Calcium in PDB 7c52: Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip

Protein crystallography data

The structure of Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip, PDB code: 7c52 was solved by L.-J.Yu, Z.-Y.Wang-Otomo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.99 / 2.89
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 96.435, 183.335, 123.857, 90, 112.58, 90
R / Rfree (%) 21.9 / 24.8

Other elements in 7c52:

The structure of Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip also contains other interesting chemical elements:

Magnesium (Mg) 36 atoms
Iron (Fe) 9 atoms

Calcium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Calcium atom in the Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip (pdb code 7c52). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 17 binding sites of Calcium where determined in the Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip, PDB code: 7c52:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 17 in 7c52

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Calcium binding site 1 out of 17 in the Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca505

b:103.6
occ:1.00
 OE1 C:GLN183 2.6 97.1 1.0
OE1 C:GLU230 2.7 105.7 1.0
OE2 C:GLU230 3.2 105.4 1.0
OE1 M:GLU96 3.2 103.0 1.0
CD C:GLU230 3.4 103.1 1.0
CD C:GLN183 3.4 94.7 1.0
OD1 C:ASN184 3.7 85.3 1.0
OE2 M:GLU96 3.8 104.3 1.0
CD M:GLU96 3.9 101.3 1.0
CG M:PRO176 4.0 84.5 1.0
NE2 C:GLN183 4.1 97.0 1.0
O M:PRO181 4.3 86.2 1.0
CG C:GLN183 4.5 89.3 1.0
CB M:PRO176 4.6 84.8 1.0
CB M:PRO181 4.6 81.3 1.0
CG C:ASN184 4.6 87.3 1.0
OD2 M:ASP184 4.7 81.9 1.0
CB M:ASP184 4.7 78.2 1.0
CA M:PRO181 4.8 80.8 1.0
CG C:GLU230 4.9 97.1 1.0
ND2 C:ASN184 4.9 88.8 1.0
C M:PRO181 4.9 83.2 1.0
O C:SER194 4.9 85.7 1.0

Calcium binding site 2 out of 17 in 7c52

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Calcium binding site 2 out of 17 in the Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca102

b:123.1
occ:1.00
 O A:TRP46 2.3 133.4 1.0
O A:ILE51 2.3 164.1 1.0
OD1 A:ASP49 2.4 168.2 1.0
O 0:TRP45 2.5 146.7 1.0
CG A:ASP49 3.3 177.6 1.0
C A:TRP46 3.4 133.1 1.0
OD2 A:ASP49 3.4 170.6 1.0
C A:ILE51 3.5 168.4 1.0
C 0:TRP45 3.6 148.5 1.0
N A:ILE51 4.0 180.1 1.0
CA A:ILE51 4.2 174.8 1.0
N A:LEU47 4.2 138.2 1.0
CA 0:TRP45 4.2 149.1 1.0
CA A:LEU47 4.3 148.6 1.0
CB A:ILE51 4.3 175.2 1.0
CA A:TRP46 4.3 127.0 1.0
C A:LEU47 4.3 165.5 1.0
O A:LEU47 4.3 173.1 1.0
N A:PRO52 4.6 166.4 1.0
CB 0:TRP45 4.6 146.2 1.0
N 0:LEU46 4.6 149.5 1.0
N A:ASP49 4.6 200.1 1.0
CB A:ASP49 4.7 195.5 1.0
CA 0:LEU46 4.8 148.0 1.0
CB A:TRP46 4.8 129.7 1.0
CD A:PRO52 4.8 164.3 1.0
N A:ASN50 4.8 187.8 1.0
N A:ASP48 5.0 175.7 1.0
CG2 A:ILE51 5.0 182.4 1.0

Calcium binding site 3 out of 17 in 7c52

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Calcium binding site 3 out of 17 in the Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca102

