Magnesium in PDB 7c9r: Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970

The structure of Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970 also contains other interesting chemical elements:

Iron	(Fe)	5 atoms
Calcium	(Ca)	17 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 37;

Binding sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 37 binding sites of Magnesium where determined in the Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970, PDB code: 7c9r:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 37 in the Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg405 b:20.0 occ:1.00 OE1 C:GLN183 3.0 40.7 1.0 OE1 C:GLU230 3.2 0.6 1.0 CD C:GLU230 3.7 83.2 1.0 OE1 M:GLU96 3.8 93.3 1.0 OE2 C:GLU230 3.8 79.5 1.0 CD C:GLN183 3.9 41.6 1.0 OE2 M:GLU96 3.9 94.3 1.0 OD1 C:ASN184 4.1 35.8 1.0 CD M:GLU96 4.2 82.7 1.0 O C:ALA194 4.5 22.0 1.0 CG C:GLN183 4.6 32.8 1.0 O M:PRO181 4.6 14.7 1.0 NE2 C:GLN183 4.6 55.5 1.0 CB M:ASP184 4.8 24.6 1.0 CG C:GLU230 4.9 39.7 1.0 CB C:GLN183 4.9 32.2 1.0 OD2 M:ASP184 4.9 45.2 1.0 CA M:PRO181 5.0 13.3 1.0 CG M:PRO176 5.0 15.5 1.0

Magnesium binding site 2 out of 37 in the Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 L:Mg301 b:8.3 occ:1.00 MG L:BCL301 0.0 8.3 1.0 ND L:BCL301 2.0 10.5 1.0 NB L:BCL301 2.0 8.2 1.0 NA L:BCL301 2.1 12.1 1.0 NC L:BCL301 2.1 9.9 1.0 NE2 L:HIS174 2.6 9.8 1.0 C4D L:BCL301 2.9 9.6 1.0 C1A L:BCL301 3.1 9.8 1.0 C1B L:BCL301 3.1 8.3 1.0 C4A L:BCL301 3.1 14.6 1.0 C4B L:BCL301 3.1 6.6 1.0 C4C L:BCL301 3.1 9.4 1.0 C1C L:BCL301 3.1 8.7 1.0 C1D L:BCL301 3.2 10.1 1.0 CE1 L:HIS174 3.4 12.5 1.0 CHC L:BCL301 3.4 6.2 1.0 CHA L:BCL301 3.4 9.3 1.0 CHB L:BCL301 3.5 9.2 1.0 CBB M:BCL403 3.5 3.6 1.0 CHD L:BCL301 3.6 7.8 1.0 CD2 L:HIS174 3.6 11.3 1.0 CAB M:BCL403 3.8 6.3 1.0 OBB M:BCL403 3.9 7.2 1.0 C3D L:BCL301 4.1 10.7 1.0 C3B L:BCL301 4.3 6.3 1.0 C2A L:BCL301 4.3 12.1 1.0 C3A L:BCL301 4.4 14.8 1.0 C2D L:BCL301 4.4 11.6 1.0 C2B L:BCL301 4.4 7.1 1.0 C3C L:BCL301 4.4 7.9 1.0 C2C L:BCL301 4.4 6.9 1.0 C3B M:BCL403 4.6 6.3 1.0 ND1 L:HIS174 4.6 13.9 1.0 CG L:HIS174 4.7 9.8 1.0 CMA L:BCL301 4.8 14.8 1.0 CBD L:BCL301 4.9 10.4 1.0 CD2 L:PHE168 4.9 12.3 1.0 CE2 L:PHE168 4.9 10.4 1.0

