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Calcium in PDB 8jc8: Cryo-Em Structure of the LH1 Complex From Thermochromatium Tepidum

Other elements in 8jc8:

The structure of Cryo-Em Structure of the LH1 Complex From Thermochromatium Tepidum also contains other interesting chemical elements:

Magnesium (Mg) 30 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Calcium atom in the Cryo-Em Structure of the LH1 Complex From Thermochromatium Tepidum (pdb code 8jc8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 15 binding sites of Calcium where determined in the Cryo-Em Structure of the LH1 Complex From Thermochromatium Tepidum, PDB code: 8jc8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 15 in 8jc8

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Calcium binding site 1 out of 15 in the Cryo-Em Structure of the LH1 Complex From Thermochromatium Tepidum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of the LH1 Complex From Thermochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Ca102

b:9.8
occ:1.00
 O 3:TRP46 2.4 9.8 1.0
O 3:ILE51 2.4 12.5 1.0
O 2:TRP45 2.5 10.0 1.0
OD1 3:ASP49 2.6 11.5 1.0
C 3:ILE51 3.5 12.5 1.0
CG 3:ASP49 3.5 11.5 1.0
C 3:TRP46 3.6 9.8 1.0
OD2 3:ASP49 3.7 11.5 1.0
C 2:TRP45 3.7 10.0 1.0
CB 3:ILE51 3.9 12.5 1.0
N 3:ILE51 4.0 12.5 1.0
CA 3:ILE51 4.0 12.5 1.0
CA 3:TRP46 4.3 9.8 1.0
O 3:LEU47 4.3 10.0 1.0
CG2 3:ILE51 4.5 12.5 1.0
CA 2:LEU46 4.5 9.9 1.0
N 2:LEU46 4.6 9.9 1.0
N 3:LEU47 4.6 10.0 1.0
N 3:PRO52 4.6 12.7 1.0
CA 2:TRP45 4.7 10.0 1.0
CA 3:LEU47 4.7 10.0 1.0
CB 3:TRP46 4.7 9.8 1.0
C 3:LEU47 4.7 10.0 1.0
OH 4:TYR42 4.9 9.8 1.0
CD 3:PRO52 4.9 12.7 1.0
CB 3:ASP49 4.9 11.5 1.0
CD2 2:LEU46 5.0 9.9 1.0

Calcium binding site 2 out of 15 in 8jc8

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Calcium binding site 2 out of 15 in the Cryo-Em Structure of the LH1 Complex From Thermochromatium Tepidum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of the LH1 Complex From Thermochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
5:Ca103

b:9.8
occ:1.00
 O 5:TRP46 2.4 9.8 1.0
O 5:ILE51 2.4 12.3 1.0
O 4:TRP45 2.5 9.8 1.0
OD1 5:ASP49 2.6 11.7 1.0
CG 5:ASP49 3.5 11.7 1.0
C 5:ILE51 3.5 12.3 1.0
C 5:TRP46 3.5 9.8 1.0
OD2 5:ASP49 3.6 11.7 1.0
C 4:TRP45 3.7 9.8 1.0
CB 5:ILE51 3.9 12.3 1.0
N 5:ILE51 4.0 12.3 1.0
CA 5:ILE51 4.0 12.3 1.0
O 5:LEU47 4.3 9.8 1.0
CA 5:TRP46 4.3 9.8 1.0
CG2 5:ILE51 4.3 12.3 1.0
CA 4:LEU46 4.5 10.0 1.0
N 5:LEU47 4.5 9.8 1.0
N 4:LEU46 4.6 10.0 1.0
N 5:PRO52 4.6 12.0 1.0
CA 4:TRP45 4.6 9.8 1.0
CA 5:LEU47 4.7 9.8 1.0
C 5:LEU47 4.7 9.8 1.0
CB 5:TRP46 4.8 9.8 1.0
OH 6:TYR42 4.9 9.9 1.0
CB 5:ASP49 4.9 11.7 1.0
CD 5:PRO52 5.0 12.0 1.0

