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

Go back to Calcium Binding Sites List in 7c9r
Calcium binding site 1 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 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

Go back to Calcium Binding Sites List in 7c9r
Calcium binding site 2 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 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

Go back to Calcium Binding Sites List in 7c9r
Calcium binding site 3 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 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

Go back to Calcium Binding Sites List in 7c9r
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

Go back to Calcium Binding Sites List in 7c9r
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

Go back to Calcium Binding Sites List in 7c9r
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

Go back to Calcium Binding Sites List in 7c9r
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

Go back to Calcium Binding Sites List in 7c9r
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

Go back to Calcium Binding Sites List in 7c9r
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

Go back to Calcium Binding Sites List in 7c9r
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: Sat Dec 12 08:04:38 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy