Calcium in PDB 8wdv: Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By CA2+-Deae
Other elements in 8wdv:
The structure of Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By CA2+-Deae 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 CA2+-Deae
(pdb code 8wdv). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By CA2+-Deae, PDB code: 8wdv:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 8wdv
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Calcium Binding Sites List in 8wdv
Calcium binding site 1 out
of 8 in the Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By CA2+-Deae
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 CA2+-Deae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca406
b:76.4
occ:1.00
|
O
|
L:HOH420
|
2.3
|
53.0
|
1.0
|
O
|
C:HOH508
|
2.6
|
48.7
|
1.0
|
O
|
L:HOH450
|
2.6
|
60.4
|
1.0
|
O
|
C:HOH575
|
2.8
|
45.7
|
1.0
|
OD1
|
C:ASP241
|
2.8
|
49.7
|
1.0
|
CG
|
C:ASP241
|
3.7
|
46.7
|
1.0
|
OD2
|
C:ASP241
|
4.0
|
51.7
|
1.0
|
O
|
C:HOH557
|
4.2
|
45.9
|
1.0
|
O
|
C:ASP241
|
4.3
|
33.1
|
1.0
|
OE2
|
L:GLU267
|
4.3
|
46.4
|
1.0
|
OE1
|
L:GLU267
|
4.4
|
47.1
|
1.0
|
CD
|
L:GLU267
|
4.8
|
42.9
|
1.0
|
|
Calcium binding site 2 out
of 8 in 8wdv
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Calcium Binding Sites List in 8wdv
Calcium binding site 2 out
of 8 in the Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By CA2+-Deae
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 CA2+-Deae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Ca401
b:78.7
occ:1.00
|
O
|
C:HOH564
|
2.1
|
58.7
|
1.0
|
OD2
|
M:ASP80
|
2.3
|
48.6
|
1.0
|
O
|
U:HOH202
|
2.4
|
47.2
|
1.0
|
O
|
U:HOH210
|
2.7
|
54.2
|
1.0
|
O
|
M:HOH502
|
2.8
|
41.0
|
1.0
|
O
|
U:HOH211
|
3.0
|
52.3
|
1.0
|
CG
|
M:ASP80
|
3.3
|
42.6
|
1.0
|
OD1
|
M:ASP80
|
3.6
|
47.8
|
1.0
|
O
|
U:SER38
|
4.1
|
49.3
|
1.0
|
OE1
|
U:GLU46
|
4.1
|
57.9
|
1.0
|
O
|
C:GLN174
|
4.3
|
44.2
|
1.0
|
CB
|
C:ASN173
|
4.4
|
47.6
|
1.0
|
O
|
U:HOH207
|
4.5
|
49.1
|
1.0
|
O
|
U:LEU37
|
4.6
|
38.2
|
1.0
|
CB
|
M:ASP80
|
4.6
|
34.2
|
1.0
|
C
|
U:SER38
|
4.8
|
33.2
|
1.0
|
CG
|
C:ASN173
|
4.9
|
52.6
|
1.0
|
ND2
|
U:ASN43
|
4.9
|
40.1
|
1.0
|
ND2
|
C:ASN173
|
4.9
|
51.8
|
1.0
|
|