b:127.7
occ:1.00
 OD1 D:ASP49 2.4 180.3 1.0
O D:TRP46 2.4 136.7 1.0
O B:TRP45 2.4 152.0 1.0
O D:ILE51 2.5 166.3 1.0
CG D:ASP49 3.1 184.1 1.0
OD2 D:ASP49 3.2 182.1 1.0
C D:TRP46 3.5 136.9 1.0
C D:ILE51 3.6 163.5 1.0
C B:TRP45 3.6 148.3 1.0
N D:ILE51 4.0 168.7 1.0
CB D:ILE51 4.0 156.9 1.0
CA D:ILE51 4.1 164.2 1.0
CA B:LEU46 4.3 147.1 1.0
N B:LEU46 4.3 148.4 1.0
N D:LEU47 4.4 147.8 1.0
CA D:TRP46 4.4 130.6 1.0
CA B:TRP45 4.5 144.4 1.0
CD2 B:LEU46 4.5 133.5 1.0
CA D:LEU47 4.5 162.2 1.0
CB D:ASP49 4.6 189.8 1.0
O D:LEU47 4.6 189.1 1.0
C D:LEU47 4.6 180.8 1.0
OH E:TYR42 4.7 144.3 1.0
N D:PRO52 4.7 158.9 1.0
CG2 D:ILE51 4.7 158.9 1.0
N D:ASP49 4.7 193.4 1.0
CB D:TRP46 4.8 129.8 1.0
CB B:TRP45 5.0 140.4 1.0
N D:ASN50 5.0 185.2 1.0
CA D:ASP49 5.0 191.6 1.0

Calcium binding site 4 out of 17 in 7c52

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Calcium binding site 4 out of 17 in the Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca102

b:129.7
occ:1.00
 OD1 F:ASP49 2.3 152.6 1.0
O F:TRP46 2.4 132.2 1.0
O F:ILE51 2.4 150.3 1.0
O E:TRP45 2.5 137.6 1.0
OD2 F:ASP49 2.9 154.1 1.0
CG F:ASP49 3.0 152.7 1.0
C F:TRP46 3.4 131.2 1.0
C F:ILE51 3.6 152.8 1.0
C E:TRP45 3.6 138.2 1.0
N F:ILE51 4.1 152.6 1.0
CA F:TRP46 4.1 131.8 1.0
CA F:ILE51 4.2 153.5 1.0
CB F:ILE51 4.2 153.2 1.0
N F:LEU47 4.3 129.2 1.0
CA E:LEU46 4.4 142.4 1.0
CA F:LEU47 4.4 131.3 1.0
CB F:ASP49 4.4 150.0 1.0
N E:LEU46 4.4 141.4 1.0
O F:LEU47 4.5 139.2 1.0
OH G:TYR42 4.5 140.1 1.0
CA E:TRP45 4.5 136.1 1.0
C F:LEU47 4.5 136.6 1.0
CB F:TRP46 4.5 135.3 1.0
N F:PRO52 4.6 155.7 1.0
N F:ASP49 4.7 142.6 1.0
CG2 F:ILE51 4.8 159.0 1.0
CD2 E:LEU46 4.9 140.8 1.0
CD F:PRO52 4.9 156.3 1.0

Calcium binding site 5 out of 17 in 7c52

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Calcium binding site 5 out of 17 in the Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca102

b:139.7
occ:1.00
 O I:ILE51 2.4 160.7 1.0
OD1 I:ASP49 2.4 162.9 1.0
O G:TRP45 2.5 146.1 1.0
O I:TRP46 2.5 141.4 1.0
CG I:ASP49 3.3 163.4 1.0
OD2 I:ASP49 3.5 163.9 1.0
C I:ILE51 3.6 162.6 1.0
C G:TRP45 3.6 145.7 1.0
C I:TRP46 3.7 139.8 1.0
N I:ILE51 4.1 166.7 1.0
O I:LEU47 4.2 151.7 1.0
CA I:ILE51 4.2 166.9 1.0
CB I:ILE51 4.3 168.3 1.0
CA G:TRP45 4.4 143.8 1.0
C I:LEU47 4.4 145.6 1.0
N G:LEU46 4.5 146.1 1.0
CA I:LEU47 4.5 140.3 1.0
N I:LEU47 4.5 138.1 1.0
CA G:LEU46 4.5 145.6 1.0
CA I:TRP46 4.6 138.1 1.0
N I:PRO52 4.6 161.4 1.0
N I:ASP49 4.7 158.5 1.0
CB I:ASP49 4.7 162.0 1.0
CD I:PRO52 4.8 161.5 1.0
CB G:TRP45 4.9 138.4 1.0
OH J:TYR42 4.9 139.5 1.0
N I:ASN50 5.0 158.2 1.0
CG2 I:ILE51 5.0 172.6 1.0

