Calcium in PDB 7vrj: Structure of Photosynthetic LH1-Rc Super-Complex of Allochromatium Tepidum
Other elements in 7vrj:
The structure of Structure of Photosynthetic LH1-Rc Super-Complex of Allochromatium Tepidum also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Structure of Photosynthetic LH1-Rc Super-Complex of Allochromatium Tepidum
(pdb code 7vrj). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Structure of Photosynthetic LH1-Rc Super-Complex of Allochromatium Tepidum, PDB code: 7vrj:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 7vrj
Go back to
Calcium Binding Sites List in 7vrj
Calcium binding site 1 out
of 6 in the Structure of Photosynthetic LH1-Rc Super-Complex of Allochromatium Tepidum
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Structure of Photosynthetic LH1-Rc Super-Complex of Allochromatium Tepidum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca104
b:33.4
occ:1.00
|
OD1
|
D:ASP47
|
2.3
|
38.6
|
1.0
|
O
|
D:TRP44
|
2.4
|
30.3
|
1.0
|
O
|
D:ILE49
|
2.4
|
39.2
|
1.0
|
OD2
|
D:ASP47
|
2.4
|
38.6
|
1.0
|
O
|
B:TRP46
|
2.4
|
32.8
|
1.0
|
CG
|
D:ASP47
|
2.7
|
38.6
|
1.0
|
C
|
D:TRP44
|
3.5
|
30.3
|
1.0
|
C
|
B:TRP46
|
3.5
|
32.8
|
1.0
|
C
|
D:ILE49
|
3.6
|
39.2
|
1.0
|
N
|
D:ILE49
|
4.1
|
39.2
|
1.0
|
CA
|
D:TRP44
|
4.2
|
30.3
|
1.0
|
CB
|
D:ASP47
|
4.2
|
38.6
|
1.0
|
CA
|
D:ILE49
|
4.3
|
39.2
|
1.0
|
CA
|
B:TRP46
|
4.3
|
32.8
|
1.0
|
N
|
B:LEU47
|
4.4
|
35.9
|
1.0
|
CA
|
B:LEU47
|
4.4
|
35.9
|
1.0
|
N
|
D:LEU45
|
4.5
|
32.0
|
1.0
|
N
|
D:PRO50
|
4.6
|
39.1
|
1.0
|
CB
|
D:TRP44
|
4.6
|
30.3
|
1.0
|
CB
|
D:ILE49
|
4.6
|
39.2
|
1.0
|
CA
|
D:LEU45
|
4.6
|
32.0
|
1.0
|
N
|
D:GLY48
|
4.7
|
41.2
|
1.0
|
CD2
|
B:LEU47
|
4.7
|
35.9
|
1.0
|
C
|
D:LEU45
|
4.8
|
32.0
|
1.0
|
N
|
D:ASP47
|
4.8
|
38.6
|
1.0
|
O
|
D:LEU45
|
4.8
|
32.0
|
1.0
|
CD
|
D:PRO50
|
4.8
|
39.1
|
1.0
|
CB
|
B:TRP46
|
4.9
|
32.8
|
1.0
|
CA
|
D:ASP47
|
4.9
|
38.6
|
1.0
|
|
Calcium binding site 2 out
of 6 in 7vrj
Go back to
Calcium Binding Sites List in 7vrj
Calcium binding site 2 out
of 6 in the Structure of Photosynthetic LH1-Rc Super-Complex of Allochromatium Tepidum
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Structure of Photosynthetic LH1-Rc Super-Complex of Allochromatium Tepidum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca102
