Magnesium in PDB 5y5s: Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution
Protein crystallography data
The structure of Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution, PDB code: 5y5s
was solved by
L.-J.Yu,
M.Suga,
Z.-Y.Wang-Otomo,
J.-R.Shen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
46.92 /
1.90
|
|
Space group
|
C 1 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
145.280,
143.810,
210.280,
90.00,
90.74,
90.00
|
|
R / Rfree (%)
|
18.1 /
21.5
|
Other elements in 5y5s:
The structure of Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution 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 -
37;
Binding sites:
The binding sites of Magnesium atom in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution
(pdb code 5y5s). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 37 binding sites of Magnesium where determined in the
Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution, PDB code: 5y5s:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 37 in 5y5s
Go back to
Magnesium Binding Sites List in 5y5s
Magnesium binding site 1 out
of 37 in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg505
b:36.8
occ:1.00
|
O
|
C:HOH617
|
2.1
|
31.6
|
1.0
|
|
O
|
M:HOH526
|
2.1
|
36.0
|
1.0
|
|
O
|
C:HOH641
|
2.1
|
38.2
|
1.0
|
|
OE1
|
C:GLN183
|
2.1
|
34.0
|
1.0
|
|
O
|
C:HOH616
|
2.2
|
34.2
|
1.0
|
|
OE1
|
C:GLU230
|
2.2
|
40.4
|
1.0
|
|
CD
|
C:GLU230
|
3.1
|
43.4
|
1.0
|
|
CD
|
C:GLN183
|
3.1
|
40.4
|
1.0
|
|
OE2
|
C:GLU230
|
3.3
|
43.7
|
1.0
|
|
NE2
|
C:GLN183
|
3.6
|
45.5
|
1.0
|
|
OE1
|
M:GLU96
|
4.1
|
49.0
|
1.0
|
|
OD1
|
C:ASN184
|
4.1
|
32.9
|
1.0
|
|
OE2
|
M:GLU96
|
4.3
|
53.2
|
1.0
|
|
O
|
C:HOH796
|
4.3
|
57.4
|
1.0
|
|
CG
|
C:GLN183
|
4.3
|
32.9
|
1.0
|
|
CG
|
C:GLU230
|
4.5
|
36.7
|
1.0
|
|
CB
|
M:ASP184
|
4.5
|
32.9
|
1.0
|
|
O
|
M:PRO181
|
4.5
|
33.0
|
1.0
|
|
OD2
|
M:ASP184
|
4.6
|
34.6
|
1.0
|
|
CD
|
M:GLU96
|
4.6
|
44.1
|
1.0
|
|
CG
|
M:PRO176
|
4.6
|
40.0
|
1.0
|
|
O
|
C:SER194
|
4.7
|
31.2
|
1.0
|
|
CB
|
M:PRO181
|
4.9
|
30.9
|
1.0
|
|
CB
|
C:GLU230
|
4.9
|
37.4
|
1.0
|
|
CB
|
C:GLN183
|
4.9
|
