Calcium in PDB 8wdu: Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By Sucrose Density
Other elements in 8wdu:
The structure of Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By Sucrose Density also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By Sucrose Density
(pdb code 8wdu). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By Sucrose Density, PDB code: 8wdu:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 8wdu
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Calcium Binding Sites List in 8wdu
Calcium binding site 1 out
of 6 in the Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By Sucrose Density
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By Sucrose Density within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca103
b:44.6
occ:1.00
|
O
|
B:TRP46
|
2.2
|
46.1
|
1.0
|
OD1
|
D:ASP47
|
2.2
|
59.5
|
1.0
|
O
|
D:TRP44
|
2.3
|
39.6
|
1.0
|
O
|
D:VAL49
|
2.3
|
58.6
|
1.0
|
O
|
D:HOH204
|
2.4
|
46.6
|
1.0
|
O
|
D:HOH201
|
2.4
|
46.5
|
1.0
|
CG
|
D:ASP47
|
3.1
|
55.7
|
1.0
|
OD2
|
D:ASP47
|
3.2
|
58.8
|
1.0
|
C
|
B:TRP46
|
3.4
|
38.3
|
1.0
|
C
|
D:TRP44
|
3.4
|
36.0
|
1.0
|
C
|
D:VAL49
|
3.4
|
56.0
|
1.0
|
N
|
D:VAL49
|
3.9
|
57.2
|
1.0
|
CA
|
D:TRP44
|
4.0
|
31.7
|
1.0
|
CA
|
D:VAL49
|
4.1
|
56.8
|
1.0
|
N
|
B:LEU47
|
4.2
|
43.9
|
1.0
|
CA
|
B:LEU47
|
4.3
|
48.4
|
1.0
|
CA
|
B:TRP46
|
4.3
|
32.4
|
1.0
|
N
|
D:LEU45
|
4.4
|
40.7
|
1.0
|
N
|
D:PRO50
|
4.4
|
59.2
|
1.0
|
CB
|
D:TRP44
|
4.5
|
26.1
|
1.0
|
CB
|
D:VAL49
|
4.5
|
59.1
|
1.0
|
CB
|
D:ASP47
|
4.5
|
50.5
|
1.0
|
CA
|
D:LEU45
|
4.6
|
38.9
|
1.0
|
N
|
D:GLY48
|
4.6
|
55.9
|
1.0
|
CD
|
D:PRO50
|
4.6
|
55.5
|
1.0
|
O
|
D:HOH202
|
4.7
|
56.6
|
1.0
|
O
|
B:HOH201
|
4.7
|
52.5
|
1.0
|
N
|
D:ASP47
|
4.8
|
50.3
|
1.0
|
C
|
D:LEU45
|
4.8
|
46.6
|
1.0
|
O
|
D:LEU45
|
4.8
|
54.2
|
1.0
|
CB
|
B:TRP46
|
4.9
|
33.5
|
1.0
|
C
|
D:GLY48
|
4.9
|
59.7
|
1.0
|
C
|
B:LEU47
|
4.9
|
57.0
|
1.0
|
|
Calcium binding site 2 out
of 6 in 8wdu
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Calcium Binding Sites List in 8wdu
Calcium binding site 2 out
of 6 in the Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By Sucrose Density
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By Sucrose Density within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca503
b:92.4
occ:1.00
|
OD1
|
F:ASP47
|
2.2
|
81.0
|
1.0
|
O
|
E:TRP46
|
2.3
|
56.1
|
1.0
|
O
|
F:VAL49
|
2.3
|
85.8
|
1.0
|
O
|
E:HOH201
|
2.4
|
67.3
|
1.0
|