Calcium binding site 3 out of 15 in 8jc8

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Calcium binding site 3 out of 15 in the Cryo-Em Structure of the LH1 Complex From Thermochromatium Tepidum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of the LH1 Complex From Thermochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
7:Ca103

b:7.4
occ:1.00
 O 7:TRP46 2.4 9.8 1.0
O 7:ILE51 2.5 11.8 1.0
O 6:TRP45 2.5 9.8 1.0
OD1 7:ASP49 2.5 11.3 1.0
OD2 7:ASP49 3.1 11.3 1.0
CG 7:ASP49 3.2 11.3 1.0
C 7:TRP46 3.5 9.8 1.0
C 7:ILE51 3.5 11.8 1.0
C 6:TRP45 3.7 9.8 1.0
CB 7:ILE51 4.0 11.8 1.0
N 7:ILE51 4.1 11.8 1.0
CA 7:ILE51 4.1 11.8 1.0
CA 7:TRP46 4.2 9.8 1.0
CA 6:LEU46 4.4 9.8 1.0
N 6:LEU46 4.5 9.8 1.0
N 7:LEU47 4.5 9.8 1.0
O 7:LEU47 4.6 9.8 1.0
CA 6:TRP45 4.6 9.8 1.0
N 7:PRO52 4.6 12.3 1.0
CB 7:ASP49 4.6 11.3 1.0
CB 7:TRP46 4.6 9.8 1.0
CA 7:LEU47 4.7 9.8 1.0
CG2 7:ILE51 4.7 11.8 1.0
OH 8:TYR42 4.8 9.9 1.0
CD2 6:LEU46 4.8 9.8 1.0
C 7:LEU47 4.8 9.8 1.0
CD 7:PRO52 4.9 12.3 1.0
C 6:LEU46 4.9 9.8 1.0

Calcium binding site 4 out of 15 in 8jc8

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Calcium binding site 4 out of 15 in the Cryo-Em Structure of the LH1 Complex From Thermochromatium Tepidum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of the LH1 Complex From Thermochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca103

b:10.3
occ:1.00
 O A:TRP46 2.4 9.8 1.0
O 8:TRP45 2.5 9.8 1.0
O A:ILE51 2.5 12.2 1.0
OD1 A:ASP49 2.5 11.4 1.0
CG A:ASP49 3.3 11.4 1.0
OD2 A:ASP49 3.3 11.4 1.0
C A:TRP46 3.5 9.8 1.0
C A:ILE51 3.6 12.2 1.0
C 8:TRP45 3.7 9.8 1.0
N A:ILE51 4.0 12.2 1.0
CB A:ILE51 4.0 12.2 1.0
CA A:ILE51 4.1 12.2 1.0
CA A:TRP46 4.3 9.8 1.0
N A:LEU47 4.5 9.8 1.0
O A:LEU47 4.5 9.8 1.0
CA 8:LEU46 4.5 9.8 1.0
N 8:LEU46 4.6 9.8 1.0
CA 8:TRP45 4.6 9.8 1.0
CA A:LEU47 4.7 9.8 1.0
N A:PRO52 4.7 12.1 1.0
CG2 A:ILE51 4.7 12.2 1.0
CB A:TRP46 4.7 9.8 1.0
CB A:ASP49 4.7 11.4 1.0
C A:LEU47 4.8 9.8 1.0
OH B:TYR42 4.9 9.8 1.0
C 8:LEU46 4.9 9.8 1.0
OXT 8:LEU46 5.0 9.8 1.0
N A:ASP49 5.0 11.4 1.0
CD A:PRO52 5.0 12.1 1.0

Calcium binding site 5 out of 15 in 8jc8

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Calcium binding site 5 out of 15 in the Cryo-Em Structure of the LH1 Complex From Thermochromatium Tepidum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cryo-Em Structure of the LH1 Complex From Thermochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca103

b:8.5
occ:1.00
 O D:TRP46 2.4 9.9 1.0
O D:ILE51 2.5 11.6 1.0
O B:TRP45 2.5 9.9 1.0
OD1 D:ASP49 2.6 11.3 1.0
CG D:ASP49 3.4 11.3 1.0
C D:ILE51 3.5 11.6 1.0
OD2 D:ASP49 3.5 11.3 1.0
C D:TRP46 3.6 9.9 1.0
C B:TRP45 3.8 9.9 1.0
CB D:ILE51 4.0 11.6 1.0
CA D:ILE51 4.0 11.6 1.0
N D:ILE51 4.1 11.6 1.0
CA D:TRP46 4.3 9.9 1.0
O D:LEU47 4.3 10.0 1.0
CA B:LEU46 4.5 10.2 1.0
CG2 D:ILE51 4.5 11.6 1.0
N D:LEU47 4.6 10.0 1.0
N B:LEU46 4.6 10.2 1.0
N D:PRO52 4.6 11.9 1.0
CA B:TRP45 4.7 9.9 1.0
CA D:LEU47 4.7 10.0 1.0
C D:LEU47 4.7 10.0 1.0
CB D:TRP46 4.7 9.9 1.0
CB D:ASP49 4.9 11.3 1.0
OH E:TYR42 4.9 9.9 1.0
CD D:PRO52 5.0 11.9 1.0