32.9
|
1.0
|
|
CD
|
C:PRO196
|
4.9
|
37.0
|
1.0
|
|
CA
|
M:PRO181
|
5.0
|
32.4
|
1.0
|
|
Magnesium binding site 2 out
of 37 in 5y5s
Go back to
Magnesium Binding Sites List in 5y5s
Magnesium binding site 2 out
of 37 in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg301
b:32.0
occ:1.00
|
MG
|
L:BCL301
|
0.0
|
32.0
|
1.0
|
|
NB
|
L:BCL301
|
2.0
|
33.0
|
1.0
|
|
ND
|
L:BCL301
|
2.1
|
33.7
|
1.0
|
|
NA
|
L:BCL301
|
2.1
|
32.3
|
1.0
|
|
NC
|
L:BCL301
|
2.1
|
27.8
|
1.0
|
|
NE2
|
L:HIS182
|
2.2
|
31.2
|
1.0
|
|
C4D
|
L:BCL301
|
2.9
|
33.4
|
1.0
|
|
C1B
|
L:BCL301
|
3.0
|
29.7
|
1.0
|
|
C4B
|
L:BCL301
|
3.0
|
31.1
|
1.0
|
|
C4A
|
L:BCL301
|
3.0
|
29.6
|
1.0
|
|
C1C
|
L:BCL301
|
3.1
|
33.1
|
1.0
|
|
C1A
|
L:BCL301
|
3.1
|
31.7
|
1.0
|
|
C4C
|
L:BCL301
|
3.1
|
29.6
|
1.0
|
|
C1D
|
L:BCL301
|
3.1
|
35.0
|
1.0
|
|
CE1
|
L:HIS182
|
3.2
|
35.9
|
1.0
|
|
CD2
|
L:HIS182
|
3.2
|
33.0
|
1.0
|
|
CHB
|
L:BCL301
|
3.4
|
27.9
|
1.0
|
|
CHC
|
L:BCL301
|
3.4
|
30.4
|
1.0
|
|
CHA
|
L:BCL301
|
3.4
|
33.0
|
1.0
|
|
CHD
|
L:BCL301
|
3.6
|
27.8
|
1.0
|
|
CBB
|
M:BCL403
|
3.6
|
33.2
|
1.0
|
|
CAB
|
M:BCL403
|
3.8
|
32.0
|
1.0
|
|
OBB
|
M:BCL403
|
4.0
|
32.3
|
1.0
|
|
C3D
|
L:BCL301
|
4.2
|
36.7
|
1.0
|
|
ND1
|
L:HIS182
|
4.3
|
31.2
|
1.0
|
|
CG
|
L:HIS182
|
4.3
|
31.6
|
1.0
|
|
C3B
|
L:BCL301
|
4.4
|
30.3
|
1.0
|
|
C2D
|
L:BCL301
|
4.4
|
34.9
|
1.0
|
|
C2B
|
L:BCL301
|
4.4
|
30.9
|
1.0
|
|
C2C
|
L:BCL301
|
4.4
|
31.1
|
1.0
|
|
C3A
|
L:BCL301
|
4.4
|
32.8
|
1.0
|
|
C2A
|
L:BCL301
|
4.4
|
32.8
|
1.0
|
|
C3C
|
L:BCL301
|
4.4
|
30.1
|
1.0
|
|
C3B
|
M:BCL403
|
4.6
|
28.9
|
1.0
|
|
CD2
|
L:PHE176
|
4.7
|
29.8
|
1.0
|
|
CE2
|
L:PHE176
|
4.7
|
33.4
|
1.0
|
|
CBD
|
L:BCL301
|
4.9
|
37.3
|
1.0
|
|
Magnesium binding site 3 out
of 37 in 5y5s
Go back to
Magnesium Binding Sites List in 5y5s
Magnesium binding site 3 out
of 37 in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg401
b:34.6
occ:1.00
|
MG
|
M:BCL401
|
0.0
|
34.6
|
1.0
|
|
ND
|
M:BCL401
|
2.0
|
36.0
|
1.0
|
|
NB
|
M:BCL401
|
2.0
|
33.1
|
1.0
|
|
NC
|
M:BCL401
|
2.1
|
34.5
|
1.0
|
|
NA
|
M:BCL401
|
2.1
|
34.9
|
1.0
|
|
NE2
|