O
|
F:HOH601
|
2.4
|
68.3
|
1.0
|
O
|
F:TRP44
|
2.5
|
52.6
|
1.0
|
CG
|
F:ASP47
|
3.0
|
79.9
|
1.0
|
OD2
|
F:ASP47
|
3.2
|
79.9
|
1.0
|
C
|
F:TRP44
|
3.3
|
43.8
|
1.0
|
C
|
E:TRP46
|
3.3
|
49.7
|
1.0
|
C
|
F:VAL49
|
3.4
|
87.4
|
1.0
|
CA
|
F:TRP44
|
3.8
|
38.8
|
1.0
|
N
|
F:VAL49
|
3.9
|
86.4
|
1.0
|
CA
|
E:TRP46
|
4.0
|
41.9
|
1.0
|
CA
|
F:VAL49
|
4.1
|
86.6
|
1.0
|
N
|
E:LEU47
|
4.3
|
60.4
|
1.0
|
CB
|
F:TRP44
|
4.3
|
40.1
|
1.0
|
N
|
F:PRO50
|
4.4
|
89.9
|
1.0
|
N
|
F:LEU45
|
4.4
|
52.4
|
1.0
|
CB
|
F:ASP47
|
4.5
|
78.1
|
1.0
|
CB
|
F:VAL49
|
4.5
|
85.8
|
1.0
|
O
|
F:HOH602
|
4.5
|
65.0
|
1.0
|
CA
|
E:LEU47
|
4.5
|
61.0
|
1.0
|
CB
|
E:TRP46
|
4.6
|
44.0
|
1.0
|
CD
|
F:PRO50
|
4.7
|
81.0
|
1.0
|
N
|
F:GLY48
|
4.7
|
87.8
|
1.0
|
N
|
F:ASP47
|
4.7
|
77.4
|
1.0
|
CA
|
F:LEU45
|
4.8
|
48.5
|
1.0
|
O
|
F:ASN43
|
4.8
|
55.8
|
1.0
|
CD2
|
E:LEU47
|
4.8
|
60.1
|
1.0
|
C
|
F:GLY48
|
5.0
|
89.8
|
1.0
|
CA
|
F:ASP47
|
5.0
|
80.3
|
1.0
|
|
Calcium binding site 3 out
of 6 in 8wdu
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Calcium Binding Sites List in 8wdu
Calcium binding site 3 out
of 6 in the Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By Sucrose Density
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By Sucrose Density within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Ca103
b:53.7
occ:1.00
|
OD1
|
S:ASP47
|
2.3
|
58.4
|
1.0
|
O
|
S:VAL49
|
2.3
|
67.0
|
1.0
|
O
|
S:TRP44
|
2.3
|
47.1
|
1.0
|
O
|
R:TRP46
|
2.4
|
45.1
|
1.0
|
O
|
S:HOH205
|
2.4
|
46.0
|
1.0
|
O
|
S:HOH202
|
2.4
|
56.1
|
1.0
|
CG
|
S:ASP47
|
3.1
|
57.3
|
1.0
|
OD2
|
S:ASP47
|
3.2
|
57.0
|
1.0
|
C
|
S:VAL49
|
3.4
|
67.2
|
1.0
|
C
|
S:TRP44
|
3.4
|
33.7
|
1.0
|
C
|
R:TRP46
|
3.5
|
35.0
|
1.0
|
N
|
S:VAL49
|
3.9
|
68.2
|
1.0
|
CA
|
S:TRP44
|
4.1
|
36.1
|
1.0
|
CA
|
S:VAL49
|
4.1
|
67.7
|
1.0
|
O
|
S:HOH201
|
4.2
|
62.6
|
1.0
|
CA
|
R:TRP46
|
4.3
|
35.8
|
1.0
|
CB
|
S:VAL49
|
4.4
|
66.4
|
1.0
|
N
|
R:LEU47
|
4.4
|
48.7
|
1.0
|
N
|
S:PRO50
|
4.4
|
70.8
|
1.0
|
N
|
S:LEU45
|
4.5
|
38.6
|
1.0
|
O
|
R:HOH201
|
4.5
|
55.7
|
1.0
|
CA
|
R:LEU47
|
4.5
|
46.7
|
1.0
|
CB
|
S:ASP47
|
4.5
|
56.1
|
1.0
|
CB
|
S:TRP44
|
4.5
|
31.2
|
1.0
|
N
|
S:GLY48
|
4.6
|
62.0
|
1.0
|
CD
|
S:PRO50
|
4.6
|
65.9
|
1.0
|
CA
|
S:LEU45
|
4.7
|
37.6
|
1.0
|
N
|
S:ASP47
|
4.7
|
59.2
|
1.0
|
CD2
|
R:LEU47
|
4.8
|
52.8
|
1.0
|
CB
|
R:TRP46
|
4.9
|
32.9
|
1.0
|
C
|
S:LEU45
|
4.9
|
44.4
|
1.0
|
C
|
S:GLY48
|
4.9
|
67.8
|
1.0
|
CA
|
S:ASP47
|
5.0
|