b:48.0
occ:1.00
|
O
|
F:ILE49
|
2.4
|
48.6
|
1.0
|
OD2
|
F:ASP47
|
2.4
|
45.4
|
1.0
|
OD1
|
F:ASP47
|
2.4
|
45.4
|
1.0
|
O
|
E:TRP46
|
2.5
|
35.8
|
1.0
|
O
|
F:TRP44
|
2.6
|
34.1
|
1.0
|
CG
|
F:ASP47
|
2.7
|
45.4
|
1.0
|
C
|
F:ILE49
|
3.6
|
48.6
|
1.0
|
C
|
E:TRP46
|
3.6
|
35.8
|
1.0
|
C
|
F:TRP44
|
3.6
|
34.1
|
1.0
|
CA
|
F:TRP44
|
4.2
|
34.1
|
1.0
|
CB
|
F:ASP47
|
4.2
|
45.4
|
1.0
|
N
|
F:ILE49
|
4.3
|
48.6
|
1.0
|
CA
|
E:TRP46
|
4.3
|
35.8
|
1.0
|
CA
|
F:ILE49
|
4.4
|
48.6
|
1.0
|
N
|
F:PRO50
|
4.5
|
48.3
|
1.0
|
CD
|
F:PRO50
|
4.6
|
48.3
|
1.0
|
N
|
E:LEU47
|
4.6
|
41.2
|
1.0
|
N
|
F:ASP47
|
4.6
|
45.4
|
1.0
|
N
|
F:LEU45
|
4.7
|
35.4
|
1.0
|
CB
|
F:TRP44
|
4.7
|
34.1
|
1.0
|
CA
|
E:LEU47
|
4.7
|
41.2
|
1.0
|
CB
|
E:TRP46
|
4.8
|
35.8
|
1.0
|
CB
|
F:ILE49
|
4.8
|
48.6
|
1.0
|
CA
|
F:ASP47
|
4.9
|
45.4
|
1.0
|
N
|
F:GLY48
|
4.9
|
48.8
|
1.0
|
CA
|
F:LEU45
|
5.0
|
35.4
|
1.0
|
|
Calcium binding site 3 out
of 6 in 7vrj
Go back to
Calcium Binding Sites List in 7vrj
Calcium binding site 3 out
of 6 in the Structure of Photosynthetic LH1-Rc Super-Complex of Allochromatium Tepidum
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Structure of Photosynthetic LH1-Rc Super-Complex of Allochromatium Tepidum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Ca103
b:33.7
occ:1.00
|
O
|
S:TRP44
|
2.3
|
27.5
|
1.0
|
OD1
|
S:ASP47
|
2.3
|
38.7
|
1.0
|
O
|
S:ILE49
|
2.4
|
42.6
|
1.0
|
OD2
|
S:ASP47
|
2.4
|
38.7
|
1.0
|
O
|
R:TRP46
|
2.4
|
32.7
|
1.0
|
CG
|
S:ASP47
|
2.7
|
38.7
|
1.0
|
C
|
S:TRP44
|
3.4
|
27.5
|
1.0
|
C
|
R:TRP46
|
3.6
|
32.7
|
1.0
|
C
|
S:ILE49
|
3.6
|
42.6
|
1.0
|
CA
|
S:TRP44
|
4.1
|
27.5
|
1.0
|
CB
|
S:ASP47
|
4.2
|
38.7
|
1.0
|
CD
|
S:PRO50
|
4.4
|
43.5
|
1.0
|
N
|
S:LEU45
|
4.4
|
31.6
|
1.0
|
CA
|
R:LEU47
|
4.4
|
35.9
|
1.0
|
N
|
S:PRO50
|
4.5
|
43.5
|
1.0
|
N
|
R:LEU47
|
4.5
|
35.9
|
1.0
|
CB
|
S:TRP44
|
4.5
|
27.5
|
1.0
|
CA
|
R:TRP46
|
4.5
|
32.7
|
1.0
|
CA
|
S:ILE49
|
4.6
|
42.6
|
1.0
|
N
|
S:ILE49
|
4.6
|
42.6
|
1.0
|
CA
|
S:LEU45
|
4.6
|
31.6
|
1.0
|
O
|
S:LEU45
|
4.8
|
31.6
|
1.0
|
N
|
S:ASP47
|
4.8
|
38.7
|
1.0
|
C
|
S:LEU45
|
4.8
|
31.6
|
1.0
|
OXT
|
R:LEU47
|
4.8
|
35.9
|
1.0
|
CB
|
S:ILE49
|
4.9
|
42.6
|
1.0
|
N
|
S:GLY48
|
4.9
|
42.9
|
1.0
|
C
|
R:LEU47
|
4.9
|
35.9
|
1.0
|
CA
|
S:ASP47
|
5.0
|
38.7
|
1.0