L:HIS162
|
2.2
|
38.4
|
1.0
|
|
C4D
|
M:BCL401
|
2.9
|
30.3
|
1.0
|
|
C1C
|
M:BCL401
|
3.0
|
40.2
|
1.0
|
|
C4B
|
M:BCL401
|
3.0
|
40.6
|
1.0
|
|
C1B
|
M:BCL401
|
3.1
|
40.7
|
1.0
|
|
C4A
|
M:BCL401
|
3.1
|
39.0
|
1.0
|
|
C4C
|
M:BCL401
|
3.1
|
32.6
|
1.0
|
|
C1A
|
M:BCL401
|
3.1
|
42.6
|
1.0
|
|
C1D
|
M:BCL401
|
3.1
|
31.6
|
1.0
|
|
CD2
|
L:HIS162
|
3.2
|
38.1
|
1.0
|
|
CE1
|
L:HIS162
|
3.2
|
34.8
|
1.0
|
|
CHC
|
M:BCL401
|
3.4
|
36.1
|
1.0
|
|
CHB
|
M:BCL401
|
3.4
|
39.3
|
1.0
|
|
CHA
|
M:BCL401
|
3.4
|
35.9
|
1.0
|
|
CHD
|
M:BCL401
|
3.6
|
30.9
|
1.0
|
|
C3D
|
M:BCL401
|
4.2
|
34.3
|
1.0
|
|
C2D
|
M:BCL401
|
4.3
|
34.3
|
1.0
|
|
C2C
|
M:BCL401
|
4.3
|
38.1
|
1.0
|
|
ND1
|
L:HIS162
|
4.3
|
36.3
|
1.0
|
|
CG
|
L:HIS162
|
4.4
|
37.6
|
1.0
|
|
C3C
|
M:BCL401
|
4.4
|
32.5
|
1.0
|
|
C3B
|
M:BCL401
|
4.4
|
33.5
|
1.0
|
|
C2B
|
M:BCL401
|
4.4
|
36.7
|
1.0
|
|
C3A
|
M:BCL401
|
4.4
|
38.1
|
1.0
|
|
C2A
|
M:BCL401
|
4.4
|
43.7
|
1.0
|
|
OBB
|
L:BPH302
|
4.5
|
48.2
|
1.0
|
|
C20
|
L:BPH302
|
4.6
|
38.9
|
1.0
|
|
CE2
|
M:TYR210
|
4.6
|
40.2
|
1.0
|
|
CBD
|
M:BCL401
|
4.9
|
33.1
|
1.0
|
|
CBC
|
M:BCL401
|
4.9
|
35.1
|
1.0
|
|
CBA
|
M:BCL401
|
5.0
|
36.2
|
1.0
|
|
CMA
|
M:BCL401
|
5.0
|
37.4
|
1.0
|
|
Magnesium binding site 4 out
of 37 in 5y5s
Go back to
Magnesium Binding Sites List in 5y5s
Magnesium binding site 4 out
of 37 in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg402
b:32.7
occ:1.00
|
MG
|
M:BCL402
|
0.0
|
32.7
|
1.0
|
|
NB
|
M:BCL402
|
2.1
|
35.2
|
1.0
|
|
NC
|
M:BCL402
|
2.1
|
32.5
|
1.0
|
|
ND
|
M:BCL402
|
2.1
|
36.6
|
1.0
|
|
NA
|
M:BCL402
|
2.1
|
35.4
|
1.0
|
|
NE2
|
M:HIS182
|
2.2
|
32.1
|
1.0
|
|
C4D
|
M:BCL402
|
2.9
|
28.5
|
1.0
|
|
CD2
|
M:HIS182
|
3.0
|
29.0
|
1.0
|
|
C4C
|
M:BCL402
|
3.0
|
28.3
|
1.0
|
|
C1C
|
M:BCL402
|
3.0
|
32.0
|
1.0
|
|
C4B
|
M:BCL402
|
3.0
|
31.9
|
1.0
|
|
C4A
|
M:BCL402
|
3.1
|
35.6
|
1.0
|
|
C1B
|
M:BCL402
|
3.1
|
30.2
|
1.0
|
|
C1A
|
M:BCL402
|
3.1
|
32.3
|
1.0
|
|
C1D
|
M:BCL402
|
3.1
|
32.4
|
1.0
|
|
CE1
|
M:HIS182
|
3.3
|
31.2
|
1.0
|
|
CHC
|
M:BCL402
|
3.4
|
30.4
|
1.0
|
|
CHA
|
M:BCL402
|
3.4
|
26.6
|
1.0