Calcium binding site 3 out
of 8 in 8wdv
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Calcium Binding Sites List in 8wdv
Calcium binding site 3 out
of 8 in the Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By CA2+-Deae
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 CA2+-Deae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca504
b:37.7
occ:1.00
|
OD1
|
D:ASP47
|
2.2
|
57.6
|
1.0
|
O
|
B:TRP46
|
2.2
|
35.6
|
1.0
|
O
|
D:VAL49
|
2.3
|
57.2
|
1.0
|
O
|
D:TRP44
|
2.3
|
40.2
|
1.0
|
O
|
D:HOH601
|
2.4
|
51.8
|
1.0
|
O
|
D:HOH605
|
2.4
|
55.6
|
1.0
|
CG
|
D:ASP47
|
3.1
|
55.4
|
1.0
|
OD2
|
D:ASP47
|
3.3
|
60.1
|
1.0
|
C
|
B:TRP46
|
3.4
|
25.0
|
1.0
|
C
|
D:TRP44
|
3.4
|
29.5
|
1.0
|
C
|
D:VAL49
|
3.4
|
54.8
|
1.0
|
N
|
D:VAL49
|
3.8
|
53.9
|
1.0
|
CA
|
D:TRP44
|
4.1
|
19.0
|
1.0
|
CA
|
D:VAL49
|
4.1
|
52.1
|
1.0
|
O
|
D:HOH606
|
4.2
|
45.5
|
1.0
|
CA
|
B:TRP46
|
4.2
|
17.4
|
1.0
|
O
|
D:HOH602
|
4.2
|
53.0
|
1.0
|
N
|
B:LEU47
|
4.4
|
37.8
|
1.0
|
CB
|
D:VAL49
|
4.4
|
52.7
|
1.0
|
N
|
D:PRO50
|
4.4
|
46.1
|
1.0
|
N
|
D:LEU45
|
4.5
|
34.3
|
1.0
|
N
|
D:GLY48
|
4.5
|
50.6
|
1.0
|
CB
|
D:TRP44
|
4.5
|
24.2
|
1.0
|
CB
|
D:ASP47
|
4.5
|
50.6
|
1.0
|
CA
|
B:LEU47
|
4.5
|
42.3
|
1.0
|
N
|
D:ASP47
|
4.6
|
48.5
|
1.0
|
CA
|
D:LEU45
|
4.7
|
26.9
|
1.0
|
O
|
E:HOH201
|
4.7
|
47.2
|
1.0
|
CD
|
D:PRO50
|
4.7
|
51.6
|
1.0
|
CB
|
B:TRP46
|
4.8
|
19.4
|
1.0
|
C
|
D:GLY48
|
4.8
|
50.6
|
1.0
|
C
|
D:LEU45
|
4.9
|
29.3
|
1.0
|
CA
|
D:ASP47
|
4.9
|
52.2
|
1.0
|
C
|
D:ASP47
|
5.0
|
55.2
|
1.0
|
|
Calcium binding site 4 out
of 8 in 8wdv
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Calcium Binding Sites List in 8wdv
Calcium binding site 4 out
of 8 in the Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By CA2+-Deae
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 CA2+-Deae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca503
b:59.2
occ:1.00
|
OD1
|
F:ASP47
|
2.1
|
52.1
|
1.0
|
O
|
E:TRP46
|
2.2
|
42.3
|
1.0
|
O
|
F:VAL49
|
2.3
|
46.2
|
1.0
|
O
|
F:HOH603
|
2.4
|
45.5
|
1.0
|
O
|
F:HOH601
|
2.4
|
40.8
|
1.0
|
O
|
F:TRP44
|
2.4
|
32.5
|
1.0
|
CG
|
F:ASP47
|
3.0
|
51.6
|
1.0
|
OD2
|
F:ASP47
|
3.1
|
54.6
|
1.0
|
C
|
E:TRP46
|
3.3
|
34.4
|
1.0
|
C
|