61.1
|
1.0
|
C
|
S:ASP47
|
5.0
|
59.3
|
1.0
|
|
Calcium binding site 4 out
of 6 in 8wdu
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Calcium Binding Sites List in 8wdu
Calcium binding site 4 out
of 6 in the Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By Sucrose Density
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By Sucrose Density within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
U:Ca102
b:42.3
occ:1.00
|
O
|
U:VAL49
|
2.2
|
58.7
|
1.0
|
O
|
T:TRP46
|
2.3
|
40.4
|
1.0
|
O
|
U:TRP44
|
2.3
|
44.9
|
1.0
|
OD1
|
U:ASP47
|
2.3
|
53.9
|
1.0
|
O
|
U:HOH208
|
2.4
|
46.0
|
1.0
|
O
|
U:HOH203
|
2.4
|
47.6
|
1.0
|
CG
|
U:ASP47
|
3.2
|
48.0
|
1.0
|
C
|
U:VAL49
|
3.3
|
53.9
|
1.0
|
C
|
T:TRP46
|
3.3
|
36.7
|
1.0
|
OD2
|
U:ASP47
|
3.3
|
48.8
|
1.0
|
C
|
U:TRP44
|
3.4
|
33.0
|
1.0
|
N
|
U:VAL49
|
3.9
|
54.3
|
1.0
|
CA
|
U:TRP44
|
4.0
|
29.6
|
1.0
|
CA
|
U:VAL49
|
4.1
|
51.1
|
1.0
|
CA
|
T:TRP46
|
4.1
|
36.3
|
1.0
|
N
|
T:LEU47
|
4.3
|
45.9
|
1.0
|
N
|
U:PRO50
|
4.3
|
55.0
|
1.0
|
O
|
T:HOH201
|
4.3
|
49.3
|
1.0
|
N
|
U:LEU45
|
4.4
|
38.5
|
1.0
|
CA
|
T:LEU47
|
4.4
|
47.0
|
1.0
|
CB
|
U:TRP44
|
4.4
|
30.6
|
1.0
|
CD
|
U:PRO50
|
4.5
|
53.4
|
1.0
|
CB
|
U:VAL49
|
4.5
|
49.9
|
1.0
|
N
|
U:GLY48
|
4.6
|
53.5
|
1.0
|
CB
|
U:ASP47
|
4.6
|
48.2
|
1.0
|
CA
|
U:LEU45
|
4.7
|
35.7
|
1.0
|
CB
|
T:TRP46
|
4.7
|
34.9
|
1.0
|
N
|
U:ASP47
|
4.8
|
43.3
|
1.0
|
O
|
U:HOH205
|
4.8
|
50.1
|
1.0
|
C
|
U:LEU45
|
4.8
|
42.0
|
1.0
|
C
|
U:GLY48
|
4.9
|
58.7
|
1.0
|
O
|
U:HOH204
|
4.9
|
53.4
|
1.0
|
O
|
U:LEU45
|
5.0
|
50.0
|
1.0
|
|
Calcium binding site 5 out
of 6 in 8wdu
Go back to
Calcium Binding Sites List in 8wdu
Calcium binding site 5 out
of 6 in the Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By Sucrose Density
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By Sucrose Density within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
W:Ca102
b:49.8
occ:1.00
|
O
|
W:VAL49
|
2.2
|
59.4
|
1.0
|
O
|
W:TRP44
|
2.2
|
48.5
|
1.0
|
O
|
V:TRP46
|
2.3
|
47.1
|
1.0
|
OD1
|
W:ASP47
|
2.4
|
57.9
|
1.0
|
O
|
W:HOH202
|
2.4
|
50.1
|
1.0
|
O
|
W:HOH207
|
2.4
|
51.6
|
1.0
|
CG
|
W:ASP47
|
3.2
|
55.4
|
1.0
|
OD2
|
W:ASP47
|
3.3
|
56.4
|
1.0
|
C
|
W:TRP44
|
3.4
|
39.0
|
1.0
|
C
|
W:VAL49
|
3.4
|
61.5
|
1.0
|
C
|
V:TRP46
|
3.5
|
47.3
|
1.0
|
N
|
W:VAL49
|
4.0
|
64.9
|
1.0
|
CA
|
W:TRP44
|
4.0
|
31.6
|
1.0
|
O
|
W:HOH203
|
4.1
|
57.3
|
1.0
|
CA
|
W:VAL49
|
4.2
|
62.2
|
1.0
|
CA
|
V:TRP46
|
4.3