|
|
CHB
|
M:BCL402
|
3.5
|
34.7
|
1.0
|
|
CHD
|
M:BCL402
|
3.5
|
35.6
|
1.0
|
|
C3D
|
M:BCL402
|
4.1
|
29.2
|
1.0
|
|
CG
|
M:HIS182
|
4.2
|
27.3
|
1.0
|
|
C2D
|
M:BCL402
|
4.3
|
28.6
|
1.0
|
|
C2C
|
M:BCL402
|
4.3
|
33.5
|
1.0
|
|
ND1
|
M:HIS182
|
4.3
|
26.4
|
1.0
|
|
C3C
|
M:BCL402
|
4.4
|
33.9
|
1.0
|
|
C3B
|
M:BCL402
|
4.4
|
26.9
|
1.0
|
|
C2B
|
M:BCL402
|
4.4
|
36.8
|
1.0
|
|
C3A
|
M:BCL402
|
4.4
|
33.2
|
1.0
|
|
C2A
|
M:BCL402
|
4.4
|
31.7
|
1.0
|
|
OBB
|
M:BPH404
|
4.5
|
49.5
|
1.0
|
|
CE2
|
L:PHE190
|
4.7
|
35.5
|
1.0
|
|
C18
|
M:CRT406
|
4.8
|
41.9
|
1.0
|
|
CBD
|
M:BCL402
|
4.8
|
35.5
|
1.0
|
|
CMA
|
M:BCL402
|
4.9
|
34.2
|
1.0
|
|
CBA
|
M:BCL402
|
5.0
|
41.5
|
1.0
|
|
Magnesium binding site 5 out
of 37 in 5y5s
Go back to
Magnesium Binding Sites List in 5y5s
Magnesium binding site 5 out
of 37 in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg403
b:32.8
occ:1.00
|
MG
|
M:BCL403
|
0.0
|
32.8
|
1.0
|
|
NB
|
M:BCL403
|
2.0
|
33.3
|
1.0
|
|
ND
|
M:BCL403
|
2.1
|
32.4
|
1.0
|
|
NC
|
M:BCL403
|
2.1
|
29.8
|
1.0
|
|
NA
|
M:BCL403
|
2.1
|
30.9
|
1.0
|
|
NE2
|
M:HIS202
|
2.2
|
34.5
|
1.0
|
|
C4D
|
M:BCL403
|
2.9
|
32.8
|
1.0
|
|
C1C
|
M:BCL403
|
3.0
|
33.5
|
1.0
|
|
C4B
|
M:BCL403
|
3.0
|
29.6
|
1.0
|
|
C1B
|
M:BCL403
|
3.0
|
29.8
|
1.0
|
|
C1A
|
M:BCL403
|
3.1
|
30.1
|
1.0
|
|
CE1
|
M:HIS202
|
3.1
|
29.0
|
1.0
|
|
C4A
|
M:BCL403
|
3.1
|
27.2
|
1.0
|
|
C4C
|
M:BCL403
|
3.1
|
27.5
|
1.0
|
|
C1D
|
M:BCL403
|
3.2
|
36.8
|
1.0
|
|
CD2
|
M:HIS202
|
3.3
|
31.9
|
1.0
|
|
CHA
|
M:BCL403
|
3.4
|
32.9
|
1.0
|
|
CHC
|
M:BCL403
|
3.4
|
30.8
|
1.0
|
|
CHB
|
M:BCL403
|
3.4
|
28.8
|
1.0
|
|
CBB
|
L:BCL301
|
3.5
|
30.5
|
1.0
|
|
CHD
|
M:BCL403
|
3.6
|
29.2
|
1.0
|
|
CAB
|
L:BCL301
|
3.8
|
29.1
|
1.0
|
|
OBB
|
L:BCL301
|
4.1
|
34.0
|
1.0
|
|
C3D
|
M:BCL403
|
4.2
|
32.8
|
1.0
|
|
ND1
|
M:HIS202
|
4.2
|
32.2
|
1.0
|
|
C2C
|
M:BCL403
|
4.3
|
31.1
|
1.0
|
|
C3B
|
M:BCL403
|
4.3
|
28.9
|
1.0
|
|
C2B
|
M:BCL403
|
4.4
|
31.3
|
1.0
|
|
CG
|
M:HIS202
|
4.4
|
29.7
|
1.0
|
|
C2D
|
M:BCL403
|
4.4
|
32.9
|
1.0
|
|
C3C
|
M:BCL403
|
4.4
|
29.9
|
1.0
|
|
C2A
|
M:BCL403
|
4.4
|
