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Calcium in PDB 7c9r: Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970

Other elements in 7c9r:

The structure of Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970 also contains other interesting chemical elements:

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

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Calcium atom in the Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970 (pdb code 7c9r). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 17 binding sites of Calcium where determined in the Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970, PDB code: 7c9r:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 17 in 7c9r

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Calcium binding site 1 out of 17 in the Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970


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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 Thiorhodovibrio Strain 970 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca406

b:51.0
occ:1.00
 OE1 C:GLN282 2.5 70.1 1.0
OD2 C:ASP278 2.7 46.0 1.0
OD2 C:ASP136 2.7 55.5 1.0
OD1 C:ASP278 2.9 47.7 1.0
CG C:ASP278 3.2 44.9 1.0
CD C:GLN282 3.6 53.4 1.0
CG C:ASP136 3.7 50.7 1.0
NE2 C:GLN282 4.1 61.8 1.0
OD1 C:ASP136 4.1 64.9 1.0
OH C:TYR283 4.4 30.6 1.0
CB C:ASP278 4.7 34.9 1.0
CE2 C:TYR283 4.7 30.3 1.0
CG C:GLN282 4.9 43.7 1.0
NE1 C:TRP141 4.9 28.5 1.0

Calcium binding site 2 out of 17 in 7c9r

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Calcium binding site 2 out of 17 in the Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970


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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 Thiorhodovibrio Strain 970 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca103

b:23.5
occ:1.00
 O A:ILE52 2.4 38.4 1.0
O 0:TRP45 2.5 15.0 1.0
O A:TRP47 2.5 22.5 1.0
OD1 A:ASP50 2.6 37.1 1.0
CG A:ASP50 3.4 35.6 1.0
OD2 A:ASP50 3.5 43.1 1.0
C A:ILE52 3.6 26.1 1.0
C A:TRP47 3.6 23.7 1.0
C 0:TRP45 3.7 18.8 1.0
N A:ILE52 4.1 18.6 1.0
CA A:ILE52 4.3 20.6 1.0
CA A:TRP47 4.3 15.6 1.0
CB A:ILE52 4.4 27.2 1.0
CA 0:LEU46 4.5 35.2 1.0
N A:HIS48 4.5 28.6 1.0
O A:HIS48 4.5 36.7 1.0
N A:PRO53 4.6 30.8 1.0
N 0:LEU46 4.6 27.2 1.0
CA 0:TRP45 4.6 16.1 1.0
CA A:HIS48 4.6 19.6 1.0
C A:HIS48 4.6 27.7 1.0
CD A:PRO53 4.7 25.9 1.0
CB A:TRP47 4.8 12.1 1.0
OH B:TYR42 4.8 41.5 1.0
N A:ASP50 4.8 30.0 1.0
CB A:ASP50 4.8 38.2 1.0
N A:GLN51 4.9 29.9 1.0
CG2 A:ILE52 4.9 24.2 1.0

Calcium binding site 3 out of 17 in 7c9r

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Calcium binding site 3 out of 17 in the Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970


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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 Thiorhodovibrio Strain 970 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca102

b:30.3
occ:1.00
 O D:ILE52 2.4 29.6 1.0
OD1 D:ASP50 2.5 58.4 1.0
O B:TRP45 2.6 16.9 1.0
O D:TRP47 2.6 30.2 1.0
CG D:ASP50 3.3 38.1 1.0
OD2 D:ASP50 3.5 47.8 1.0
C D:ILE52 3.6 23.9 1.0
C D:TRP47 3.6 22.2 1.0
C B:TRP45 3.7 15.0 1.0
N D:ILE52 4.0 24.2 1.0
CA D:ILE52 4.2 22.0 1.0
CA D:TRP47 4.3 22.1 1.0
CB D:ILE52 4.3 27.1 1.0
CA B:LEU46 4.5 34.2 1.0
N B:LEU46 4.6 25.7 1.0
N D:HIS48 4.6 24.7 1.0
N D:PRO53 4.6 27.1 1.0
CA B:TRP45 4.6 14.9 1.0
O D:HIS48 4.7 26.2 1.0
CA D:HIS48 4.7 23.4 1.0
CB D:TRP47 4.7 19.1 1.0
CD D:PRO53 4.7 25.8 1.0
C D:HIS48 4.7 22.3 1.0
CB D:ASP50 4.8 35.6 1.0
N D:ASP50 4.8 31.6 1.0
N D:GLN51 4.9 31.6 1.0
CG2 D:ILE52 4.9 29.2 1.0
C B:LEU46 5.0 60.7 1.0
OH E:TYR42 5.0 33.1 1.0

