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Calcium in PDB 5y5s: Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution

Protein crystallography data

The structure of Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution, PDB code: 5y5s was solved by L.-J.Yu, M.Suga, Z.-Y.Wang-Otomo, J.-R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.92 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 145.280, 143.810, 210.280, 90.00, 90.74, 90.00
R / Rfree (%) 18.1 / 21.5

Other elements in 5y5s:

The structure of Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution 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 - 16;

Binding sites:

The binding sites of Calcium atom in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution (pdb code 5y5s). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution, PDB code: 5y5s:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 16 in 5y5s

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Calcium binding site 1 out of 16 in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution


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 at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca102

b:64.5
occ:1.00
 O A:ILE51 2.3 70.4 1.0
O A:HOH206 2.3 57.5 1.0
O 0:TRP45 2.3 60.2 1.0
O A:HOH201 2.3 60.4 1.0
O A:TRP46 2.4 56.9 1.0
OD1 A:ASP49 2.5 63.4 1.0
CG A:ASP49 3.3 65.3 1.0
OD2 A:ASP49 3.4 62.7 1.0
C 0:TRP45 3.4 61.4 1.0
C A:ILE51 3.4 70.5 1.0
C A:TRP46 3.5 55.9 1.0
N A:ILE51 4.0 74.3 1.0
CA A:ILE51 4.1 69.0 1.0
CB A:ILE51 4.2 71.6 1.0
CA 0:LEU46 4.2 74.9 1.0
N 0:LEU46 4.2 65.1 1.0
CA A:TRP46 4.3 57.9 1.0
CA 0:TRP45 4.3 64.5 1.0
N A:LEU47 4.4 66.2 1.0
N A:PRO52 4.5 74.6 1.0
CA A:LEU47 4.5 70.8 1.0
C A:LEU47 4.6 71.9 1.0
O A:LEU47 4.6 68.8 1.0
CB A:TRP46 4.7 57.3 1.0
CD A:PRO52 4.7 75.6 1.0
O 9:HOH204 4.7 69.4 1.0
CD2 0:LEU46 4.7 64.0 1.0
CB A:ASP49 4.8 64.0 1.0
CB 0:TRP45 4.8 60.0 1.0
OH B:TYR42 4.8 71.3 1.0
CG2 A:ILE51 4.9 63.9 1.0
N A:ASP49 4.9 62.9 1.0
C 0:LEU46 5.0 79.5 1.0

Calcium binding site 2 out of 16 in 5y5s

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Calcium binding site 2 out of 16 in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution


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 at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca102

b:64.3
occ:1.00
 O D:TRP46 2.4 63.1 1.0
O B:TRP45 2.4 65.8 1.0
O D:HOH205 2.4 57.9 1.0
O D:ILE51 2.4 68.9 1.0
O E:HOH202 2.4 68.9 1.0
OD1 D:ASP49 2.5 67.7 1.0
CG D:ASP49 3.3 65.1 1.0
OD2 D:ASP49 3.5 66.0 1.0
C D:TRP46 3.5 58.9 1.0
C B:TRP45 3.5 65.9 1.0
C D:ILE51 3.5 69.4 1.0
CB D:ILE51 4.0 73.8 1.0
N D:ILE51 4.0 76.4 1.0
CA D:ILE51 4.1 73.3 1.0
CA D:TRP46 4.3 58.1 1.0
N B:LEU46 4.3 68.2 1.0
CA B:LEU46 4.3 70.8 1.0
N D:LEU47 4.4 63.5 1.0
CA B:TRP45 4.4 72.5 1.0
CA D:LEU47 4.5 64.8 1.0
N D:PRO52 4.6 76.3 1.0
CD2 B:LEU46 4.6 69.8 1.0
CG2 D:ILE51 4.6 71.1 1.0
O D:LEU47 4.7 59.7 1.0
C D:LEU47 4.7 66.5 1.0
CB D:TRP46 4.7 63.7 1.0
O A:HOH203 4.7 71.3 1.0
CB D:ASP49 4.8 58.0 1.0
OH E:TYR42 4.8 75.1 1.0
CD D:PRO52 4.8 71.0 1.0
N D:ASP49 4.8 61.1 1.0
CB B:TRP45 4.8 66.8 1.0