F:TRP44
|
3.4
|
23.3
|
1.0
|
C
|
F:VAL49
|
3.4
|
47.4
|
1.0
|
O
|
F:HOH602
|
3.8
|
38.7
|
1.0
|
N
|
F:VAL49
|
3.9
|
45.3
|
1.0
|
CA
|
F:TRP44
|
3.9
|
18.8
|
1.0
|
CA
|
F:VAL49
|
4.1
|
48.5
|
1.0
|
CA
|
E:TRP46
|
4.1
|
28.0
|
1.0
|
N
|
E:LEU47
|
4.2
|
43.9
|
1.0
|
CA
|
E:LEU47
|
4.3
|
45.0
|
1.0
|
CB
|
F:VAL49
|
4.4
|
47.7
|
1.0
|
CB
|
F:TRP44
|
4.4
|
11.1
|
1.0
|
CB
|
F:ASP47
|
4.4
|
45.9
|
1.0
|
N
|
F:LEU45
|
4.4
|
25.4
|
1.0
|
N
|
F:PRO50
|
4.5
|
45.2
|
1.0
|
N
|
F:GLY48
|
4.6
|
41.5
|
1.0
|
CD
|
F:PRO50
|
4.7
|
45.1
|
1.0
|
N
|
F:ASP47
|
4.7
|
48.8
|
1.0
|
CB
|
E:TRP46
|
4.7
|
28.3
|
1.0
|
CA
|
F:LEU45
|
4.8
|
24.2
|
1.0
|
CA
|
F:ASP47
|
4.9
|
48.7
|
1.0
|
C
|
E:LEU47
|
4.9
|
55.9
|
1.0
|
CD2
|
E:LEU47
|
4.9
|
45.5
|
1.0
|
C
|
F:GLY48
|
5.0
|
43.2
|
1.0
|
C
|
F:ASP47
|
5.0
|
49.9
|
1.0
|
|
Calcium binding site 5 out
of 8 in 8wdv
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Calcium Binding Sites List in 8wdv
Calcium binding site 5 out
of 8 in the Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By CA2+-Deae
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 CA2+-Deae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Ca102
b:37.9
occ:1.00
|
O
|
S:VAL49
|
2.2
|
58.3
|
1.0
|
OD1
|
S:ASP47
|
2.3
|
61.3
|
1.0
|
O
|
S:TRP44
|
2.3
|
46.5
|
1.0
|
O
|
S:HOH206
|
2.3
|
44.5
|
1.0
|
O
|
R:TRP46
|
2.4
|
34.5
|
1.0
|
O
|
S:HOH201
|
2.4
|
44.0
|
1.0
|
CG
|
S:ASP47
|
3.1
|
56.2
|
1.0
|
OD2
|
S:ASP47
|
3.2
|
62.3
|
1.0
|
C
|
S:TRP44
|
3.3
|
31.8
|
1.0
|
C
|
S:VAL49
|
3.4
|
56.0
|
1.0
|
C
|
R:TRP46
|
3.5
|
19.3
|
1.0
|
CA
|
S:TRP44
|
3.9
|
24.7
|
1.0
|
N
|
S:VAL49
|
3.9
|
58.5
|
1.0
|
CA
|
S:VAL49
|
4.1
|
58.2
|
1.0
|
N
|
S:LEU45
|
4.3
|
33.1
|
1.0
|
CA
|
R:TRP46
|
4.4
|
17.0
|
1.0
|
CB
|
S:VAL49
|
4.4
|
59.9
|
1.0
|
N
|
R:LEU47
|
4.4
|
33.5
|
1.0
|
CB
|
S:TRP44
|
4.4
|
29.5
|
1.0
|
N
|
S:PRO50
|
4.4
|
55.5
|
1.0
|
CA
|
R:LEU47
|
4.4
|
37.6
|
1.0
|
O
|
R:HOH201
|
4.5
|
45.6
|
1.0
|
CB
|
S:ASP47
|
4.5
|
49.2
|
1.0
|
O
|
S:HOH203
|
4.6
|
53.6
|
1.0
|
CD
|
S:PRO50
|
4.6
|
59.0
|
1.0
|
CA
|
S:LEU45
|
4.6
|
33.5
|
1.0
|
N
|
S:GLY48
|
4.7
|
56.5
|
1.0
|
N
|
S:ASP47
|
4.7
|
51.3
|
1.0
|
O
|
S:HOH202
|
4.8
|
57.2
|
1.0
|
C
|
S:LEU45
|
4.8
|
36.3
|
1.0
|
CD2
|
