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Calcium in PDB 8ypb: Cryo-Em Structure of the LH1 Complex From Allochromatium Tepidum

Other elements in 8ypb:

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

Magnesium (Mg) 28 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Calcium atom in the Cryo-Em Structure of the LH1 Complex From Allochromatium Tepidum (pdb code 8ypb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 14 binding sites of Calcium where determined in the Cryo-Em Structure of the LH1 Complex From Allochromatium Tepidum, PDB code: 8ypb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 14 in 8ypb

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Calcium binding site 1 out of 14 in the Cryo-Em Structure of the LH1 Complex From Allochromatium 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 Allochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca102

b:3.8
occ:1.00
 OD1 F:ASP47 1.9 5.1 1.0
O F:ILE49 2.0 5.0 1.0
O F:TRP44 2.1 4.0 1.0
O C:TRP46 2.2 4.1 1.0
CG F:ASP47 2.8 5.1 1.0
OD2 F:ASP47 2.9 5.1 1.0
C F:ILE49 3.2 5.0 1.0
C F:TRP44 3.3 4.0 1.0
C C:TRP46 3.3 4.1 1.0
N F:ILE49 3.9 5.0 1.0
CA F:TRP44 3.9 4.0 1.0
CA F:ILE49 4.0 5.0 1.0
CA C:TRP46 4.1 4.1 1.0
CB F:ASP47 4.2 5.1 1.0
N F:PRO50 4.2 5.3 1.0
N F:LEU45 4.3 4.4 1.0
N C:LEU47 4.3 4.3 1.0
CB F:TRP44 4.4 4.0 1.0
CD F:PRO50 4.4 5.3 1.0
CB F:ILE49 4.5 5.0 1.0
CA C:LEU47 4.5 4.3 1.0
CA F:LEU45 4.5 4.4 1.0
N F:ASP47 4.5 5.1 1.0
CB C:TRP46 4.6 4.1 1.0
C F:LEU45 4.7 4.4 1.0
N F:GLY48 4.8 5.3 1.0
CA F:ASP47 4.8 5.1 1.0
O F:LEU45 4.9 4.4 1.0
CD2 C:LEU47 5.0 4.3 1.0

Calcium binding site 2 out of 14 in 8ypb

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Calcium binding site 2 out of 14 in the Cryo-Em Structure of the LH1 Complex From Allochromatium 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 Allochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca102

b:3.8
occ:1.00
 OD1 B:ASP47 2.0 5.1 1.0
O B:ILE49 2.0 5.0 1.0
O B:TRP44 2.1 4.4 1.0
O N:TRP46 2.2 3.9 1.0
CG B:ASP47 2.7 5.1 1.0
OD2 B:ASP47 2.8 5.1 1.0
C B:ILE49 3.3 5.0 1.0
C B:TRP44 3.3 4.4 1.0
C N:TRP46 3.3 3.9 1.0
N B:ILE49 3.9 5.0 1.0
CA B:TRP44 3.9 4.4 1.0
CA B:ILE49 4.1 5.0 1.0
CA N:TRP46 4.1 3.9 1.0
CB B:ASP47 4.1 5.1 1.0
N B:PRO50 4.2 5.2 1.0
N N:LEU47 4.3 4.2 1.0
N B:LEU45 4.3 4.5 1.0
CB B:TRP44 4.4 4.4 1.0
CA N:LEU47 4.4 4.2 1.0
CD B:PRO50 4.5 5.2 1.0
CB B:ILE49 4.5 5.0 1.0
CB N:TRP46 4.6 3.9 1.0
CA B:LEU45 4.6 4.5 1.0
N B:ASP47 4.6 5.1 1.0
C B:LEU45 4.7 4.5 1.0
O B:LEU45 4.7 4.5 1.0
N B:GLY48 4.8 5.2 1.0
CA B:ASP47 4.8 5.1 1.0
CD2 N:LEU47 4.9 4.2 1.0

Calcium binding site 3 out of 14 in 8ypb

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Calcium binding site 3 out of 14 in the Cryo-Em Structure of the LH1 Complex From Allochromatium 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 Allochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca102