Calcium binding site 6 out of 17 in 7c52

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Calcium binding site 6 out of 17 in the Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca102

b:120.1
occ:1.00
 O K:TRP46 2.4 128.7 1.0
OD1 K:ASP49 2.4 149.2 1.0
O J:TRP45 2.5 136.7 1.0
O K:ILE51 2.5 171.4 1.0
OD2 K:ASP49 2.9 151.2 1.0
CG K:ASP49 3.0 152.5 1.0
C K:TRP46 3.4 127.3 1.0
C K:ILE51 3.6 169.8 1.0
C J:TRP45 3.7 139.3 1.0
CB K:ILE51 3.9 163.5 1.0
CA K:TRP46 4.0 123.5 1.0
N K:ILE51 4.1 160.7 1.0
CA K:ILE51 4.1 164.9 1.0
OH N:TYR42 4.2 141.4 1.0
CA J:LEU46 4.3 142.6 1.0
CB K:TRP46 4.4 126.2 1.0
N J:LEU46 4.4 141.9 1.0
N K:LEU47 4.5 129.8 1.0
CB K:ASP49 4.5 157.2 1.0
CG2 K:ILE51 4.6 165.6 1.0
CA J:TRP45 4.6 140.3 1.0
N K:PRO52 4.7 173.7 1.0
CD2 J:LEU46 4.7 132.9 1.0
CA K:LEU47 4.7 136.5 1.0
NH2 N:ARG43 4.8 137.6 1.0
N K:ASP49 4.9 162.8 1.0
C K:LEU47 4.9 145.8 1.0
O K:LEU47 4.9 148.5 1.0
C J:LEU46 4.9 149.9 1.0

Calcium binding site 7 out of 17 in 7c52

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Calcium binding site 7 out of 17 in the Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca102

b:121.7
occ:1.00
 OD1 O:ASP49 2.4 152.1 1.0
O O:TRP46 2.4 136.5 1.0
O O:ILE51 2.5 155.4 1.0
O N:TRP45 2.6 128.8 1.0
OD2 O:ASP49 3.0 153.6 1.0
CG O:ASP49 3.0 154.2 1.0
C O:TRP46 3.5 135.9 1.0
C O:ILE51 3.6 154.6 1.0
C N:TRP45 3.6 132.4 1.0
CB O:ILE51 4.0 150.7 1.0
CA O:TRP46 4.1 134.1 1.0
CA N:LEU46 4.1 137.8 1.0
N O:ILE51 4.1 158.4 1.0
CA O:ILE51 4.1 155.2 1.0
OH P:TYR42 4.2 129.7 1.0
N N:LEU46 4.3 137.3 1.0
CB O:TRP46 4.4 134.2 1.0
CB O:ASP49 4.5 157.8 1.0
N O:LEU47 4.5 137.3 1.0
OXT N:LEU46 4.6 143.3 1.0
CG2 O:ILE51 4.6 150.6 1.0
CA N:TRP45 4.6 131.4 1.0
C N:LEU46 4.7 141.7 1.0
N O:PRO52 4.7 153.6 1.0
CD2 N:LEU46 4.7 130.4 1.0
CA O:LEU47 4.7 142.4 1.0
O O:LEU47 4.8 155.4 1.0
N O:ASP49 4.8 160.7 1.0
C O:LEU47 4.9 150.5 1.0
CD O:PRO52 5.0 153.2 1.0

Calcium binding site 8 out of 17 in 7c52

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Calcium binding site 8 out of 17 in the Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip


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Stereo pair view

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

b:116.8
occ:1.00
 O Q:TRP46 2.2 126.6 1.0
OD1 Q:ASP49 2.4 138.3 1.0
O Q:ILE51 2.4 153.8 1.0
O P:TRP45 2.4 140.9 1.0
OD2 Q:ASP49 2.9 141.2 1.0
CG Q:ASP49 3.0 140.9 1.0
C Q:TRP46 3.3 123.6 1.0
C Q:ILE51 3.5 155.0 1.0
C P:TRP45 3.5 143.3 1.0
N Q:ILE51 4.0 157.3 1.0
CB Q:ILE51 4.1 151.6 1.0
CA Q:ILE51 4.1 154.7 1.0
CA Q:TRP46 4.1 124.4 1.0
CA P:LEU46 4.3 158.6 1.0
N Q:LEU47 4.3 119.9 1.0
OH R:TYR42 4.4 135.9 1.0
N P:LEU46 4.4 151.9 1.0
CB Q:TRP46 4.4 127.4 1.0
CA P:TRP45 4.5 138.7 1.0
CB Q:ASP49 4.5 142.8 1.0
CA Q:LEU47 4.5 120.0 1.0
N Q:PRO52 4.6 154.9 1.0
CG2 Q:ILE51 4.7 154.9 1.0
C Q:LEU47 4.7 126.2 1.0
O Q:LEU47 4.7 132.2 1.0
N Q:ASP49 4.8 139.7 1.0
CD2 P:LEU46 4.9 155.6 1.0
CD Q:PRO52 4.9 154.8 1.0
C P:LEU46 4.9 168.1 1.0
CB P:TRP45 4.9 134.0 1.0