Calcium binding site 3 out of 16 in 5y5s

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Calcium binding site 3 out of 16 in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution


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 at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca102

b:65.8
occ:1.00
 O F:ILE51 2.3 70.5 1.0
O F:HOH207 2.3 67.6 1.0
O E:TRP45 2.4 73.3 1.0
OD1 F:ASP49 2.4 66.5 1.0
O F:TRP46 2.5 62.1 1.0
O F:HOH201 2.7 61.8 1.0
CG F:ASP49 3.3 66.6 1.0
OD2 F:ASP49 3.4 65.6 1.0
C E:TRP45 3.4 73.5 1.0
C F:ILE51 3.5 69.4 1.0
C F:TRP46 3.5 57.1 1.0
N F:ILE51 4.0 64.0 1.0
CA F:ILE51 4.1 69.2 1.0
CA E:TRP45 4.3 73.0 1.0
CB F:ILE51 4.3 69.4 1.0
N E:LEU46 4.3 75.8 1.0
N F:LEU47 4.3 66.5 1.0
CA E:LEU46 4.4 76.8 1.0
CA F:TRP46 4.4 54.5 1.0
CA F:LEU47 4.4 69.1 1.0
O F:LEU47 4.5 71.5 1.0
N F:PRO52 4.5 69.2 1.0
C F:LEU47 4.5 69.2 1.0
O D:HOH201 4.6 67.1 1.0
CB F:ASP49 4.7 61.2 1.0
CD F:PRO52 4.7 67.0 1.0
CB E:TRP45 4.8 71.0 1.0
OH G:TYR42 4.8 72.3 1.0
N F:ASP49 4.8 62.1 1.0
CD2 E:LEU46 4.8 60.1 1.0
CB F:TRP46 4.8 57.0 1.0
CG2 F:ILE51 5.0 62.0 1.0
N F:ASN50 5.0 67.3 1.0

Calcium binding site 4 out of 16 in 5y5s

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Calcium binding site 4 out of 16 in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution


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 at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca103

b:64.0
occ:1.00
 O I:ILE51 2.2 71.1 1.0
O I:TRP46 2.3 68.0 1.0
O J:HOH202 2.4 66.7 1.0
O G:TRP45 2.4 64.4 1.0
OD1 I:ASP49 2.4 66.2 1.0
O I:HOH204 2.4 62.8 1.0
CG I:ASP49 3.3 65.6 1.0
C I:ILE51 3.4 67.5 1.0
OD2 I:ASP49 3.4 64.1 1.0
C I:TRP46 3.5 64.7 1.0
C G:TRP45 3.5 68.4 1.0
N I:ILE51 4.1 64.7 1.0
CA I:ILE51 4.1 68.1 1.0
CB I:ILE51 4.2 70.8 1.0
CA I:TRP46 4.3 64.3 1.0
N G:LEU46 4.3 69.0 1.0
CA G:LEU46 4.3 74.0 1.0
CA G:TRP45 4.4 68.4 1.0
N I:LEU47 4.4 65.8 1.0
O I:LEU47 4.4 72.1 1.0
N I:PRO52 4.4 67.4 1.0
CA I:LEU47 4.5 65.7 1.0
C I:LEU47 4.5 66.2 1.0
CD I:PRO52 4.5 62.7 1.0
CD2 G:LEU46 4.7 66.6 1.0
OH J:TYR42 4.7 75.5 1.0
CB I:ASP49 4.7 64.0 1.0
O F:HOH203 4.7 69.6 1.0
CB I:TRP46 4.8 64.8 1.0
N I:ASP49 4.8 66.4 1.0
CG2 I:ILE51 4.8 71.0 1.0
CB G:TRP45 4.8 64.7 1.0