Magnesium binding site 3 out of 37 in the Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 L:Mg304 b:21.4 occ:1.00 MG L:BCL304 0.0 21.4 1.0 ND L:BCL304 2.0 21.6 1.0 NC L:BCL304 2.0 20.6 1.0 NA L:BCL304 2.0 28.9 1.0 NB L:BCL304 2.1 24.9 1.0 NE2 L:HIS154 2.6 7.4 1.0 C4D L:BCL304 2.9 19.5 1.0 C4C L:BCL304 3.0 17.1 1.0 C1C L:BCL304 3.0 20.8 1.0 C1A L:BCL304 3.1 26.4 1.0 C4A L:BCL304 3.1 31.3 1.0 C1B L:BCL304 3.1 26.3 1.0 C4B L:BCL304 3.1 20.3 1.0 C1D L:BCL304 3.1 20.0 1.0 CHA L:BCL304 3.4 20.9 1.0 CHC L:BCL304 3.4 15.3 1.0 CHB L:BCL304 3.4 23.2 1.0 CD2 L:HIS154 3.5 11.8 1.0 CHD L:BCL304 3.5 16.1 1.0 CE1 L:HIS154 3.7 13.6 1.0 C3D L:BCL304 4.1 19.9 1.0 C2D L:BCL304 4.4 18.1 1.0 C3B L:BCL304 4.4 27.6 1.0 C3C L:BCL304 4.4 16.9 1.0 C2C L:BCL304 4.4 20.2 1.0 C2B L:BCL304 4.4 26.0 1.0 C3A L:BCL304 4.4 29.1 1.0 C2A L:BCL304 4.4 24.0 1.0 OBB L:BPH302 4.6 24.4 1.0 CG L:HIS154 4.7 13.7 1.0 ND1 L:HIS154 4.8 15.3 1.0 CBA L:BCL304 4.8 46.5 1.0 CBD L:BCL304 4.9 21.1 1.0 CBC L:BCL304 4.9 15.4 1.0 CE2 M:TYR210 4.9 15.1 1.0

Magnesium binding site 4 out of 37 in the Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 M:Mg402 b:17.1 occ:1.00 MG M:BCL402 0.0 17.1 1.0 ND M:BCL402 2.0 16.4 1.0 NB M:BCL402 2.0 19.5 1.0 NC M:BCL402 2.1 17.1 1.0 NA M:BCL402 2.1 21.5 1.0 C4D M:BCL402 2.9 12.4 1.0 NE2 M:HIS182 3.0 8.3 1.0 C4C M:BCL402 3.0 14.8 1.0 C1B M:BCL402 3.0 18.6 1.0 C1A M:BCL402 3.0 17.4 1.0 C1C M:BCL402 3.1 17.8 1.0 C4B M:BCL402 3.1 20.2 1.0 C4A M:BCL402 3.1 19.1 1.0 C1D M:BCL402 3.2 11.1 1.0 CHA M:BCL402 3.4 12.9 1.0 CHB M:BCL402 3.4 18.2 1.0 CHC M:BCL402 3.4 16.7 1.0 CHD M:BCL402 3.5 10.4 1.0 CD2 M:HIS182 3.6 11.1 1.0 C3D M:BCL402 4.1 10.2 1.0 CE1 M:HIS182 4.2 16.3 1.0 C3B M:BCL402 4.3 24.2 1.0 C3C M:BCL402 4.3 18.2 1.0 C2A M:BCL402 4.3 19.0 1.0 C2B M:BCL402 4.3 22.4 1.0 C2D M:BCL402 4.4 8.6 1.0 C2C M:BCL402 4.4 17.7 1.0 C3A M:BCL402 4.4 16.4 1.0 CE2 L:PHE182 4.4 19.4 1.0 CBD M:BCL402 4.8 13.0 1.0 CAA M:BCL402 4.9 31.8 1.0 CG M:HIS182 4.9 16.5 1.0 CD2 L:PHE182 4.9 16.4 1.0