Calcium binding site 6 out of 15 in 8jc8

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Calcium binding site 6 out of 15 in the Cryo-Em Structure of the LH1 Complex From Thermochromatium Tepidum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cryo-Em Structure of the LH1 Complex From Thermochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca102

b:9.8
occ:1.00
 O F:TRP46 2.4 9.8 1.0
O F:ILE51 2.5 11.7 1.0
O E:TRP45 2.5 9.8 1.0
OD1 F:ASP49 2.6 10.7 1.0
CG F:ASP49 3.4 10.7 1.0
C F:ILE51 3.5 11.7 1.0
OD2 F:ASP49 3.6 10.7 1.0
C F:TRP46 3.6 9.8 1.0
C E:TRP45 3.7 9.8 1.0
CB F:ILE51 3.9 11.7 1.0
CA F:ILE51 4.0 11.7 1.0
N F:ILE51 4.0 11.7 1.0
CA F:TRP46 4.3 9.8 1.0
O F:LEU47 4.4 9.8 1.0
CG2 F:ILE51 4.5 11.7 1.0
CA E:LEU46 4.5 9.8 1.0
N E:LEU46 4.6 9.8 1.0
N F:LEU47 4.6 9.8 1.0
N F:PRO52 4.6 11.8 1.0
CA E:TRP45 4.7 9.8 1.0
CA F:LEU47 4.7 9.8 1.0
CB F:TRP46 4.8 9.8 1.0
C F:LEU47 4.8 9.8 1.0
OH G:TYR42 4.8 9.8 1.0
CB F:ASP49 4.9 10.7 1.0
CD F:PRO52 4.9 11.8 1.0
C E:LEU46 4.9 9.8 1.0
OXT E:LEU46 5.0 9.8 1.0

Calcium binding site 7 out of 15 in 8jc8

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Calcium binding site 7 out of 15 in the Cryo-Em Structure of the LH1 Complex From Thermochromatium Tepidum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cryo-Em Structure of the LH1 Complex From Thermochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca103

b:9.8
occ:1.00
 O I:TRP46 2.4 9.8 1.0
O I:ILE51 2.5 12.0 1.0
O G:TRP45 2.6 9.8 1.0
OD1 I:ASP49 2.6 11.5 1.0
CG I:ASP49 3.5 11.5 1.0
C I:ILE51 3.5 12.0 1.0
C I:TRP46 3.6 9.8 1.0
OD2 I:ASP49 3.6 11.5 1.0
C G:TRP45 3.7 9.8 1.0
CB I:ILE51 3.9 12.0 1.0
CA I:ILE51 4.0 12.0 1.0
N I:ILE51 4.0 12.0 1.0
CA I:TRP46 4.3 9.8 1.0
O I:LEU47 4.3 9.8 1.0
CG2 I:ILE51 4.4 12.0 1.0
CA G:LEU46 4.5 9.8 1.0
N G:LEU46 4.5 9.8 1.0
N I:LEU47 4.6 9.8 1.0
N I:PRO52 4.6 12.4 1.0
CA G:TRP45 4.7 9.8 1.0
CA I:LEU47 4.7 9.8 1.0
CB I:TRP46 4.7 9.8 1.0
C I:LEU47 4.7 9.8 1.0
OH J:TYR42 4.9 9.8 1.0
CB I:ASP49 4.9 11.5 1.0
CD I:PRO52 4.9 12.4 1.0
C G:LEU46 5.0 9.8 1.0

Calcium binding site 8 out of 15 in 8jc8

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Calcium binding site 8 out of 15 in the Cryo-Em Structure of the LH1 Complex From Thermochromatium Tepidum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Cryo-Em Structure of the LH1 Complex From Thermochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca102

b:9.8
occ:1.00
 O K:TRP46 2.4 9.8 1.0
O K:ILE51 2.5 11.5 1.0
O J:TRP45 2.5 9.9 1.0
OD1 K:ASP49 2.6 11.2 1.0
CG K:ASP49 3.5 11.2 1.0
C K:ILE51 3.5 11.5 1.0
C K:TRP46 3.6 9.8 1.0
OD2 K:ASP49 3.6 11.2 1.0
C J:TRP45 3.7 9.9 1.0
CB K:ILE51 4.0 11.5 1.0
N K:ILE51 4.0 11.5 1.0
CA K:ILE51 4.0 11.5 1.0
O K:LEU47 4.2 9.8 1.0
CA K:TRP46 4.4 9.8 1.0
CG2 K:ILE51 4.5 11.5 1.0
N K:LEU47 4.6 9.8 1.0
CA J:TRP45 4.6 9.9 1.0
N J:LEU46 4.6 9.8 1.0
CA J:LEU46 4.6 9.8 1.0
C K:LEU47 4.6 9.8 1.0
CA K:LEU47 4.6 9.8 1.0
N K:PRO52 4.6 11.8 1.0
CB K:TRP46 4.8 9.8 1.0
CB K:ASP49 4.9 11.2 1.0
N K:ASP49 5.0 11.2 1.0
CD K:PRO52 5.0 11.8 1.0
OH N:TYR42 5.0 9.8 1.0
CB J:TRP45 5.0 9.9 1.0