Calcium binding site 4 out of 17 in 7c9r

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Calcium binding site 4 out of 17 in the Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970


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 Thiorhodovibrio Strain 970 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca102

b:23.0
occ:1.00
 O E:TRP45 2.4 18.7 1.0
O F:ILE52 2.5 37.9 1.0
O F:TRP47 2.5 28.6 1.0
OD1 F:ASP50 2.6 44.4 1.0
CG F:ASP50 3.4 38.2 1.0
OD2 F:ASP50 3.5 49.7 1.0
C F:TRP47 3.6 17.8 1.0
C E:TRP45 3.6 17.5 1.0
C F:ILE52 3.6 28.4 1.0
N F:ILE52 4.1 24.1 1.0
CA F:TRP47 4.3 17.0 1.0
CA F:ILE52 4.4 23.8 1.0
CA E:LEU46 4.5 35.3 1.0
N E:LEU46 4.5 24.4 1.0
CB F:ILE52 4.5 30.9 1.0
CA E:TRP45 4.5 15.4 1.0
N F:HIS48 4.5 18.0 1.0
CA F:HIS48 4.6 22.2 1.0
O F:HIS48 4.6 44.7 1.0
N F:PRO53 4.6 25.7 1.0
C F:HIS48 4.7 28.5 1.0
CB F:TRP47 4.7 15.3 1.0
CD F:PRO53 4.7 22.5 1.0
N F:ASP50 4.8 29.4 1.0
CB F:ASP50 4.8 32.9 1.0
CB E:TRP45 5.0 17.6 1.0
N F:GLN51 5.0 24.5 1.0

Calcium binding site 5 out of 17 in 7c9r

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Calcium binding site 5 out of 17 in the Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970


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 Thiorhodovibrio Strain 970 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca101

b:23.4
occ:1.00
 O G:TRP45 2.5 22.1 1.0
O I:ILE52 2.5 33.1 1.0
O I:TRP47 2.5 20.3 1.0
OD1 I:ASP50 2.6 38.9 1.0
CG I:ASP50 3.4 34.0 1.0
OD2 I:ASP50 3.5 38.1 1.0
C I:TRP47 3.6 18.1 1.0
C G:TRP45 3.6 22.5 1.0
C I:ILE52 3.6 24.6 1.0
N I:ILE52 4.1 27.5 1.0
CA I:TRP47 4.3 15.1 1.0
CA I:ILE52 4.3 25.2 1.0
CA G:LEU46 4.4 33.6 1.0
N G:LEU46 4.5 28.7 1.0
CB I:ILE52 4.5 30.6 1.0
N I:HIS48 4.5 20.0 1.0
CA G:TRP45 4.5 17.5 1.0
O I:HIS48 4.6 42.0 1.0
CA I:HIS48 4.6 23.5 1.0
N I:PRO53 4.6 26.1 1.0
C I:HIS48 4.6 30.4 1.0
CB I:TRP47 4.7 18.4 1.0
CD I:PRO53 4.7 23.1 1.0
N I:ASP50 4.8 32.4 1.0
CB I:ASP50 4.9 32.1 1.0
N I:GLN51 5.0 28.2 1.0
C G:LEU46 5.0 58.7 1.0
CB G:TRP45 5.0 20.3 1.0

Calcium binding site 6 out of 17 in 7c9r

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Calcium binding site 6 out of 17 in the Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970


