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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:

Magnesium (Mg) 37 atoms
Iron (Fe) 5 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 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 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 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 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 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 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

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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

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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

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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: Thu Jul 10 08:09:27 2025

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