|
42.7
|
1.0
|
N
|
W:LEU45
|
4.4
|
43.8
|
1.0
|
N
|
W:PRO50
|
4.4
|
63.4
|
1.0
|
N
|
V:LEU47
|
4.5
|
53.2
|
1.0
|
CB
|
W:VAL49
|
4.5
|
61.1
|
1.0
|
CB
|
W:TRP44
|
4.5
|
34.8
|
1.0
|
CD
|
W:PRO50
|
4.5
|
62.2
|
1.0
|
CA
|
V:LEU47
|
4.6
|
52.3
|
1.0
|
O
|
V:HOH203
|
4.6
|
58.0
|
1.0
|
CD2
|
V:LEU47
|
4.6
|
56.4
|
1.0
|
N
|
W:GLY48
|
4.6
|
62.8
|
1.0
|
CB
|
W:ASP47
|
4.6
|
53.6
|
1.0
|
CA
|
W:LEU45
|
4.6
|
41.2
|
1.0
|
N
|
W:ASP47
|
4.7
|
53.7
|
1.0
|
CB
|
V:TRP46
|
4.8
|
39.9
|
1.0
|
C
|
W:LEU45
|
4.8
|
47.7
|
1.0
|
C
|
W:GLY48
|
4.9
|
64.4
|
1.0
|
|
Calcium binding site 6 out
of 6 in 8wdu
Go back to
Calcium Binding Sites List in 8wdu
Calcium binding site 6 out
of 6 in the Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By Sucrose Density
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By Sucrose Density within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Y:Ca103
b:63.0
occ:1.00
|
O
|
Y:TRP44
|
2.2
|
56.4
|
1.0
|
O
|
X:TRP46
|
2.3
|
62.7
|
1.0
|
O
|
Y:VAL49
|
2.3
|
73.2
|
1.0
|
O
|
Y:HOH205
|
2.4
|
61.4
|
1.0
|
O
|
Y:HOH204
|
2.4
|
62.1
|
1.0
|
OD1
|
Y:ASP47
|
2.6
|
63.8
|
1.0
|
C
|
Y:TRP44
|
3.3
|
47.7
|
1.0
|
C
|
X:TRP46
|
3.4
|
56.3
|
1.0
|
CG
|
Y:ASP47
|
3.4
|
64.6
|
1.0
|
OD2
|
Y:ASP47
|
3.5
|
67.7
|
1.0
|
C
|
Y:VAL49
|
3.5
|
74.6
|
1.0
|
O
|
Y:HOH202
|
3.8
|
64.4
|
1.0
|
CD
|
Y:PRO50
|
3.8
|
74.4
|
1.0
|
CA
|
Y:TRP44
|
4.0
|
45.5
|
1.0
|
CA
|
X:TRP46
|
4.2
|
49.8
|
1.0
|
N
|
Y:PRO50
|
4.2
|
73.0
|
1.0
|
N
|
Y:LEU45
|
4.2
|
52.2
|
1.0
|
N
|
X:LEU47
|
4.3
|
62.9
|
1.0
|
CA
|
X:LEU47
|
4.4
|
61.4
|
1.0
|
CA
|
Y:LEU45
|
4.4
|
48.1
|
1.0
|
CB
|
Y:TRP44
|
4.5
|
42.9
|
1.0
|
CB
|
X:TRP46
|
4.6
|
52.5
|
1.0
|
CA
|
Y:VAL49
|
4.6
|
75.1
|
1.0
|
C
|
Y:LEU45
|
4.7
|
52.0
|
1.0
|
CB
|
Y:ASP47
|
4.8
|
65.1
|
1.0
|
CG
|
Y:PRO50
|
4.8
|
73.2
|
1.0
|
N
|
Y:ASP47
|
4.8
|
66.1
|
1.0
|
CB
|
Y:VAL49
|
4.9
|
75.9
|
1.0
|
N
|
Y:VAL49
|
4.9
|
73.1
|
1.0
|
CD2
|
X:LEU47
|
4.9
|
61.2
|
1.0
|
|
Reference:
K.Tani,
R.Kanno,
A.Harada,
Y.Kobayashi,
A.Minamino,
S.Takenaka,
N.Nakamura,
X.C.Ji,
E.R.Purba,
M.Hall,
L.J.Yu,
M.T.Madigan,
A.Mizoguchi,
K.Iwasaki,
B.M.Humbel,
Y.Kimura,
Z.Y.Wang-Otomo.
High-Resolution Structure and Biochemical Properties of the LH1-Rc Photocomplex From the Model Purple Sulfur Bacterium, Allochromatium Vinosum Commun Biol V. 7 176 2024.
ISSN: ESSN 2399-3642
DOI: 10.1038/S42003-024-05863-W
Page generated: Fri Jul 19 12:36:33 2024
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