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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:

Iron (Fe) 5 atoms
Magnesium (Mg) 37 atoms

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 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 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 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 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

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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

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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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