b:4.0
occ:1.00
 O D:ILE49 1.9 5.3 1.0
O D:TRP44 2.1 4.4 1.0
OD1 D:ASP47 2.2 5.5 1.0
O E:TRP46 2.2 4.2 1.0
CG D:ASP47 3.0 5.5 1.0
OD2 D:ASP47 3.2 5.5 1.0
C D:ILE49 3.2 5.3 1.0
C D:TRP44 3.3 4.4 1.0
C E:TRP46 3.3 4.2 1.0
N D:ILE49 3.8 5.3 1.0
CA D:ILE49 3.9 5.3 1.0
CA D:TRP44 4.0 4.4 1.0
CA E:TRP46 4.1 4.2 1.0
N D:PRO50 4.2 5.8 1.0
N E:LEU47 4.3 4.6 1.0
N D:LEU45 4.3 4.6 1.0
CB D:ASP47 4.4 5.5 1.0
CA E:LEU47 4.5 4.6 1.0
CB D:ILE49 4.5 5.3 1.0
CB D:TRP44 4.5 4.4 1.0
CD D:PRO50 4.5 5.8 1.0
CA D:LEU45 4.5 4.6 1.0
CB E:TRP46 4.6 4.2 1.0
N D:ASP47 4.6 5.5 1.0
C D:LEU45 4.6 4.6 1.0
O D:LEU45 4.7 4.6 1.0
N D:GLY48 4.7 5.7 1.0
C D:GLY48 4.9 5.7 1.0
CA D:ASP47 5.0 5.5 1.0

Calcium binding site 4 out of 14 in 8ypb

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Calcium binding site 4 out of 14 in the Cryo-Em Structure of the LH1 Complex From Allochromatium 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 Allochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca102

b:3.4
occ:1.00
 O G:ILE49 2.0 5.0 1.0
OD1 G:ASP47 2.1 5.3 1.0
O G:TRP44 2.1 4.6 1.0
O H:TRP46 2.2 4.3 1.0
CG G:ASP47 2.8 5.3 1.0
OD2 G:ASP47 2.9 5.3 1.0
C G:ILE49 3.2 5.0 1.0
C G:TRP44 3.2 4.6 1.0
C H:TRP46 3.3 4.3 1.0
N G:ILE49 3.9 5.0 1.0
CA G:TRP44 3.9 4.6 1.0
CA G:ILE49 4.0 5.0 1.0
CA H:TRP46 4.1 4.3 1.0
N G:PRO50 4.2 5.2 1.0
CB G:ASP47 4.2 5.3 1.0
N H:LEU47 4.3 4.6 1.0
N G:LEU45 4.3 4.5 1.0
CB G:TRP44 4.4 4.6 1.0
CA H:LEU47 4.4 4.6 1.0
CB G:ILE49 4.5 5.0 1.0
CD G:PRO50 4.5 5.2 1.0
CA G:LEU45 4.6 4.5 1.0
CB H:TRP46 4.6 4.3 1.0
N G:ASP47 4.7 5.3 1.0
C G:LEU45 4.7 4.5 1.0
N G:GLY48 4.7 5.4 1.0
O G:LEU45 4.7 4.5 1.0
CA G:ASP47 4.9 5.3 1.0
CD2 H:LEU47 5.0 4.6 1.0

Calcium binding site 5 out of 14 in 8ypb

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Calcium binding site 5 out of 14 in the Cryo-Em Structure of the LH1 Complex From Allochromatium 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 Allochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca102

b:4.6
occ:1.00
 OD1 I:ASP47 1.8 5.3 1.0
O I:ILE49 2.0 5.1 1.0
O I:TRP44 2.1 4.4 1.0
O J:TRP46 2.2 4.2 1.0
CG I:ASP47 2.6 5.3 1.0
OD2 I:ASP47 2.8 5.3 1.0
C I:ILE49 3.1 5.1 1.0
C I:TRP44 3.3 4.4 1.0
C J:TRP46 3.3 4.2 1.0
N I:ILE49 3.9 5.1 1.0
CA I:TRP44 3.9 4.4 1.0
CA I:ILE49 4.0 5.1 1.0
CB I:ASP47 4.0 5.3 1.0
CA J:TRP46 4.1 4.2 1.0
N I:PRO50 4.1 5.3 1.0
N I:LEU45 4.2 4.5 1.0
N J:LEU47 4.3 4.5 1.0
CD I:PRO50 4.4 5.3 1.0
CB I:TRP44 4.4 4.4 1.0
CA J:LEU47 4.5 4.5 1.0
CB I:ILE49 4.5 5.1 1.0
CA I:LEU45 4.5 4.5 1.0
N I:ASP47 4.6 5.3 1.0
CB J:TRP46 4.6 4.2 1.0
O I:LEU45 4.6 4.5 1.0
C I:LEU45 4.7 4.5 1.0
N I:GLY48 4.7 5.6 1.0
CA I:ASP47 4.7 5.3 1.0