34.0
|
1.0
|
|
C3A
|
M:BCL403
|
4.4
|
34.9
|
1.0
|
|
C3B
|
L:BCL301
|
4.4
|
30.3
|
1.0
|
|
CBD
|
M:BCL403
|
4.8
|
35.7
|
1.0
|
|
CD1
|
M:ILE206
|
4.9
|
33.5
|
1.0
|
|
Magnesium binding site 6 out
of 37 in 5y5s
Go back to
Magnesium Binding Sites List in 5y5s
Magnesium binding site 6 out
of 37 in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg101
b:61.5
occ:1.00
|
MG
|
A:BCL101
|
0.0
|
61.5
|
1.0
|
|
NB
|
A:BCL101
|
2.0
|
64.4
|
1.0
|
|
ND
|
A:BCL101
|
2.0
|
65.5
|
1.0
|
|
NC
|
A:BCL101
|
2.1
|
71.0
|
1.0
|
|
NA
|
A:BCL101
|
2.1
|
63.5
|
1.0
|
|
NE2
|
A:HIS36
|
2.2
|
62.4
|
1.0
|
|
C4D
|
A:BCL101
|
2.9
|
67.2
|
1.0
|
|
C1C
|
A:BCL101
|
3.0
|
69.9
|
1.0
|
|
C4B
|
A:BCL101
|
3.0
|
57.9
|
1.0
|
|
C1B
|
A:BCL101
|
3.0
|
57.7
|
1.0
|
|
CE1
|
A:HIS36
|
3.1
|
54.7
|
1.0
|
|
C1A
|
A:BCL101
|
3.1
|
64.6
|
1.0
|
|
C4A
|
A:BCL101
|
3.1
|
62.7
|
1.0
|
|
C4C
|
A:BCL101
|
3.1
|
69.6
|
1.0
|
|
C1D
|
A:BCL101
|
3.2
|
72.2
|
1.0
|
|
CD2
|
A:HIS36
|
3.3
|
58.3
|
1.0
|
|
CHC
|
A:BCL101
|
3.4
|
61.5
|
1.0
|
|
CHA
|
A:BCL101
|
3.4
|
64.7
|
1.0
|
|
CHB
|
A:BCL101
|
3.4
|
56.6
|
1.0
|
|
CHD
|
A:BCL101
|
3.6
|
59.6
|
1.0
|
|
C3D
|
A:BCL101
|
4.2
|
60.8
|
1.0
|
|
CMD
|
A:BCL103
|
4.2
|
59.1
|
1.0
|
|
ND1
|
A:HIS36
|
4.2
|
54.9
|
1.0
|
|
C3B
|
A:BCL101
|
4.3
|
56.4
|
1.0
|
|
C2B
|
A:BCL101
|
4.4
|
62.6
|
1.0
|
|
C2D
|
A:BCL101
|
4.4
|
69.2
|
1.0
|
|
C2C
|
A:BCL101
|
4.4
|
75.5
|
1.0
|
|
CG
|
A:HIS36
|
4.4
|
56.0
|
1.0
|
|
C3C
|
A:BCL101
|
4.4
|
71.7
|
1.0
|
|
C2A
|
A:BCL101
|
4.4
|
67.4
|
1.0
|
|
C3A
|
A:BCL101
|
4.5
|
68.3
|
1.0
|
|
C13
|
B:UNL101
|
4.6
|
69.3
|
1.0
|
|
CBB
|
0:BCL102
|
4.7
|
65.6
|
1.0
|
|
CMB
|
0:BCL102
|
4.8
|
64.1
|
1.0
|
|
CBD
|
A:BCL101
|
4.8
|
66.2
|
1.0
|
|
C12
|
B:UNL101
|
4.8
|
72.1
|
1.0
|
|
Magnesium binding site 7 out
of 37 in 5y5s
Go back to
Magnesium Binding Sites List in 5y5s
Magnesium binding site 7 out
of 37 in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg103
b:70.1
occ:1.00
|
MG
|
A:BCL103
|
0.0
|
70.1
|
1.0
|
|
NB
|
A:BCL103
|
2.0
|
67.0
|
1.0
|
|
ND
|
A:BCL103
|
2.1
|
70.3
|
1.0
|
|
NC
|
A:BCL103
|
2.1
|
68.4
|
1.0
|
|
NA
|