R:LEU47
|
4.9
|
37.8
|
1.0
|
CB
|
R:TRP46
|
4.9
|
22.5
|
1.0
|
C
|
S:GLY48
|
4.9
|
57.9
|
1.0
|
CA
|
S:ASP47
|
5.0
|
53.6
|
1.0
|
|
Calcium binding site 6 out
of 8 in 8wdv
Go back to
Calcium Binding Sites List in 8wdv
Calcium binding site 6 out
of 8 in the Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By CA2+-Deae
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 CA2+-Deae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
U:Ca102
b:37.7
occ:1.00
|
O
|
U:VAL49
|
2.2
|
58.2
|
1.0
|
O
|
T:TRP46
|
2.2
|
42.2
|
1.0
|
O
|
U:TRP44
|
2.3
|
44.0
|
1.0
|
OD1
|
U:ASP47
|
2.3
|
58.2
|
1.0
|
O
|
U:HOH209
|
2.4
|
56.0
|
1.0
|
O
|
U:HOH201
|
2.4
|
49.6
|
1.0
|
CG
|
U:ASP47
|
3.1
|
48.7
|
1.0
|
OD2
|
U:ASP47
|
3.2
|
54.6
|
1.0
|
C
|
U:VAL49
|
3.4
|
55.5
|
1.0
|
C
|
U:TRP44
|
3.4
|
36.2
|
1.0
|
C
|
T:TRP46
|
3.4
|
32.9
|
1.0
|
N
|
U:VAL49
|
3.9
|
53.9
|
1.0
|
CA
|
U:TRP44
|
3.9
|
27.9
|
1.0
|
CA
|
U:VAL49
|
4.0
|
51.5
|
1.0
|
CA
|
T:TRP46
|
4.2
|
22.5
|
1.0
|
CB
|
U:VAL49
|
4.3
|
52.8
|
1.0
|
N
|
T:LEU47
|
4.4
|
36.0
|
1.0
|
CB
|
U:TRP44
|
4.4
|
27.8
|
1.0
|
N
|
U:PRO50
|
4.4
|
51.8
|
1.0
|
N
|
U:LEU45
|
4.4
|
35.9
|
1.0
|
O
|
U:HOH205
|
4.4
|
48.4
|
1.0
|
CA
|
T:LEU47
|
4.5
|
42.5
|
1.0
|
CB
|
U:ASP47
|
4.6
|
41.5
|
1.0
|
CD
|
U:PRO50
|
4.6
|
54.6
|
1.0
|
O
|
U:HOH206
|
4.6
|
56.0
|
1.0
|
O
|
T:HOH201
|
4.6
|
45.1
|
1.0
|
CA
|
U:LEU45
|
4.7
|
27.6
|
1.0
|
CB
|
T:TRP46
|
4.7
|
21.8
|
1.0
|
N
|
U:GLY48
|
4.8
|
47.3
|
1.0
|
N
|
U:ASP47
|
4.8
|
41.2
|
1.0
|
C
|
U:LEU45
|
5.0
|
32.6
|
1.0
|
|
Calcium binding site 7 out
of 8 in 8wdv
Go back to
Calcium Binding Sites List in 8wdv
Calcium binding site 7 out
of 8 in the Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By CA2+-Deae
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By CA2+-Deae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
W:Ca102
b:41.8
occ:1.00
|
O
|
W:VAL49
|
2.2
|
54.0
|
1.0
|
O
|
W:TRP44
|
2.3
|
40.4
|
1.0
|
O
|
V:TRP46
|
2.3
|
32.5
|
1.0
|
OD1
|
W:ASP47
|
2.3
|
64.4
|
1.0
|
O
|
W:HOH205
|
2.4
|
51.8
|
1.0
|
O
|
W:HOH201
|
2.4
|
50.4
|
1.0
|
CG
|
W:ASP47
|
3.2
|
57.2
|
1.0
|
C
|
W:TRP44
|
3.4
|
32.9
|
1.0
|
OD2
|
W:ASP47
|
3.4
|
62.4
|
1.0
|
C
|
W:VAL49
|
3.5
|
53.5
|
1.0
|
C
|
V:TRP46
|