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 Thiorhodovibrio Strain 970 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca104

b:23.5
occ:1.00
 O K:TRP47 2.4 29.9 1.0
O J:TRP45 2.5 27.0 1.0
O K:ILE52 2.5 32.4 1.0
OD1 K:ASP50 2.6 41.3 1.0
CG K:ASP50 3.4 34.3 1.0
C K:TRP47 3.5 20.8 1.0
OD2 K:ASP50 3.5 41.3 1.0
C J:TRP45 3.6 23.5 1.0
C K:ILE52 3.7 28.2 1.0
CA K:TRP47 4.2 17.6 1.0
N K:ILE52 4.2 28.6 1.0
CA K:ILE52 4.4 32.6 1.0
CA J:LEU46 4.4 38.2 1.0
N K:HIS48 4.4 22.3 1.0
N J:LEU46 4.5 29.7 1.0
CB K:ILE52 4.5 35.1 1.0
CB K:TRP47 4.5 16.0 1.0
CA J:TRP45 4.5 19.6 1.0
CA K:HIS48 4.6 20.2 1.0
O K:HIS48 4.7 38.6 1.0
C K:HIS48 4.7 27.8 1.0
N K:PRO53 4.7 27.9 1.0
CD K:PRO53 4.8 29.5 1.0
N K:ASP50 4.8 25.2 1.0
CB K:ASP50 4.8 31.0 1.0
OH N:TYR42 5.0 44.1 1.0
C J:LEU46 5.0 61.9 1.0
CB J:TRP45 5.0 18.1 1.0

Calcium binding site 7 out of 17 in 7c9r

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Calcium binding site 7 out of 17 in the Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970 within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca103

b:27.3
occ:1.00
 O N:TRP45 2.4 30.5 1.0
O O:ILE52 2.4 31.8 1.0
O O:TRP47 2.5 25.7 1.0
OD1 O:ASP50 2.7 49.1 1.0
CG O:ASP50 3.5 41.6 1.0
C N:TRP45 3.6 24.3 1.0
OD2 O:ASP50 3.6 53.7 1.0
C O:TRP47 3.6 25.3 1.0
C O:ILE52 3.6 26.3 1.0
N O:ILE52 4.1 31.4 1.0
CA O:TRP47 4.3 20.2 1.0
CA O:ILE52 4.3 25.1 1.0
CA N:LEU46 4.4 36.8 1.0
N N:LEU46 4.4 30.3 1.0
CA N:TRP45 4.5 20.9 1.0
CB O:ILE52 4.5 30.2 1.0
N O:HIS48 4.5 23.1 1.0
N O:PRO53 4.6 29.4 1.0
O O:HIS48 4.6 41.3 1.0
CA O:HIS48 4.6 24.9 1.0
C O:HIS48 4.7 31.3 1.0
CB O:TRP47 4.7 15.5 1.0
CD O:PRO53 4.7 23.1 1.0
N O:ASP50 4.9 26.4 1.0
CB O:ASP50 4.9 35.7 1.0
CB N:TRP45 4.9 26.1 1.0
C N:LEU46 4.9 65.5 1.0
N O:GLN51 5.0 33.7 1.0

Calcium binding site 8 out of 17 in 7c9r

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Calcium binding site 8 out of 17 in the Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970 within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Ca102

b:22.6
occ:1.00
 O Q:ILE52 2.5 29.7 1.0
O P:TRP45 2.5 26.2 1.0
OD1 Q:ASP50 2.5 43.0 1.0
O Q:TRP47 2.6 25.4 1.0
CG Q:ASP50 3.4 32.5 1.0
OD2 Q:ASP50 3.5 41.7 1.0
C Q:TRP47 3.6 21.0 1.0
C Q:ILE52 3.7 23.6 1.0
C P:TRP45 3.7 21.7 1.0
N Q:ILE52 4.2 21.0 1.0
CA Q:TRP47 4.3 20.0 1.0
O Q:HIS48 4.3 27.0 1.0
CA Q:ILE52 4.3 21.3 1.0
CB Q:ILE52 4.5 28.2 1.0
CA P:LEU46 4.5 38.8 1.0
N Q:HIS48 4.5 16.9 1.0
N P:LEU46 4.5 33.8 1.0
CA P:TRP45 4.5 18.3 1.0
C Q:HIS48 4.6 21.6 1.0
CA Q:HIS48 4.6 17.5 1.0
N Q:PRO53 4.7 29.7 1.0
CB Q:TRP47 4.7 16.0 1.0
N Q:ASP50 4.7 19.8 1.0
CB Q:ASP50 4.8 28.3 1.0
CD Q:PRO53 4.8 30.2 1.0
CG2 Q:ILE52 4.9 24.7 1.0
CB P:TRP45 5.0 19.7 1.0