Calcium binding site 6 out of 14 in 8ypb

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Calcium binding site 6 out of 14 in the Cryo-Em Structure of the LH1 Complex From Allochromatium 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 Allochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca102

b:3.8
occ:1.00
 O K:ILE49 2.0 4.3 1.0
OD1 K:ASP47 2.0 4.7 1.0
O K:TRP44 2.1 4.2 1.0
O L:TRP46 2.2 3.9 1.0
CG K:ASP47 2.7 4.7 1.0
OD2 K:ASP47 2.9 4.7 1.0
C K:ILE49 3.2 4.3 1.0
C K:TRP44 3.2 4.2 1.0
C L:TRP46 3.3 3.9 1.0
CA K:TRP44 3.8 4.2 1.0
N K:ILE49 3.9 4.3 1.0
CA K:ILE49 4.0 4.3 1.0
N K:PRO50 4.2 4.5 1.0
CA L:TRP46 4.2 3.9 1.0
CB K:ASP47 4.2 4.7 1.0
N L:LEU47 4.2 4.0 1.0
CB K:TRP44 4.3 4.2 1.0
N K:LEU45 4.3 4.3 1.0
CA L:LEU47 4.4 4.0 1.0
CD K:PRO50 4.4 4.5 1.0
CB K:ILE49 4.5 4.3 1.0
CA K:LEU45 4.6 4.3 1.0
N K:ASP47 4.7 4.7 1.0
CB L:TRP46 4.7 3.9 1.0
C K:LEU45 4.8 4.3 1.0
N K:GLY48 4.8 4.5 1.0
CA K:ASP47 4.9 4.7 1.0
CD2 L:LEU47 4.9 4.0 1.0
O K:LEU45 5.0 4.3 1.0

Calcium binding site 7 out of 14 in 8ypb

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Calcium binding site 7 out of 14 in the Cryo-Em Structure of the LH1 Complex From Allochromatium 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 Allochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca103

b:4.0
occ:1.00
 O M:ILE49 2.0 5.1 1.0
O M:TRP44 2.2 4.3 1.0
O A:TRP46 2.2 4.2 1.0
OD1 M:ASP47 2.2 5.2 1.0
CG M:ASP47 2.9 5.2 1.0
OD2 M:ASP47 2.9 5.2 1.0
C M:ILE49 3.2 5.1 1.0
C M:TRP44 3.2 4.3 1.0
C A:TRP46 3.3 4.2 1.0
CA M:TRP44 3.8 4.3 1.0
N M:ILE49 3.9 5.1 1.0
CA M:ILE49 4.0 5.1 1.0
CA A:TRP46 4.2 4.2 1.0
N M:PRO50 4.3 5.5 1.0
N A:LEU47 4.3 4.4 1.0
CB M:TRP44 4.3 4.3 1.0
N M:LEU45 4.3 4.5 1.0
CB M:ASP47 4.3 5.2 1.0
CA A:LEU47 4.4 4.4 1.0
CB M:ILE49 4.5 5.1 1.0
CD M:PRO50 4.6 5.5 1.0
CB A:TRP46 4.7 4.2 1.0
CA M:LEU45 4.7 4.5 1.0
N M:ASP47 4.7 5.2 1.0
N M:GLY48 4.8 5.2 1.0
C M:LEU45 4.8 4.5 1.0
CD2 A:LEU47 4.9 4.4 1.0
CA M:ASP47 4.9 5.2 1.0
O M:LEU45 5.0 4.5 1.0

Calcium binding site 8 out of 14 in 8ypb

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Calcium binding site 8 out of 14 in the Cryo-Em Structure of the LH1 Complex From Allochromatium 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 Allochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca102

b:3.4
occ:1.00
 O O:ILE49 2.0 4.8 1.0
O O:TRP44 2.1 4.3 1.0
O P:TRP46 2.2 4.2 1.0
OD1 O:ASP47 2.2 5.1 1.0
CG O:ASP47 3.0 5.1 1.0
OD2 O:ASP47 3.1 5.1 1.0
C O:ILE49 3.1 4.8 1.0
C O:TRP44 3.3 4.3 1.0
C P:TRP46 3.3 4.2 1.0
N O:ILE49 3.9 4.8 1.0
CA O:ILE49 3.9 4.8 1.0
CA O:TRP44 3.9 4.3 1.0
CA P:TRP46 4.1 4.2 1.0
N O:PRO50 4.2 5.2 1.0
N O:LEU45 4.3 4.5 1.0
N P:LEU47 4.3 4.3 1.0
CB O:ASP47 4.4 5.1 1.0
CB O:TRP44 4.4 4.3 1.0
CB O:ILE49 4.4 4.8 1.0
CA P:LEU47 4.5 4.3 1.0
CD O:PRO50 4.5 5.2 1.0
CA O:LEU45 4.5 4.5 1.0
CB P:TRP46 4.6 4.2 1.0
N O:ASP47 4.6 5.1 1.0
C O:LEU45 4.7 4.5 1.0
N O:GLY48 4.8 5.2 1.0
O O:LEU45 4.9 4.5 1.0
CA O:ASP47 4.9 5.1 1.0
CD2 P:LEU47 5.0 4.3 1.0