Calcium binding site 5 out of 16 in 5y5s

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Calcium binding site 5 out of 16 in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution


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 at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca104

b:63.3
occ:1.00
 O K:ILE51 2.3 66.8 1.0
O J:TRP45 2.3 61.6 1.0
O K:TRP46 2.4 57.0 1.0
OD1 K:ASP49 2.4 63.5 1.0
O K:HOH206 2.5 63.4 1.0
O K:HOH204 2.5 65.4 1.0
CG K:ASP49 3.3 64.9 1.0
C K:ILE51 3.4 70.2 1.0
OD2 K:ASP49 3.5 62.7 1.0
C K:TRP46 3.5 62.3 1.0
C J:TRP45 3.5 62.8 1.0
N K:ILE51 4.0 70.5 1.0
CA K:ILE51 4.0 71.6 1.0
CB K:ILE51 4.1 71.5 1.0
CA K:TRP46 4.2 56.9 1.0
N J:LEU46 4.3 69.8 1.0
CA J:TRP45 4.4 64.8 1.0
CA J:LEU46 4.4 72.0 1.0
N K:LEU47 4.4 64.7 1.0
N K:PRO52 4.5 70.4 1.0
CA K:LEU47 4.5 66.3 1.0
O K:LEU47 4.6 66.6 1.0
C K:LEU47 4.7 65.7 1.0
O I:HOH206 4.7 63.3 1.0
CB K:TRP46 4.7 54.4 1.0
CD K:PRO52 4.7 69.3 1.0
CB K:ASP49 4.7 57.1 1.0
CD2 J:LEU46 4.8 60.5 1.0
CG2 K:ILE51 4.8 65.9 1.0
CB J:TRP45 4.8 60.4 1.0
OH N:TYR42 4.8 73.2 1.0
N K:ASP49 4.8 52.9 1.0
N K:ASN50 5.0 74.1 1.0

Calcium binding site 6 out of 16 in 5y5s

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Calcium binding site 6 out of 16 in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution


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 at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Ca102

b:56.1
occ:1.00
 O O:ILE51 2.3 58.8 1.0
O N:TRP45 2.4 57.5 1.0
O O:TRP46 2.4 48.3 1.0
O O:HOH211 2.4 54.3 1.0
OD1 O:ASP49 2.4 58.1 1.0
O O:HOH202 2.5 55.2 1.0
CG O:ASP49 3.3 56.6 1.0
OD2 O:ASP49 3.4 58.5 1.0
C O:ILE51 3.4 56.1 1.0
C N:TRP45 3.5 55.4 1.0
C O:TRP46 3.5 51.5 1.0
N O:ILE51 4.0 57.7 1.0
CA O:ILE51 4.1 56.0 1.0
CB O:ILE51 4.2 56.6 1.0
CA O:TRP46 4.3 45.4 1.0
N N:LEU46 4.3 55.5 1.0
CA N:LEU46 4.3 59.6 1.0
CA N:TRP45 4.4 53.3 1.0
N O:LEU47 4.4 49.2 1.0
O O:LEU47 4.5 58.8 1.0
N O:PRO52 4.5 60.6 1.0
CA O:LEU47 4.5 52.5 1.0
C O:LEU47 4.6 59.1 1.0
CB O:TRP46 4.7 45.9 1.0
CB O:ASP49 4.7 50.0 1.0
CD O:PRO52 4.8 61.4 1.0
O O:HOH205 4.8 59.5 1.0
CD2 N:LEU46 4.8 47.2 1.0
N O:ASP49 4.8 51.9 1.0
CB N:TRP45 4.8 56.6 1.0
N O:ASN50 4.9 60.0 1.0
OH P:TYR42 4.9 67.9 1.0
CG2 O:ILE51 5.0 55.2 1.0

Calcium binding site 7 out of 16 in 5y5s

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Calcium binding site 7 out of 16 in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution


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 at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Ca103

b:47.3
occ:1.00
 O P:TRP45 2.3 50.3 1.0
O Q:TRP46 2.3 43.9 1.0
O Q:HOH203 2.3 46.1 1.0
OD1 Q:ASP49 2.3 45.0 1.0
O Q:ILE51 2.4 53.1 1.0
O Q:HOH209 2.5 45.8 1.0
CG Q:ASP49 3.2 48.8 1.0
C Q:TRP46 3.4 39.6 1.0
OD2 Q:ASP49 3.4 46.7 1.0
C P:TRP45 3.5 45.6 1.0
C Q:ILE51 3.5 50.6 1.0
N Q:ILE51 4.1 47.9 1.0
CA Q:ILE51 4.2 47.1 1.0
CA Q:TRP46 4.2 39.6 1.0
CB Q:ILE51 4.2 47.7 1.0
CA P:LEU46 4.3 49.5 1.0
N P:LEU46 4.3 48.0 1.0
N Q:LEU47 4.3 42.2 1.0
CA P:TRP45 4.4 51.7 1.0
CA Q:LEU47 4.5 50.7 1.0
N Q:PRO52 4.6 52.1 1.0
CB Q:TRP46 4.6 40.4 1.0
CD2 P:LEU46 4.6 46.6 1.0
C Q:LEU47 4.7 48.9 1.0
O Q:LEU47 4.7 46.7 1.0
O Q:HOH202 4.7 56.8 1.0
CB Q:ASP49 4.7 49.4 1.0
CG2 Q:ILE51 4.7 44.7 1.0
CD Q:PRO52 4.8 56.2 1.0
OH R:TYR42 4.8 57.1 1.0
CB P:TRP45 4.8 49.5 1.0
N Q:ASP49 4.8 50.8 1.0
C P:LEU46 5.0 60.2 1.0

Calcium binding site 8 out of 16 in 5y5s

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Calcium binding site 8 out of 16 in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution


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 at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Ca102

b:44.5
occ:1.00
 O R:TRP45 2.3 45.8 1.0
O S:TRP46 2.3 42.0 1.0
O S:HOH207 2.4 45.6 1.0
O S:HOH201 2.4 45.1 1.0
OD1 S:ASP49 2.4 45.4 1.0
O S:ILE51 2.4 53.3 1.0
CG S:ASP49 3.3 44.2 1.0
C S:TRP46 3.4 39.1 1.0
C R:TRP45 3.5 43.9 1.0
OD2 S:ASP49 3.5 45.6 1.0
C S:ILE51 3.5 51.5 1.0
N S:ILE51 4.0 46.2 1.0
CA S:ILE51 4.1 47.6 1.0
CB S:ILE51 4.1 51.5 1.0
CA S:TRP46 4.2 43.1 1.0
N S:LEU47 4.3 40.4 1.0
CA R:TRP45 4.3 44.9 1.0
N R:LEU46 4.4 46.6 1.0
CA R:LEU46 4.4 50.0 1.0
CA S:LEU47 4.5 45.5 1.0
O S:LEU47 4.6 48.1 1.0
N S:PRO52 4.6 50.7 1.0
C S:LEU47 4.6 44.4 1.0
CG2 S:ILE51 4.6 47.2 1.0
O Q:HOH205 4.6 53.9 1.0
CB S:TRP46 4.7 47.1 1.0
CD2 R:LEU46 4.7 45.5 1.0
CB S:ASP49 4.7 44.2 1.0
CB R:TRP45 4.8 46.8 1.0
N S:ASP49 4.8 47.8 1.0
CD S:PRO52 4.8 51.1 1.0
OH T:TYR42 4.9 49.4 1.0
N S:ASN50 5.0 53.4 1.0

Calcium binding site 9 out of 16 in 5y5s

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Calcium binding site 9 out of 16 in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution


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 at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Ca102

b:48.4
occ:1.00
 O T:TRP45 2.2 50.0 1.0
O U:HOH204 2.3 45.3 1.0
O U:HOH208 2.3 46.6 1.0
O U:ILE51 2.3 47.2 1.0
O U:TRP46 2.3 49.8 1.0
OD1 U:ASP49 2.5 49.9 1.0
C T:TRP45 3.4 44.9 1.0
C U:TRP46 3.4 48.1 1.0
CG U:ASP49 3.4 49.9 1.0
C U:ILE51 3.5 54.9 1.0
OD2 U:ASP49 3.6 48.2 1.0
N U:ILE51 4.0 54.0 1.0
CA U:ILE51 4.1 57.9 1.0
N T:LEU46 4.2 48.5 1.0
CA T:LEU46 4.2 53.9 1.0
CA U:TRP46 4.2 53.0 1.0
CB U:ILE51 4.2 59.9 1.0
CA T:TRP45 4.3 51.5 1.0
N U:LEU47 4.3 49.5 1.0
CA U:LEU47 4.4 47.3 1.0
N U:PRO52 4.5 53.0 1.0
O U:LEU47 4.5 46.5 1.0
CD2 T:LEU46 4.6 45.2 1.0
C U:LEU47 4.6 50.7 1.0
CB U:TRP46 4.7 50.5 1.0
CB T:TRP45 4.7 44.9 1.0
CD U:PRO52 4.7 54.9 1.0
O S:HOH202 4.7 52.5 1.0
CG2 U:ILE51 4.8 60.2 1.0
CB U:ASP49 4.9 47.5 1.0
N U:ASN50 5.0 48.6 1.0
OH V:TYR42 5.0 56.7 1.0
N U:ASP49 5.0 49.6 1.0

Calcium binding site 10 out of 16 in 5y5s

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Calcium binding site 10 out of 16 in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution


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 at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Ca103

b:52.9
occ:1.00
 O W:HOH204 2.2 48.9 1.0
O W:TRP46 2.3 48.4 1.0
O V:TRP45 2.3 50.3 1.0
O W:ILE51 2.3 61.6 1.0
O W:HOH203 2.4 55.6 1.0
OD1 W:ASP49 2.5 56.0 1.0
CG W:ASP49 3.4 55.6 1.0
C V:TRP45 3.4 51.2 1.0
C W:TRP46 3.4 49.2 1.0
C W:ILE51 3.5 64.4 1.0
OD2 W:ASP49 3.6 54.2 1.0
N W:ILE51 4.0 61.0 1.0
CA W:ILE51 4.1 58.3 1.0
CB W:ILE51 4.1 65.8 1.0
CA W:TRP46 4.3 52.8 1.0
CA V:TRP45 4.3 48.6 1.0
N V:LEU46 4.3 51.9 1.0
CA V:LEU46 4.3 54.4 1.0
N W:LEU47 4.4 49.4 1.0
CA W:LEU47 4.5 48.5 1.0
O W:LEU47 4.5 57.5 1.0
N W:PRO52 4.5 64.2 1.0
C W:LEU47 4.6 54.9 1.0
CG2 W:ILE51 4.6 64.3 1.0
CB W:TRP46 4.7 55.1 1.0
CD2 V:LEU46 4.7 63.2 1.0
CB V:TRP45 4.7 50.5 1.0
O U:HOH203 4.7 51.6 1.0
CB W:ASP49 4.8 48.1 1.0
CD W:PRO52 4.8 58.9 1.0
N W:ASP49 4.8 52.8 1.0
OH X:TYR42 5.0 64.5 1.0

Reference:

L.-J.Yu, M.Suga, Z.-Y.Wang-Otomo, J.R.Shen. Structure of Photosynthetic LH1-Rc Supercomplex at 1.9 Angstrom Resolution. Nature V. 556 209 2018.
ISSN: ESSN 1476-4687
PubMed: 29618814
DOI: 10.1038/S41586-018-0002-9
Page generated: Mon Jul 15 15:17:35 2024

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