|
CD2
|
R:LEU47
|
5.0
|
35.9
|
1.0
|
|
Calcium binding site 4 out
of 6 in 7vrj
Go back to
Calcium Binding Sites List in 7vrj
Calcium binding site 4 out
of 6 in the Structure of Photosynthetic LH1-Rc Super-Complex of Allochromatium Tepidum
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Structure of Photosynthetic LH1-Rc Super-Complex of Allochromatium Tepidum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
U:Ca102
b:35.5
occ:1.00
|
O
|
U:ILE49
|
2.3
|
39.1
|
1.0
|
OD1
|
U:ASP47
|
2.3
|
37.0
|
1.0
|
O
|
U:TRP44
|
2.4
|
27.6
|
1.0
|
OD2
|
U:ASP47
|
2.5
|
37.0
|
1.0
|
O
|
T:TRP46
|
2.7
|
28.5
|
1.0
|
CG
|
U:ASP47
|
2.7
|
37.0
|
1.0
|
C
|
U:ILE49
|
3.5
|
39.1
|
1.0
|
C
|
U:TRP44
|
3.5
|
27.6
|
1.0
|
C
|
T:TRP46
|
3.7
|
28.5
|
1.0
|
N
|
U:ILE49
|
4.1
|
39.1
|
1.0
|
CA
|
U:TRP44
|
4.2
|
27.6
|
1.0
|
CB
|
U:ASP47
|
4.2
|
37.0
|
1.0
|
CA
|
U:ILE49
|
4.3
|
39.1
|
1.0
|
N
|
U:PRO50
|
4.5
|
40.3
|
1.0
|
CA
|
T:TRP46
|
4.5
|
28.5
|
1.0
|
N
|
U:LEU45
|
4.5
|
29.4
|
1.0
|
CD
|
U:PRO50
|
4.6
|
40.3
|
1.0
|
N
|
T:LEU47
|
4.6
|
32.5
|
1.0
|
CB
|
U:TRP44
|
4.7
|
27.6
|
1.0
|
CB
|
U:ILE49
|
4.7
|
39.1
|
1.0
|
CA
|
T:LEU47
|
4.7
|
32.5
|
1.0
|
O
|
U:LEU45
|
4.8
|
29.4
|
1.0
|
CA
|
U:LEU45
|
4.8
|
29.4
|
1.0
|
N
|
U:GLY48
|
4.9
|
39.0
|
1.0
|
N
|
U:ASP47
|
4.9
|
37.0
|
1.0
|
C
|
U:LEU45
|
4.9
|
29.4
|
1.0
|
CD2
|
T:LEU47
|
5.0
|
32.5
|
1.0
|
|
Calcium binding site 5 out
of 6 in 7vrj
Go back to
Calcium Binding Sites List in 7vrj
Calcium binding site 5 out
of 6 in the Structure of Photosynthetic LH1-Rc Super-Complex of Allochromatium Tepidum
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Structure of Photosynthetic LH1-Rc Super-Complex of Allochromatium Tepidum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
W:Ca102
b:36.2
occ:1.00
|
O
|
W:ILE49
|
2.1
|
42.7
|
1.0
|
OD1
|
W:ASP47
|
2.3
|
38.2
|
1.0
|
O
|
W:TRP44
|
2.4
|
29.5
|
1.0
|
OD2
|
W:ASP47
|
2.5
|
38.2
|
1.0
|
O
|
V:TRP46
|
2.7
|
33.6
|
1.0
|
CG
|
W:ASP47
|
2.7
|
38.2
|
1.0
|
C
|
W:ILE49
|
3.3
|
42.7
|
1.0
|
C
|
W:TRP44
|
3.5
|
29.5
|
1.0
|
C
|
V:TRP46
|
3.9
|
33.6
|
1.0
|
N
|
W:ILE49
|
4.0
|
42.7
|
1.0
|
CA
|
W:ILE49
|
4.0
|
42.7
|
1.0
|
CA
|
W:TRP44
|
4.1
|
29.5
|
1.0
|
CB
|
W:ILE49
|
4.2
|
42.7
|
1.0
|
CB
|
W:ASP47
|
4.2
|
38.2
|
1.0
|
N
|
W:PRO50
|
4.3
|
46.6
|
1.0
|
N
|
W:LEU45
