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:

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

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

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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

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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

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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

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Calcium binding site 4 out of 6 in the Structure of Photosynthetic LH1-Rc Super-Complex of Allochromatium Tepidum


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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

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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

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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
Page generated: Tue Apr 4 19:04:08 2023

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