A:BCL103
|
2.1
|
67.8
|
1.0
|
|
NE2
|
B:HIS36
|
2.2
|
66.4
|
1.0
|
|
C4D
|
A:BCL103
|
2.9
|
60.4
|
1.0
|
|
CE1
|
B:HIS36
|
3.0
|
63.8
|
1.0
|
|
C4B
|
A:BCL103
|
3.0
|
66.0
|
1.0
|
|
C1C
|
A:BCL103
|
3.0
|
64.4
|
1.0
|
|
C1B
|
A:BCL103
|
3.0
|
69.2
|
1.0
|
|
C4A
|
A:BCL103
|
3.1
|
68.3
|
1.0
|
|
C1A
|
A:BCL103
|
3.1
|
64.4
|
1.0
|
|
C4C
|
A:BCL103
|
3.1
|
63.8
|
1.0
|
|
C1D
|
A:BCL103
|
3.2
|
64.9
|
1.0
|
|
CD2
|
B:HIS36
|
3.3
|
66.0
|
1.0
|
|
CHC
|
A:BCL103
|
3.4
|
60.9
|
1.0
|
|
CHB
|
A:BCL103
|
3.4
|
70.1
|
1.0
|
|
CHA
|
A:BCL103
|
3.4
|
62.6
|
1.0
|
|
CHD
|
A:BCL103
|
3.6
|
59.7
|
1.0
|
|
C3D
|
A:BCL103
|
4.2
|
58.1
|
1.0
|
|
ND1
|
B:HIS36
|
4.2
|
65.5
|
1.0
|
|
CMB
|
D:BCL101
|
4.2
|
60.4
|
1.0
|
|
C3B
|
A:BCL103
|
4.3
|
68.2
|
1.0
|
|
C2D
|
A:BCL103
|
4.4
|
60.2
|
1.0
|
|
CG
|
B:HIS36
|
4.4
|
69.0
|
1.0
|
|
C2B
|
A:BCL103
|
4.4
|
68.2
|
1.0
|
|
C2C
|
A:BCL103
|
4.4
|
67.3
|
1.0
|
|
C3C
|
A:BCL103
|
4.4
|
65.9
|
1.0
|
|
CBB
|
D:BCL101
|
4.4
|
56.3
|
1.0
|
|
C3A
|
A:BCL103
|
4.4
|
66.7
|
1.0
|
|
C2A
|
A:BCL103
|
4.4
|
62.0
|
1.0
|
|
CMD
|
A:BCL101
|
4.6
|
74.5
|
1.0
|
|
C2B
|
D:BCL101
|
4.7
|
62.9
|
1.0
|
|
CG2
|
A:ILE35
|
4.7
|
58.9
|
1.0
|
|
CD1
|
A:ILE35
|
4.8
|
59.2
|
1.0
|
|
CBD
|
A:BCL103
|
4.9
|
65.2
|
1.0
|
|
Magnesium binding site 8 out
of 37 in 5y5s
Go back to
Magnesium Binding Sites List in 5y5s
Magnesium binding site 8 out
of 37 in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg101
b:66.1
occ:1.00
|
MG
|
D:BCL101
|
0.0
|
66.1
|
1.0
|
|
NB
|
D:BCL101
|
2.0
|
65.7
|
1.0
|
|
ND
|
D:BCL101
|
2.0
|
67.7
|
1.0
|
|
NC
|
D:BCL101
|
2.1
|
67.0
|
1.0
|
|
NA
|
D:BCL101
|
2.1
|
65.0
|
1.0
|
|
NE2
|
D:HIS36
|
2.2
|
63.1
|
1.0
|
|
C4D
|
D:BCL101
|
2.9
|
67.7
|
1.0
|
|
CE1
|
D:HIS36
|
3.0
|
59.0
|
1.0
|
|
C1C
|
D:BCL101
|
3.0
|
71.2
|
1.0
|
|
C4B
|
D:BCL101
|
3.0
|
61.9
|
1.0
|
|
C1B
|
D:BCL101
|
3.0
|
62.5
|
1.0
|
|
C1A
|
D:BCL101
|
3.1
|
62.5
|
1.0
|
|
C4A
|
D:BCL101
|
3.1
|
61.6
|
1.0
|
|
C4C
|
D:BCL101
|
3.1
|
69.5
|
1.0
|
|
C1D
|
D:BCL101
|
3.2
|
71.9
|
1.0
|
|
CD2
|
D:HIS36
|
3.3
|
57.5
|
1.0
|
|
CHC
|
D:BCL101
|
3.3
|
67.5
|
1.0
|
|
CHA
|