Magnesium binding site 5 out of 37 in the Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 M:Mg403 b:8.4 occ:1.00 MG M:BCL403 0.0 8.4 1.0 ND M:BCL403 2.0 10.7 1.0 NB M:BCL403 2.0 6.8 1.0 NC M:BCL403 2.0 7.4 1.0 NA M:BCL403 2.1 10.8 1.0 NE2 M:HIS202 2.6 12.1 1.0 C4D M:BCL403 2.9 11.0 1.0 C4B M:BCL403 3.0 6.6 1.0 C1A M:BCL403 3.0 10.4 1.0 C1C M:BCL403 3.0 8.5 1.0 C1B M:BCL403 3.1 5.1 1.0 C4C M:BCL403 3.1 6.1 1.0 C4A M:BCL403 3.1 11.1 1.0 C1D M:BCL403 3.2 10.2 1.0 CHA M:BCL403 3.4 11.2 1.0 CHC M:BCL403 3.4 7.3 1.0 CHB M:BCL403 3.4 6.2 1.0 CD2 M:HIS202 3.5 14.6 1.0 CBB L:BCL301 3.5 4.2 1.0 CHD M:BCL403 3.6 6.7 1.0 CE1 M:HIS202 3.6 16.2 1.0 CAB L:BCL301 3.8 7.2 1.0 OBB L:BCL301 4.0 8.9 1.0 C3D M:BCL403 4.1 11.2 1.0 C3B M:BCL403 4.3 6.3 1.0 C2D M:BCL403 4.3 10.1 1.0 C2A M:BCL403 4.4 12.0 1.0 C2B M:BCL403 4.4 5.2 1.0 C3C M:BCL403 4.4 5.4 1.0 C2C M:BCL403 4.4 4.8 1.0 C3A M:BCL403 4.4 11.9 1.0 C3B L:BCL301 4.5 6.3 1.0 CG M:HIS202 4.7 15.5 1.0 ND1 M:HIS202 4.7 18.6 1.0 CBD M:BCL403 4.8 12.5 1.0

Magnesium binding site 6 out of 37 in the Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 A:Mg102 b:27.8 occ:1.00 MG A:BCL102 0.0 27.8 1.0 ND A:BCL102 2.0 29.1 1.0 NB A:BCL102 2.0 22.8 1.0 NA A:BCL102 2.0 28.2 1.0 NC A:BCL102 2.1 29.7 1.0 NE2 A:HIS37 2.9 15.0 1.0 C4D A:BCL102 2.9 29.2 1.0 C1B A:BCL102 3.0 22.9 1.0 C4A A:BCL102 3.0 26.3 1.0 C1A A:BCL102 3.1 26.8 1.0 C4B A:BCL102 3.1 17.8 1.0 C4C A:BCL102 3.1 23.1 1.0 C1C A:BCL102 3.1 27.3 1.0 C10 B:LMT104 3.1 14.7 1.0 C1D A:BCL102 3.1 24.9 1.0 C11 B:LMT104 3.3 15.5 1.0 CHB A:BCL102 3.3 22.0 1.0 CHC A:BCL102 3.4 22.9 1.0 CHA A:BCL102 3.4 26.5 1.0 CHD A:BCL102 3.5 23.6 1.0 CE1 A:HIS37 3.6 15.3 1.0 CD2 A:HIS37 4.1 17.4 1.0 C3D A:BCL102 4.1 24.4 1.0 C3B A:BCL102 4.3 16.9 1.0 C2B A:BCL102 4.3 18.6 1.0 C2D A:BCL102 4.3 23.1 1.0 C3A A:BCL102 4.4 23.2 1.0 C3C A:BCL102 4.4 22.6 1.0 C2A A:BCL102 4.4 22.5 1.0 C2C A:BCL102 4.4 19.8 1.0 CMB 9:BCL104 4.5 26.8 1.0 CMD B:BCL103 4.6 16.5 1.0 C9 B:LMT104 4.6 19.6 1.0 CBB 9:BCL104 4.8 21.6 1.0 ND1 A:HIS37 4.9 14.9 1.0 C12 B:LMT104 4.9 26.7 1.0 CBD A:BCL102 4.9 24.4 1.0