Calcium binding site 9 out of 14 in 8ypb

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Calcium binding site 9 out of 14 in the Cryo-Em Structure of the LH1 Complex From Allochromatium 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 Allochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Ca102

b:3.9
occ:1.00
 O Q:ILE49 2.0 5.1 1.0
O Q:TRP44 2.1 4.4 1.0
OD1 Q:ASP47 2.2 5.4 1.0
O R:TRP46 2.2 4.1 1.0
CG Q:ASP47 3.0 5.4 1.0
OD2 Q:ASP47 3.1 5.4 1.0
C Q:ILE49 3.2 5.1 1.0
C Q:TRP44 3.3 4.4 1.0
C R:TRP46 3.3 4.1 1.0
N Q:ILE49 3.8 5.1 1.0
CA Q:ILE49 4.0 5.1 1.0
CA Q:TRP44 4.0 4.4 1.0
CA R:TRP46 4.1 4.1 1.0
N Q:PRO50 4.2 5.2 1.0
N Q:LEU45 4.3 4.5 1.0
N R:LEU47 4.3 4.2 1.0
CB Q:ASP47 4.4 5.4 1.0
CA R:LEU47 4.5 4.2 1.0
CB Q:TRP44 4.5 4.4 1.0
CB Q:ILE49 4.5 5.1 1.0
CD Q:PRO50 4.5 5.2 1.0
CA Q:LEU45 4.5 4.5 1.0
N Q:GLY48 4.6 5.5 1.0
N Q:ASP47 4.6 5.4 1.0
CB R:TRP46 4.6 4.1 1.0
C Q:LEU45 4.7 4.5 1.0
O Q:LEU45 4.7 4.5 1.0
CA Q:ASP47 4.9 5.4 1.0
C Q:GLY48 4.9 5.5 1.0

Calcium binding site 10 out of 14 in 8ypb

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Calcium binding site 10 out of 14 in the Cryo-Em Structure of the LH1 Complex From Allochromatium 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 Allochromatium Tepidum within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Ca102

b:3.4
occ:1.00
 O S:ILE49 2.0 4.9 1.0
OD1 S:ASP47 2.0 5.0 1.0
O S:TRP44 2.1 4.5 1.0
O T:TRP46 2.2 4.4 1.0
CG S:ASP47 2.8 5.0 1.0
OD2 S:ASP47 2.9 5.0 1.0
C S:ILE49 3.2 4.9 1.0
C S:TRP44 3.2 4.5 1.0
C T:TRP46 3.3 4.4 1.0
N S:ILE49 3.9 4.9 1.0
CA S:TRP44 3.9 4.5 1.0
CA S:ILE49 3.9 4.9 1.0
CA T:TRP46 4.1 4.4 1.0
N S:PRO50 4.2 5.2 1.0
CB S:ASP47 4.2 5.0 1.0
N T:LEU47 4.3 4.7 1.0
N S:LEU45 4.3 4.4 1.0
CB S:TRP44 4.4 4.5 1.0
CB S:ILE49 4.4 4.9 1.0
CA T:LEU47 4.4 4.7 1.0
CD S:PRO50 4.5 5.2 1.0
CA S:LEU45 4.6 4.4 1.0
CB T:TRP46 4.6 4.4 1.0
N S:ASP47 4.7 5.0 1.0
C S:LEU45 4.7 4.4 1.0
N S:GLY48 4.7 5.2 1.0
O S:LEU45 4.8 4.4 1.0
CA S:ASP47 4.8 5.0 1.0
CD2 T:LEU47 5.0 4.7 1.0

Reference:

M.J.Zou, S.Sun, G.L.Wang, Y.H.Yan, W.Ji, Z.Y.Wang-Otomo, M.T.Madigan, L.J.Yu. Probing the Dual Role of Ca 2+ in the Allochromatium Tepidum LH1-Rc Complex By Constructing and Analyzing Ca 2+ -Bound and Ca 2+ -Free LH1 Complexes. Biomolecules V. 15 2025.
ISSN: ESSN 2218-273X
PubMed: 39858518
DOI: 10.3390/BIOM15010124
Page generated: Thu Jul 10 08:33:18 2025

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