D:BCL101
|
3.4
|
65.4
|
1.0
|
|
CHB
|
D:BCL101
|
3.4
|
60.1
|
1.0
|
|
CHD
|
D:BCL101
|
3.6
|
69.3
|
1.0
|
|
C12
|
E:UNL101
|
3.9
|
78.8
|
1.0
|
|
CMD
|
D:BCL102
|
4.1
|
57.0
|
1.0
|
|
C3D
|
D:BCL101
|
4.2
|
67.4
|
1.0
|
|
ND1
|
D:HIS36
|
4.2
|
60.1
|
1.0
|
|
C3B
|
D:BCL101
|
4.3
|
61.8
|
1.0
|
|
C2D
|
D:BCL101
|
4.3
|
71.0
|
1.0
|
|
C2B
|
D:BCL101
|
4.4
|
62.9
|
1.0
|
|
C2C
|
D:BCL101
|
4.4
|
72.5
|
1.0
|
|
CG
|
D:HIS36
|
4.4
|
57.0
|
1.0
|
|
C3C
|
D:BCL101
|
4.4
|
67.1
|
1.0
|
|
C2A
|
D:BCL101
|
4.4
|
66.0
|
1.0
|
|
C3A
|
D:BCL101
|
4.4
|
63.1
|
1.0
|
|
C13
|
E:UNL101
|
4.6
|
78.8
|
1.0
|
|
CMB
|
A:BCL103
|
4.8
|
74.4
|
1.0
|
|
CBB
|
A:BCL103
|
4.8
|
77.8
|
1.0
|
|
CBD
|
D:BCL101
|
4.8
|
70.4
|
1.0
|
|
C11
|
E:UNL101
|
4.8
|
85.5
|
1.0
|
|
C2D
|
D:BCL102
|
5.0
|
61.5
|
1.0
|
|
Magnesium binding site 9 out
of 37 in 5y5s
Go back to
Magnesium Binding Sites List in 5y5s
Magnesium binding site 9 out
of 37 in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg102
b:68.0
occ:1.00
|
MG
|
D:BCL102
|
0.0
|
68.0
|
1.0
|
|
NB
|
D:BCL102
|
2.0
|
67.4
|
1.0
|
|
ND
|
D:BCL102
|
2.0
|
65.9
|
1.0
|
|
NC
|
D:BCL102
|
2.1
|
70.3
|
1.0
|
|
NA
|
D:BCL102
|
2.1
|
63.5
|
1.0
|
|
NE2
|
E:HIS36
|
2.2
|
71.5
|
1.0
|
|
C4D
|
D:BCL102
|
2.9
|
66.6
|
1.0
|
|
C1C
|
D:BCL102
|
3.0
|
69.2
|
1.0
|
|
C4B
|
D:BCL102
|
3.0
|
66.9
|
1.0
|
|
C1B
|
D:BCL102
|
3.0
|
67.2
|
1.0
|
|
C4A
|
D:BCL102
|
3.0
|
64.7
|
1.0
|
|
C1A
|
D:BCL102
|
3.1
|
65.6
|
1.0
|
|
CE1
|
E:HIS36
|
3.1
|
67.8
|
1.0
|
|
C4C
|
D:BCL102
|
3.1
|
69.6
|
1.0
|
|
C1D
|
D:BCL102
|
3.2
|
65.4
|
1.0
|
|
CD2
|
E:HIS36
|
3.2
|
66.9
|
1.0
|
|
CHC
|
D:BCL102
|
3.4
|
67.5
|
1.0
|
|
CHB
|
D:BCL102
|
3.4
|
65.8
|
1.0
|
|
CHA
|
D:BCL102
|
3.4
|
67.9
|
1.0
|
|
CHD
|
D:BCL102
|
3.6
|
66.1
|
1.0
|
|
C3D
|
D:BCL102
|
4.2
|
62.8
|
1.0
|
|
ND1
|
E:HIS36
|
4.2
|
71.8
|
1.0
|
|
CMB
|
F:BCL101
|
4.3
|
64.0
|
1.0
|
|
CG
|
E:HIS36
|
4.3
|
71.7
|
1.0
|
|
C3B
|
D:BCL102
|
4.4
|
65.5
|
1.0
|
|
C2D
|
D:BCL102
|
4.4
|
61.5
|
1.0
|
|
C2C
|
D:BCL102
|
4.4
|
71.1
|
1.0
|
|
C2B
|
D:BCL102
|
4.4
|
63.1
|
1.0
|
|
C3C
|
D:BCL102
|
4.4
|
73.2
|
1.0
|
|
C3A
|