Magnesium binding site 7 out of 37 in the Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 B:Mg103 b:20.1 occ:1.00 MG B:BCL103 0.0 20.1 1.0 ND B:BCL103 2.0 19.5 1.0 NB B:BCL103 2.1 23.8 1.0 NA B:BCL103 2.1 28.6 1.0 NC B:BCL103 2.1 22.7 1.0 NE2 B:HIS36 2.5 10.4 1.0 C4D B:BCL103 2.9 18.4 1.0 C1C B:BCL103 3.0 21.4 1.0 C4C B:BCL103 3.1 16.6 1.0 C4A B:BCL103 3.1 32.5 1.0 C1A B:BCL103 3.1 25.1 1.0 C1B B:BCL103 3.1 22.1 1.0 C4B B:BCL103 3.1 21.8 1.0 C1D B:BCL103 3.1 20.0 1.0 CHC B:BCL103 3.4 21.1 1.0 CHB B:BCL103 3.4 24.3 1.0 CHA B:BCL103 3.5 21.3 1.0 CE1 B:HIS36 3.5 12.6 1.0 CD2 B:HIS36 3.5 15.9 1.0 CHD B:BCL103 3.6 16.1 1.0 C3D B:BCL103 4.1 19.0 1.0 CBB D:BCL103 4.3 15.4 1.0 C2D B:BCL103 4.3 18.3 1.0 C3C B:BCL103 4.3 16.8 1.0 C2C B:BCL103 4.4 19.1 1.0 CMD A:BCL102 4.4 24.9 1.0 CMB D:BCL103 4.4 20.2 1.0 C3B B:BCL103 4.4 21.1 1.0 C3A B:BCL103 4.4 30.9 1.0 C2A B:BCL103 4.4 27.3 1.0 C2B B:BCL103 4.4 17.8 1.0 ND1 B:HIS36 4.6 16.0 1.0 CG B:HIS36 4.6 16.0 1.0 CBD B:BCL103 4.9 20.2 1.0 CG2 A:ILE36 5.0 9.3 1.0 CAB D:BCL103 5.0 22.9 1.0

Magnesium binding site 8 out of 37 in the Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 D:Mg103 b:31.7 occ:1.00 MG D:BCL103 0.0 31.7 1.0 ND D:BCL103 2.0 35.7 1.0 NB D:BCL103 2.0 23.4 1.0 NC D:BCL103 2.1 30.5 1.0 NA D:BCL103 2.1 35.1 1.0 C4D D:BCL103 2.9 32.6 1.0 C10 E:LMT102 3.0 17.8 1.0 C4C D:BCL103 3.0 24.9 1.0 C1B D:BCL103 3.0 21.4 1.0 C1C D:BCL103 3.1 26.2 1.0 C4B D:BCL103 3.1 20.2 1.0 NE2 D:HIS37 3.1 10.3 1.0 C1A D:BCL103 3.1 28.5 1.0 C4A D:BCL103 3.1 29.6 1.0 C1D D:BCL103 3.1 31.9 1.0 CHC D:BCL103 3.4 21.9 1.0 CHB D:BCL103 3.4 21.2 1.0 CHA D:BCL103 3.4 32.4 1.0 C11 E:LMT102 3.5 26.7 1.0 CHD D:BCL103 3.5 28.8 1.0 CD2 D:HIS37 4.0 13.1 1.0 CE1 D:HIS37 4.0 20.5 1.0 C3D D:BCL103 4.1 26.4 1.0 C3B D:BCL103 4.3 21.5 1.0 C3C D:BCL103 4.3 19.9 1.0 C2B D:BCL103 4.3 22.4 1.0 CMB B:BCL103 4.3 18.8 1.0 C2D D:BCL103 4.3 23.3 1.0 C9 E:LMT102 4.4 28.7 1.0 C2C D:BCL103 4.4 19.0 1.0 C2A D:BCL103 4.4 24.0 1.0 C3A D:BCL103 4.5 20.0 1.0 CBB B:BCL103 4.7 20.6 1.0 CMD D:BCL104 4.8 26.7 1.0 CBD D:BCL103 4.9 29.3 1.0 C8 E:LMT102 4.9 32.0 1.0