|
4.5
|
31.1
|
1.0
|
CA
|
V:LEU47
|
4.5
|
35.7
|
1.0
|
CB
|
W:TRP44
|
4.5
|
29.5
|
1.0
|
CD
|
W:PRO50
|
4.6
|
46.6
|
1.0
|
N
|
V:LEU47
|
4.7
|
35.7
|
1.0
|
CD2
|
V:LEU47
|
4.7
|
35.7
|
1.0
|
CA
|
W:LEU45
|
4.8
|
31.1
|
1.0
|
CA
|
V:TRP46
|
4.8
|
33.6
|
1.0
|
N
|
W:ASP47
|
4.9
|
38.2
|
1.0
|
O
|
W:LEU45
|
4.9
|
31.1
|
1.0
|
CG2
|
W:ILE49
|
4.9
|
42.7
|
1.0
|
C
|
W:LEU45
|
5.0
|
31.1
|
1.0
|
|
Calcium binding site 6 out
of 6 in 7vrj
Go back to
Calcium Binding Sites List in 7vrj
Calcium binding site 6 out
of 6 in the Structure of Photosynthetic LH1-Rc Super-Complex of Allochromatium Tepidum
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Structure of Photosynthetic LH1-Rc Super-Complex of Allochromatium Tepidum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Y:Ca102
b:42.1
occ:1.00
|
O
|
Y:TRP44
|
2.3
|
38.1
|
1.0
|
O
|
X:TRP46
|
2.3
|
39.1
|
1.0
|
OD1
|
Y:ASP47
|
2.4
|
46.3
|
1.0
|
O
|
Y:ILE49
|
2.4
|
48.9
|
1.0
|
OD2
|
Y:ASP47
|
2.4
|
46.3
|
1.0
|
CG
|
Y:ASP47
|
2.7
|
46.3
|
1.0
|
C
|
Y:TRP44
|
3.4
|
38.1
|
1.0
|
C
|
Y:ILE49
|
3.5
|
48.9
|
1.0
|
C
|
X:TRP46
|
3.5
|
39.1
|
1.0
|
CA
|
X:LEU47
|
4.1
|
43.5
|
1.0
|
CA
|
Y:TRP44
|
4.1
|
38.1
|
1.0
|
CB
|
Y:ILE49
|
4.1
|
48.9
|
1.0
|
CA
|
Y:ILE49
|
4.2
|
48.9
|
1.0
|
N
|
Y:ILE49
|
4.2
|
48.9
|
1.0
|
CB
|
Y:ASP47
|
4.2
|
46.3
|
1.0
|
N
|
X:LEU47
|
4.3
|
43.5
|
1.0
|
C
|
X:LEU47
|
4.4
|
43.5
|
1.0
|
OXT
|
X:LEU47
|
4.5
|
43.5
|
1.0
|
N
|
Y:LEU45
|
4.5
|
39.5
|
1.0
|
CB
|
Y:TRP44
|
4.5
|
38.1
|
1.0
|
N
|
Y:PRO50
|
4.5
|
48.8
|
1.0
|
CA
|
X:TRP46
|
4.6
|
39.1
|
1.0
|
CD
|
Y:PRO50
|
4.7
|
48.8
|
1.0
|
CA
|
Y:LEU45
|
4.8
|
39.5
|
1.0
|
N
|
Y:ASP47
|
4.8
|
46.3
|
1.0
|
O
|
Y:LEU45
|
4.9
|
39.5
|
1.0
|
C
|
Y:LEU45
|
4.9
|
39.5
|
1.0
|
CG2
|
Y:ILE49
|
4.9
|
48.9
|
1.0
|
O
|
X:LEU47
|
5.0
|
43.5
|
1.0
|
|
Reference:
K.Tani,
K.Kobayashi,
N.Hosogi,
X.C.Ji,
S.Nagashima,
K.V.P.Nagashima,
A.Izumida,
K.Inoue,
Y.Tsukatani,
R.Kanno,
M.Hall,
L.J.Yu,
I.Ishikawa,
Y.Okura,
M.T.Madigan,
A.Mizoguchi,
B.M.Humbel,
Y.Kimura,
Z.Y.Wang-Otomo.
A Ca 2+ -Binding Motif Underlies the Unusual Properties of Certain Photosynthetic Bacterial Core Light-Harvesting Complexes. J.Biol.Chem. V. 298 01967 2022.
ISSN: ESSN 1083-351X
PubMed: 35460693
DOI: 10.1016/J.JBC.2022.101967
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