Calcium binding site 9 out of 17 in 7c9r

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Calcium binding site 9 out of 17 in the Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970 within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Ca102

b:20.4
occ:1.00
 O S:ILE52 2.4 33.3 1.0
O R:TRP45 2.5 13.6 1.0
O S:TRP47 2.6 27.4 1.0
OD1 S:ASP50 2.6 28.5 1.0
CG S:ASP50 3.4 29.6 1.0
OD2 S:ASP50 3.5 27.9 1.0
C S:ILE52 3.6 27.0 1.0
C S:TRP47 3.6 19.3 1.0
C R:TRP45 3.6 19.2 1.0
N S:ILE52 4.1 23.7 1.0
CA S:ILE52 4.2 24.5 1.0
CA S:TRP47 4.3 15.9 1.0
CB S:ILE52 4.4 27.0 1.0
CA R:LEU46 4.4 34.0 1.0
N R:LEU46 4.5 29.0 1.0
CA R:TRP45 4.5 17.7 1.0
N S:HIS48 4.5 19.4 1.0
N S:PRO53 4.6 28.5 1.0
CA S:HIS48 4.7 21.7 1.0
CB S:TRP47 4.7 10.9 1.0
O S:HIS48 4.7 44.5 1.0
CD S:PRO53 4.7 30.2 1.0
C S:HIS48 4.7 30.0 1.0
N S:ASP50 4.8 26.1 1.0
CB S:ASP50 4.8 26.8 1.0
CG2 S:ILE52 4.9 17.8 1.0
C R:LEU46 4.9 59.2 1.0
N S:GLN51 5.0 29.1 1.0
OH T:TYR42 5.0 38.1 1.0

Calcium binding site 10 out of 17 in 7c9r

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Calcium binding site 10 out of 17 in the Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970 within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Ca101

b:29.9
occ:1.00
 O U:ILE52 2.4 33.7 1.0
OD1 U:ASP50 2.5 45.8 1.0
O U:TRP47 2.5 37.5 1.0
O T:TRP45 2.6 21.2 1.0
CG U:ASP50 3.3 35.2 1.0
OD2 U:ASP50 3.4 48.3 1.0
C U:TRP47 3.5 25.3 1.0
C U:ILE52 3.6 28.0 1.0
C T:TRP45 3.7 21.7 1.0
N U:ILE52 4.0 23.8 1.0
CA U:TRP47 4.2 20.5 1.0
CA U:ILE52 4.3 26.3 1.0
CB U:ILE52 4.4 30.2 1.0
N U:HIS48 4.5 24.6 1.0
CA T:LEU46 4.6 34.2 1.0
CA T:TRP45 4.6 21.8 1.0
O U:HIS48 4.6 37.9 1.0
N T:LEU46 4.6 28.3 1.0
N U:PRO53 4.6 33.4 1.0
CA U:HIS48 4.6 23.7 1.0
C U:HIS48 4.6 27.7 1.0
CB U:TRP47 4.7 18.5 1.0
N U:ASP50 4.7 24.9 1.0
CB U:ASP50 4.7 35.4 1.0
CD U:PRO53 4.8 28.9 1.0
N U:GLN51 4.9 23.3 1.0
CG2 U:ILE52 4.9 24.4 1.0

Reference:

K.Tani, R.Kanno, Y.Makino, M.Hall, M.Takenouchi, M.Imanishi, L.J.Yu, J.Overmann, M.T.Madigan, Y.Kimura, A.Mizoguchi, B.M.Humbel, Z.Y.Wang-Otomo. Cryo-Em Structure of A Ca 2+ -Bound Photosynthetic LH1-Rc Complex Containing Multiple Alpha Beta-Polypeptides. Nat Commun V. 11 4955 2020.
ISSN: ESSN 2041-1723
PubMed: 33009385
DOI: 10.1038/S41467-020-18748-3
Page generated: Thu Jul 18 23:35:11 2024

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