3.5
|
25.6
|
1.0
|
CA
|
W:TRP44
|
4.1
|
23.9
|
1.0
|
N
|
W:VAL49
|
4.2
|
53.7
|
1.0
|
CA
|
W:VAL49
|
4.3
|
50.8
|
1.0
|
CA
|
V:TRP46
|
4.3
|
21.5
|
1.0
|
N
|
W:LEU45
|
4.4
|
32.4
|
1.0
|
N
|
V:LEU47
|
4.4
|
38.5
|
1.0
|
N
|
W:PRO50
|
4.4
|
49.3
|
1.0
|
O
|
V:HOH201
|
4.5
|
40.7
|
1.0
|
CA
|
V:LEU47
|
4.5
|
42.5
|
1.0
|
CD
|
W:PRO50
|
4.5
|
50.2
|
1.0
|
CB
|
W:VAL49
|
4.5
|
52.4
|
1.0
|
CA
|
W:LEU45
|
4.6
|
31.0
|
1.0
|
CB
|
W:TRP44
|
4.6
|
23.6
|
1.0
|
CB
|
W:ASP47
|
4.6
|
50.8
|
1.0
|
C
|
W:GLY48
|
4.7
|
52.2
|
1.0
|
C
|
W:LEU45
|
4.7
|
32.4
|
1.0
|
N
|
W:ASP47
|
4.8
|
49.2
|
1.0
|
N
|
W:GLY48
|
4.8
|
50.6
|
1.0
|
CB
|
V:TRP46
|
4.8
|
21.4
|
1.0
|
O
|
W:LEU45
|
4.9
|
46.0
|
1.0
|
O
|
W:HOH204
|
4.9
|
53.6
|
1.0
|
CD2
|
V:LEU47
|
5.0
|
38.2
|
1.0
|
|
Calcium binding site 8 out
of 8 in 8wdv
Go back to
Calcium Binding Sites List in 8wdv
Calcium binding site 8 out
of 8 in the Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By CA2+-Deae
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By CA2+-Deae within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Y:Ca102
b:46.4
occ:1.00
|
O
|
Y:TRP44
|
2.2
|
34.3
|
1.0
|
O
|
X:TRP46
|
2.3
|
39.8
|
1.0
|
O
|
Y:HOH201
|
2.4
|
48.4
|
1.0
|
O
|
Y:VAL49
|
2.4
|
63.6
|
1.0
|
O
|
Y:HOH203
|
2.4
|
47.1
|
1.0
|
OD1
|
Y:ASP47
|
2.6
|
54.5
|
1.0
|
C
|
Y:TRP44
|
3.3
|
30.0
|
1.0
|
CG
|
Y:ASP47
|
3.4
|
50.8
|
1.0
|
C
|
X:TRP46
|
3.4
|
29.3
|
1.0
|
OD2
|
Y:ASP47
|
3.4
|
57.5
|
1.0
|
C
|
Y:VAL49
|
3.6
|
63.0
|
1.0
|
CD
|
Y:PRO50
|
3.9
|
65.7
|
1.0
|
CA
|
Y:TRP44
|
4.1
|
20.8
|
1.0
|
CA
|
X:TRP46
|
4.2
|
25.4
|
1.0
|
O
|
X:HOH202
|
4.3
|
43.8
|
1.0
|
N
|
Y:PRO50
|
4.3
|
62.5
|
1.0
|
N
|
Y:LEU45
|
4.3
|
26.9
|
1.0
|
N
|
X:LEU47
|
4.3
|
42.1
|
1.0
|
CA
|
X:LEU47
|
4.4
|
46.4
|
1.0
|
CA
|
Y:LEU45
|
4.5
|
29.9
|
1.0
|
CB
|
Y:TRP44
|
4.6
|
18.3
|
1.0
|
CG1
|
Y:VAL49
|
4.7
|
58.1
|
1.0
|
CA
|
Y:VAL49
|
4.7
|
61.9
|
1.0
|
C
|
Y:LEU45
|
4.7
|
36.6
|
1.0
|
CB
|
X:TRP46
|
4.8
|
25.7
|
1.0
|
N
|
Y:VAL49
|
4.8
|
59.1
|
1.0
|
CB
|
Y:ASP47
|
4.8
|
48.6
|
1.0
|
N
|
Y:ASP47
|
4.9
|
50.3
|
1.0
|
O
|
Y:LEU45
|
5.0
|
45.0
|
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 12:36:51 2024
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