA605
|
3.7
|
40.8
|
1.0
|
C14
|
B:CLA613
|
4.0
|
43.0
|
1.0
|
C3D
|
B:CLA605
|
4.3
|
34.6
|
1.0
|
ND1
|
B:HIS455
|
4.3
|
44.7
|
1.0
|
CG
|
B:HIS455
|
4.3
|
50.4
|
1.0
|
C3B
|
B:CLA605
|
4.4
|
41.8
|
1.0
|
C2B
|
B:CLA605
|
4.4
|
35.5
|
1.0
|
C2C
|
B:CLA605
|
4.4
|
36.4
|
1.0
|
C3A
|
B:CLA605
|
4.4
|
35.2
|
1.0
|
C3C
|
B:CLA605
|
4.5
|
34.2
|
1.0
|
C2A
|
B:CLA605
|
4.5
|
36.8
|
1.0
|
C2D
|
B:CLA605
|
4.5
|
38.7
|
1.0
|
C13
|
B:CLA613
|
4.7
|
48.1
|
1.0
|
C15
|
B:CLA613
|
4.9
|
43.3
|
1.0
|
CBD
|
B:CLA605
|
5.0
|
54.5
|
1.0
|
CE1
|
B:PHE451
|
5.0
|
49.1
|
1.0
|
|
Magnesium binding site 9 out
of 72 in 6jlm
Go back to
Magnesium Binding Sites List in 6jlm
Magnesium binding site 9 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II (Dark 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 (Dark State, DATASET2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg606
b:44.0
occ:1.00
|
MG
|
B:CLA606
|
0.0
|
44.0
|
1.0
|
ND
|
B:CLA606
|
2.0
|
43.3
|
1.0
|
NB
|
B:CLA606
|
2.0
|
35.1
|
1.0
|
NC
|
B:CLA606
|
2.1
|
45.3
|
1.0
|
NA
|
B:CLA606
|
2.1
|
38.6
|
1.0
|
NE2
|
B:HIS100
|
2.2
|
45.6
|
1.0
|
C4D
|
B:CLA606
|
3.0
|
37.7
|
1.0
|
C4B
|
B:CLA606
|
3.0
|
35.9
|
1.0
|
C1C
|
B:CLA606
|
3.0
|
38.5
|
1.0
|
C1B
|
B:CLA606
|
3.1
|
39.6
|
1.0
|
C4A
|
B:CLA606
|
3.1
|
43.8
|
1.0
|
C1A
|
B:CLA606
|
3.1
|
34.2
|
1.0
|
CE1
|
B:HIS100
|
3.1
|
42.3
|
1.0
|
C4C
|
B:CLA606
|
3.2
|
47.9
|
1.0
|
C1D
|
B:CLA606
|
3.3
|
41.8
|
1.0
|
CD2
|
B:HIS100
|
3.3
|
40.4
|
1.0
|
CHC
|
B:CLA606
|
3.4
|
40.0
|
1.0
|
CHB
|
B:CLA606
|
3.4
|
42.7
|
1.0
|
CHA
|
B:CLA606
|
3.5
|
28.6
|
1.0
|
CHD
|
B:CLA606
|
3.7
|
41.7
|
1.0
|
C1
|
B:CLA605
|
4.1
|
57.0
|
1.0
|
C2
|
B:CLA605
|
4.1
|
66.4
|
1.0
|
ND1
|
B:HIS100
|
4.3
|
37.4
|
1.0
|
C3D
|
B:CLA606
|
4.3
|
38.0
|
1.0
|
C3B
|
B:CLA606
|
4.4
|
36.3
|
1.0
|
CG
|
B:HIS100
|
4.4
|
41.6
|
1.0
|
C2B
|
B:CLA606
|
4.4
|
31.5
|
1.0
|
C2C
|
B:CLA606
|
4.4
|
41.6
|
1.0
|
C2A
|
B:CLA606
|
4.4
|
37.7
|
1.0
|
C3A
|
B:CLA606
|
4.4
|
40.6
|
1.0
|
C3C
|
B:CLA606
|
4.5
|
38.2
|
1.0
|
C2D
|
B:CLA606
|
4.5
|
33.9
|
1.0
|
C4
|
B:CLA607
|
4.8
|
39.5
|
1.0
|
CBD
|
B:CLA606
|
4.9
|
29.8
|
1.0
|
|
Magnesium binding site 10 out
of 72 in 6jlm
Go back to
Magnesium Binding Sites List in 6jlm
Magnesium binding site 10 out
of 72 in the Xfel Structure of Cyanobacterial Photosystem II (Dark 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 (Dark State, DATASET2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg607
b:57.0
occ:1.00
|
MG
|
B:CLA607
|
0.0
|
57.0
|
1.0
|
ND
|
B:CLA607
|
2.0
|
59.6
|
1.0
|
NB
|
B:CLA607
|
2.0
|
46.2
|
1.0
|
NC
|
B:CLA607
|
2.1
|
44.4
|
1.0
|
NA
|
B:CLA607
|
2.1
|
44.4
|
1.0
|
ND1
|
B:HIS157
|
2.2
|
49.3
|
1.0
|
CE1
|
B:HIS157
|
2.8
|
55.6
|
1.0
|
C4D
|
B:CLA607
|
3.0
|
63.7
|
1.0
|
C1C
|
B:CLA607
|
3.0
|
54.0
|
1.0
|
C4B
|
B:CLA607
|
3.0
|
38.3
|
1.0
|
C1B
|
B:CLA607
|
3.0
|
47.5
|
1.0
|
C4A
|
B:CLA607
|
3.1
|
46.7
|
1.0
|
C1A
|
B:CLA607
|
3.1
|
48.4
|
1.0
|
C4C
|
B:CLA607
|
3.1
|
48.9
|
1.0
|
C1D
|
B:CLA607
|
3.3
|
62.4
|
1.0
|
CHB
|
B:CLA607
|
3.4
|
54.9
|
1.0
|
CHC
|
B:CLA607
|
3.4
|
54.9
|
1.0
|
CG
|
B:HIS157
|
3.5
|
54.8
|
1.0
|
CHA
|
B:CLA607
|
3.5
|
50.2
|
1.0
|
CHD
|
B:CLA607
|
3.7
|
60.2
|
1.0
|
C15
|
B:UNL634
|
4.0
|
57.5
|
1.0
|
C14
|
B:UNL634
|
4.0
|
56.5
|
1.0
|
NE2
|
B:HIS157
|
4.1
|
42.3
|
1.0
|
CB
|
B:HIS157
|
4.1
|
50.5
|
1.0
|
C13
|
B:UNL634
|
4.2
|
66.5
|
1.0
|
C3D
|
B:CLA607
|
4.3
|
55.7
|
1.0
|
C3B
|
B:CLA607
|
4.3
|
49.0
|
1.0
|
C2B
|
B:CLA607
|
4.4
|
42.1
|
1.0
|
C2C
|
B:CLA607
|
4.4
|
55.9
|
1.0
|
CD2
|
B:HIS157
|
4.4
|
41.0
|
1.0
|
C3C
|
B:CLA607
|
4.4
|
57.3
|
1.0
|
C3A
|
B:CLA607
|
4.4
|
31.0
|
1.0
|
C2A
|
B:CLA607
|
4.5
|
48.1
|
1.0
|
C2D
|
B:CLA607
|
4.5
|
51.0
|
1.0
|
C16
|
B:UNL634
|
4.8
|
61.2
|
1.0
|
CBD
|
B:CLA607
|
5.0
|
63.0
|
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 05:03:32 2024
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