Calcium binding site 9 out of 17 in 7c52

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Calcium binding site 9 out of 17 in the Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip


Mono view


Stereo pair view

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

b:111.7
occ:1.00
 OD1 S:ASP49 2.4 128.8 1.0
O R:TRP45 2.5 127.8 1.0
O S:TRP46 2.5 122.4 1.0
O S:ILE51 2.5 138.7 1.0
OD2 S:ASP49 2.9 129.3 1.0
CG S:ASP49 3.0 130.1 1.0
C S:TRP46 3.5 121.6 1.0
C S:ILE51 3.6 139.8 1.0
C R:TRP45 3.6 131.6 1.0
CB S:ILE51 3.8 144.1 1.0
CA S:ILE51 4.0 142.0 1.0
N S:ILE51 4.0 142.1 1.0
CA S:TRP46 4.0 123.6 1.0
OH T:TYR42 4.1 136.1 1.0
CA R:LEU46 4.1 138.4 1.0
N R:LEU46 4.3 136.8 1.0
CG2 S:ILE51 4.3 148.9 1.0
CB S:TRP46 4.4 125.8 1.0
CB S:ASP49 4.5 131.8 1.0
CD2 R:LEU46 4.5 126.7 1.0
N S:LEU47 4.6 118.4 1.0
CA R:TRP45 4.6 131.8 1.0
N S:PRO52 4.7 140.8 1.0
C R:LEU46 4.8 145.1 1.0
OXT R:LEU46 4.8 148.1 1.0
CA S:LEU47 4.9 119.3 1.0
N S:ASP49 5.0 127.9 1.0

Calcium binding site 10 out of 17 in 7c52

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Calcium binding site 10 out of 17 in the Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Co-Crystal Structure of A Photosynthetic LH1-Rc in Complex with Electron Donor Hipip within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Ca102

b:112.2
occ:1.00
 OD1 U:ASP49 2.3 141.6 1.0
O U:TRP46 2.4 121.4 1.0
O U:ILE51 2.4 123.9 1.0
O T:TRP45 2.5 125.1 1.0
CG U:ASP49 3.2 140.8 1.0
OD2 U:ASP49 3.4 142.5 1.0
C U:TRP46 3.4 120.6 1.0
C U:ILE51 3.5 127.5 1.0
C T:TRP45 3.6 127.9 1.0
N U:ILE51 3.8 128.3 1.0
CA U:ILE51 4.1 127.8 1.0
CB U:ILE51 4.2 126.5 1.0
N U:LEU47 4.2 118.3 1.0
CA U:TRP46 4.3 122.1 1.0
CA T:TRP45 4.4 127.2 1.0
CA U:LEU47 4.4 119.5 1.0
O U:LEU47 4.4 130.0 1.0
C U:LEU47 4.5 124.0 1.0
N T:LEU46 4.5 132.8 1.0
CA T:LEU46 4.6 136.1 1.0
CB U:ASP49 4.6 139.0 1.0
N U:PRO52 4.7 131.8 1.0
N U:ASN50 4.7 135.4 1.0
CB T:TRP45 4.7 123.7 1.0
N U:ASP49 4.7 134.9 1.0
CB U:TRP46 4.8 124.1 1.0
CG2 U:ILE51 4.9 127.5 1.0
CD U:PRO52 4.9 132.6 1.0
C U:ASN50 5.0 131.6 1.0
C U:ASP49 5.0 141.2 1.0

Reference:

T.Kawakami, L.J.Yu, T.Liang, K.Okazaki, M.T.Madigan, Y.Kimura, Z.Y.Wang-Otomo. Crystal Structure of A Photosynthetic LH1-Rc in Complex with Its Electron Donor Hipip. Nat Commun V. 12 1104 2021.
ISSN: ESSN 2041-1723
PubMed: 33597527
DOI: 10.1038/S41467-021-21397-9
Page generated: Sat Apr 17 14:07:29 2021

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