Calcium binding site 9 out of 15 in 8jc8

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Calcium binding site 9 out of 15 in the Cryo-Em Structure of the LH1 Complex From Thermochromatium Tepidum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Cryo-Em Structure of the LH1 Complex From Thermochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca102

b:10.0
occ:1.00
 O O:TRP46 2.4 9.9 1.0
O O:ILE51 2.5 11.8 1.0
O N:TRP45 2.5 9.8 1.0
OD1 O:ASP49 2.5 11.5 1.0
CG O:ASP49 3.3 11.5 1.0
OD2 O:ASP49 3.3 11.5 1.0
C O:ILE51 3.6 11.8 1.0
C O:TRP46 3.6 9.9 1.0
C N:TRP45 3.7 9.8 1.0
N O:ILE51 4.1 11.8 1.0
CB O:ILE51 4.1 11.8 1.0
CA O:ILE51 4.1 11.8 1.0
CA O:TRP46 4.3 9.9 1.0
O O:LEU47 4.5 10.0 1.0
CA N:LEU46 4.5 9.8 1.0
N N:LEU46 4.5 9.8 1.0
N O:LEU47 4.5 10.0 1.0
CA N:TRP45 4.6 9.8 1.0
CA O:LEU47 4.6 10.0 1.0
N O:PRO52 4.6 11.6 1.0
CB O:ASP49 4.7 11.5 1.0
CB O:TRP46 4.8 9.9 1.0
C O:LEU47 4.8 10.0 1.0
CG2 O:ILE51 4.8 11.8 1.0
CD O:PRO52 4.9 11.6 1.0
N O:ASP49 5.0 11.5 1.0

Calcium binding site 10 out of 15 in 8jc8

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Calcium binding site 10 out of 15 in the Cryo-Em Structure of the LH1 Complex From Thermochromatium Tepidum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Cryo-Em Structure of the LH1 Complex From Thermochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Ca102

b:9.8
occ:1.00
 O Q:TRP46 2.4 9.8 1.0
O Q:ILE51 2.4 12.5 1.0
O P:TRP45 2.5 9.8 1.0
OD1 Q:ASP49 2.6 11.0 1.0
CG Q:ASP49 3.4 11.0 1.0
C Q:ILE51 3.5 12.5 1.0
OD2 Q:ASP49 3.5 11.0 1.0
C Q:TRP46 3.6 9.8 1.0
C P:TRP45 3.7 9.8 1.0
CB Q:ILE51 4.0 12.5 1.0
N Q:ILE51 4.0 12.5 1.0
CA Q:ILE51 4.0 12.5 1.0
CA Q:TRP46 4.3 9.8 1.0
O Q:LEU47 4.3 9.8 1.0
CA P:LEU46 4.5 9.9 1.0
N Q:LEU47 4.6 9.8 1.0
N P:LEU46 4.6 9.9 1.0
N Q:PRO52 4.6 12.9 1.0
CG2 Q:ILE51 4.6 12.5 1.0
CA P:TRP45 4.6 9.8 1.0
CA Q:LEU47 4.7 9.8 1.0
C Q:LEU47 4.7 9.8 1.0
CB Q:TRP46 4.7 9.8 1.0
CB Q:ASP49 4.8 11.0 1.0
OH R:TYR42 4.9 9.8 1.0
CD Q:PRO52 4.9 12.9 1.0
C P:LEU46 5.0 9.9 1.0

Reference:

Y.H.Yan, G.L.Wang, X.Y.Yue, F.Ma, M.T.Madigan, Z.Y.Wang-Otomo, M.J.Zou, L.J.Yu. Molecular Structure and Characterization of the Thermochromatium Tepidum Light-Harvesting 1 Photocomplex Produced in A Foreign Host. Biochim Biophys Acta V.1865 49050 2024BIOENERG.
ISSN: ISSN 1879-2650
PubMed: 38806091
DOI: 10.1016/J.BBABIO.2024.149050
Page generated: Wed Nov 27 16:34:46 2024

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