D:BCL102
|
4.4
|
63.6
|
1.0
|
|
C2A
|
D:BCL102
|
4.4
|
65.1
|
1.0
|
|
CBB
|
F:BCL101
|
4.4
|
63.6
|
1.0
|
|
CMD
|
D:BCL101
|
4.4
|
69.2
|
1.0
|
|
CG2
|
D:ILE35
|
4.8
|
53.9
|
1.0
|
|
C2B
|
F:BCL101
|
4.8
|
64.1
|
1.0
|
|
CBD
|
D:BCL102
|
4.9
|
61.8
|
1.0
|
|
Magnesium binding site 10 out
of 37 in 5y5s
Go back to
Magnesium Binding Sites List in 5y5s
Magnesium binding site 10 out
of 37 in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg101
b:67.8
occ:1.00
|
MG
|
F:BCL101
|
0.0
|
67.8
|
1.0
|
|
NB
|
F:BCL101
|
2.0
|
67.2
|
1.0
|
|
ND
|
F:BCL101
|
2.0
|
69.4
|
1.0
|
|
NC
|
F:BCL101
|
2.1
|
63.9
|
1.0
|
|
NA
|
F:BCL101
|
2.1
|
67.8
|
1.0
|
|
NE2
|
F:HIS36
|
2.2
|
59.9
|
1.0
|
|
C4D
|
F:BCL101
|
2.9
|
68.5
|
1.0
|
|
C1C
|
F:BCL101
|
3.0
|
65.6
|
1.0
|
|
C4B
|
F:BCL101
|
3.0
|
64.1
|
1.0
|
|
CE1
|
F:HIS36
|
3.0
|
61.6
|
1.0
|
|
C1B
|
F:BCL101
|
3.1
|
63.6
|
1.0
|
|
C1A
|
F:BCL101
|
3.1
|
66.3
|
1.0
|
|
C4A
|
F:BCL101
|
3.1
|
65.9
|
1.0
|
|
C4C
|
F:BCL101
|
3.1
|
65.2
|
1.0
|
|
C1D
|
F:BCL101
|
3.2
|
70.2
|
1.0
|
|
CD2
|
F:HIS36
|
3.3
|
57.1
|
1.0
|
|
CHC
|
F:BCL101
|
3.4
|
67.5
|
1.0
|
|
CHA
|
F:BCL101
|
3.4
|
67.0
|
1.0
|
|
CHB
|
F:BCL101
|
3.4
|
57.1
|
1.0
|
|
CHD
|
F:BCL101
|
3.6
|
65.8
|
1.0
|
|
CMD
|
F:BCL102
|
4.1
|
55.8
|
1.0
|
|
C3D
|
F:BCL101
|
4.2
|
69.5
|
1.0
|
|
ND1
|
F:HIS36
|
4.2
|
57.4
|
1.0
|
|
C12
|
G:UNL102
|
4.2
|
79.2
|
1.0
|
|
C3B
|
F:BCL101
|
4.3
|
66.0
|
1.0
|
|
C13
|
G:UNL102
|
4.3
|
77.0
|
1.0
|
|
C2D
|
F:BCL101
|
4.4
|
64.3
|
1.0
|
|
CG
|
F:HIS36
|
4.4
|
54.2
|
1.0
|
|
C2B
|
F:BCL101
|
4.4
|
64.1
|
1.0
|
|
C2C
|
F:BCL101
|
4.4
|
68.9
|
1.0
|
|
C3C
|
F:BCL101
|
4.4
|
68.6
|
1.0
|
|
C2A
|
F:BCL101
|
4.4
|
70.4
|
1.0
|
|
C3A
|
F:BCL101
|
4.4
|
69.7
|
1.0
|
|
CBB
|
D:BCL102
|
4.8
|
73.2
|
1.0
|
|
CBD
|
F:BCL101
|
4.8
|
70.2
|
1.0
|
|
CMB
|
D:BCL102
|
4.9
|
64.9
|
1.0
|
|
Reference:
L.-J.Yu,
M.Suga,
Z.-Y.Wang-Otomo,
J.R.Shen.
Structure of Photosynthetic LH1-Rc Supercomplex at 1.9 Angstrom Resolution. Nature V. 556 209 2018.
ISSN: ESSN 1476-4687
PubMed: 29618814
DOI: 10.1038/S41586-018-0002-9
Page generated: Wed Aug 13 00:45:13 2025
|