Magnesium binding site 9 out of 37 in the Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 D:Mg104 b:22.5 occ:1.00 MG D:BCL104 0.0 22.5 1.0 ND D:BCL104 2.0 22.7 1.0 NC D:BCL104 2.0 25.0 1.0 NB D:BCL104 2.1 24.4 1.0 NA D:BCL104 2.1 33.0 1.0 NE2 E:HIS36 2.5 7.1 1.0 C4D D:BCL104 2.9 20.2 1.0 C1C D:BCL104 3.0 24.9 1.0 C4C D:BCL104 3.1 19.1 1.0 C1A D:BCL104 3.1 32.7 1.0 C1B D:BCL104 3.1 24.3 1.0 C4B D:BCL104 3.1 22.5 1.0 C4A D:BCL104 3.1 31.0 1.0 C1D D:BCL104 3.1 23.7 1.0 CHC D:BCL104 3.4 23.2 1.0 CHB D:BCL104 3.4 23.1 1.0 CHA D:BCL104 3.4 24.6 1.0 CE1 E:HIS36 3.5 15.8 1.0 CD2 E:HIS36 3.5 12.6 1.0 CHD D:BCL104 3.5 19.8 1.0 C3D D:BCL104 4.1 22.9 1.0 C2D D:BCL104 4.3 24.6 1.0 C2C D:BCL104 4.3 20.7 1.0 C3C D:BCL104 4.4 16.7 1.0 C3B D:BCL104 4.4 21.7 1.0 CMD D:BCL103 4.4 20.9 1.0 CMB F:BCL103 4.4 20.6 1.0 C2B D:BCL104 4.4 23.0 1.0 C2A D:BCL104 4.4 29.6 1.0 C3A D:BCL104 4.4 30.4 1.0 CBB F:BCL103 4.5 13.6 1.0 ND1 E:HIS36 4.6 17.6 1.0 CG E:HIS36 4.6 16.8 1.0 CG2 D:ILE36 4.8 7.2 1.0 CBD D:BCL104 4.9 24.9 1.0

Magnesium binding site 10 out of 37 in the Structure of Photosynthetic LH1-Rc Super-Complex of Thiorhodovibrio Strain 970


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 F:Mg103 b:31.6 occ:1.00 MG F:BCL103 0.0 31.6 1.0 NB F:BCL103 2.0 28.0 1.0 NA F:BCL103 2.1 32.0 1.0 ND F:BCL103 2.1 36.5 1.0 NC F:BCL103 2.1 31.8 1.0 C4D F:BCL103 2.9 29.8 1.0 NE2 F:HIS37 3.0 10.2 1.0 C1B F:BCL103 3.0 23.8 1.0 C4C F:BCL103 3.0 26.2 1.0 C1A F:BCL103 3.0 32.0 1.0 C1C F:BCL103 3.1 29.2 1.0 C4A F:BCL103 3.1 25.8 1.0 C4B F:BCL103 3.1 23.1 1.0 C10 G:LMT102 3.1 14.4 1.0 C1D F:BCL103 3.2 29.3 1.0 CHB F:BCL103 3.4 23.8 1.0 C11 G:LMT102 3.4 16.0 1.0 CHA F:BCL103 3.4 33.4 1.0 CHC F:BCL103 3.4 21.8 1.0 CHD F:BCL103 3.5 24.5 1.0 CE1 F:HIS37 3.7 11.1 1.0 CD2 F:HIS37 4.1 16.2 1.0 C3D F:BCL103 4.2 27.2 1.0 C3B F:BCL103 4.3 18.7 1.0 C2B F:BCL103 4.4 19.6 1.0 C3C F:BCL103 4.4 25.2 1.0 CMB D:BCL104 4.4 19.1 1.0 C2D F:BCL103 4.4 23.7 1.0 C2C F:BCL103 4.4 24.0 1.0 C2A F:BCL103 4.4 23.7 1.0 C3A F:BCL103 4.4 19.1 1.0 C9 G:LMT102 4.5 22.1 1.0 CBB D:BCL104 4.7 23.9 1.0 CMD F:BCL105 4.7 20.9 1.0 ND1 F:HIS37 4.9 13.2 1.0 C12 G:LMT102 4.9 33.8 1.0 CBD F:BCL103 4.9 32.1 1.0

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