Magnesium in PDB 7oy8: Cryo-Em Structure of the Rhodospirillum Rubrum Rc-LH1 Complex

The structure of Cryo-Em Structure of the Rhodospirillum Rubrum Rc-LH1 Complex also contains other interesting chemical elements:

Iron	(Fe)	1 atom
Chlorine	(Cl)	1 atom

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 Cryo-Em Structure of the Rhodospirillum Rubrum Rc-LH1 Complex (pdb code 7oy8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 37 binding sites of Magnesium where determined in the Cryo-Em Structure of the Rhodospirillum Rubrum Rc-LH1 Complex, PDB code: 7oy8:
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 Cryo-Em Structure of the Rhodospirillum Rubrum Rc-LH1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of the Rhodospirillum Rubrum Rc-LH1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg1001 b:8.0 occ:1.00 MG 1:07D1001 0.0 8.0 1.0 NE2 1:HIS39 1.9 4.8 1.0 NB 1:07D1001 2.1 6.5 1.0 ND 1:07D1001 2.1 5.1 1.0 NA 1:07D1001 2.2 8.2 1.0 NC 1:07D1001 2.2 6.3 1.0 CE1 1:HIS39 2.8 5.4 1.0 C4D 1:07D1001 3.0 5.7 1.0 CD2 1:HIS39 3.0 5.9 1.0 C1B 1:07D1001 3.0 7.2 1.0 C4B 1:07D1001 3.0 5.5 1.0 C1C 1:07D1001 3.0 4.5 1.0 C4A 1:07D1001 3.1 7.4 1.0 C1A 1:07D1001 3.1 8.7 1.0 C1D 1:07D1001 3.2 3.5 1.0 C4C 1:07D1001 3.3 6.3 1.0 CHC 1:07D1001 3.3 5.5 1.0 CHB 1:07D1001 3.4 8.2 1.0 CHA 1:07D1001 3.4 6.8 1.0 CHD 1:07D1001 3.6 4.4 1.0 ND1 1:HIS39 4.0 7.4 1.0 CG 1:HIS39 4.1 6.9 1.0 C3D 1:07D1001 4.1 5.0 1.0 CBB X:07D1001 4.2 9.9 1.0 CMB X:07D1001 4.2 9.2 1.0 C2B 1:07D1001 4.2 6.2 1.0 C2D 1:07D1001 4.3 4.5 1.0 C3B 1:07D1001 4.3 4.8 1.0 C3A 1:07D1001 4.4 9.7 1.0 C2C 1:07D1001 4.4 4.3 1.0 C2A 1:07D1001 4.4 10.2 1.0 C3C 1:07D1001 4.5 5.3 1.0 CAB X:07D1001 4.7 9.3 1.0 C2B X:07D1001 4.9 9.3 1.0 CBD 1:07D1001 4.9 4.8 1.0

Magnesium binding site 2 out of 37 in the Cryo-Em Structure of the Rhodospirillum Rubrum Rc-LH1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of the Rhodospirillum Rubrum Rc-LH1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1001 b:7.9 occ:1.00 MG 2:07D1001 0.0 7.9 1.0 NE2 2:HIS29 1.9 6.0 1.0 NB 2:07D1001 2.1 6.9 1.0 ND 2:07D1001 2.1 6.8 1.0 NA 2:07D1001 2.2 7.8 1.0 NC 2:07D1001 2.2 6.4 1.0 CE1 2:HIS29 2.8 6.6 1.0 C4D 2:07D1001 3.0 6.5 1.0 CD2 2:HIS29 3.0 6.0 1.0 C1B 2:07D1001 3.0 6.6 1.0 C4B 2:07D1001 3.0 5.7 1.0 C1C 2:07D1001 3.0 6.8 1.0 C4A 2:07D1001 3.1 7.1 1.0 C1A 2:07D1001 3.1 8.4 1.0 C1D 2:07D1001 3.2 6.4 1.0 C4C 2:07D1001 3.3 6.5 1.0 CHC 2:07D1001 3.3 6.5 1.0 CHB 2:07D1001 3.4 6.8 1.0 CHA 2:07D1001 3.4 7.9 1.0 CHD 2:07D1001 3.6 6.7 1.0 ND1 2:HIS29 4.0 6.9 1.0 CG 2:HIS29 4.1 7.0 1.0 C3D 2:07D1001 4.1 6.2 1.0 C2B 2:07D1001 4.2 6.0 1.0 CBB 5:07D102 4.2 7.2 1.0 C3B 2:07D1001 4.3 5.8 1.0 C2D 2:07D1001 4.3 6.0 1.0 CMD 3:07D102 4.4 8.4 1.0 C2C 2:07D1001 4.4 6.6 1.0 C3A 2:07D1001 4.4 9.2 1.0 C2A 2:07D1001 4.5 9.8 1.0 C3C 2:07D1001 4.5 6.4 1.0 CBD 2:07D1001 4.9 7.7 1.0 CMB 5:07D102 4.9 10.7 1.0

Magnesium binding site 3 out of 37 in the Cryo-Em Structure of the Rhodospirillum Rubrum Rc-LH1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of the Rhodospirillum Rubrum Rc-LH1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ 3:Mg102 b:12.6 occ:1.00 MG 3:07D102 0.0 12.6 1.0 NE2 3:HIS39 1.9 8.6 1.0 NB 3:07D102 2.1 9.9 1.0 ND 3:07D102 2.1 8.3 1.0 NA 3:07D102 2.2 10.6 1.0 NC 3:07D102 2.2 9.2 1.0 CE1 3:HIS39 2.8 8.3 1.0 C4D 3:07D102 3.0 8.4 1.0 CD2 3:HIS39 3.0 9.6 1.0 C1B 3:07D102 3.0 10.8 1.0 C4B 3:07D102 3.0 10.0 1.0 C1C 3:07D102 3.0 8.7 1.0 C4A 3:07D102 3.1 11.9 1.0 C1A 3:07D102 3.1 10.7 1.0 C1D 3:07D102 3.2 7.8 1.0 C4C 3:07D102 3.3 8.4 1.0 CHC 3:07D102 3.3 9.5 1.0 CHB 3:07D102 3.4 12.1 1.0 CHA 3:07D102 3.4 9.9 1.0 CHD 3:07D102 3.6 8.0 1.0 ND1 3:HIS39 4.0 8.8 1.0 CG 3:HIS39 4.1 9.3 1.0 CMB Z:07D1001 4.1 10.9 1.0 C3D 3:07D102 4.1 7.9 1.0 CBB Z:07D1001 4.2 9.7 1.0 C2B 3:07D102 4.2 11.7 1.0 C2D 3:07D102 4.3 8.3 1.0 C3B 3:07D102 4.3 10.9 1.0 C3A 3:07D102 4.4 13.7 1.0 C2C 3:07D102 4.4 8.8 1.0 C2A 3:07D102 4.5 11.7 1.0 C3C 3:07D102 4.5 8.8 1.0 CAB Z:07D1001 4.7 10.7 1.0 C2B Z:07D1001 4.8 10.3 1.0 CBD 3:07D102 4.9 8.9 1.0

Magnesium binding site 4 out of 37 in the Cryo-Em Structure of the Rhodospirillum Rubrum Rc-LH1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of the Rhodospirillum Rubrum Rc-LH1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ 4:Mg1001 b:6.5 occ:1.00 MG 4:07D1001 0.0 6.5 1.0 NE2 4:HIS29 1.9 4.3 1.0 NB 4:07D1001 2.1 5.0 1.0 ND 4:07D1001 2.1 5.0 1.0 NA 4:07D1001 2.2 5.2 1.0 NC 4:07D1001 2.2 5.2 1.0 CE1 4:HIS29 2.8 4.3 1.0 C4D 4:07D1001 3.0 5.1 1.0 CD2 4:HIS29 3.0 4.2 1.0 C1B 4:07D1001 3.0 4.6 1.0 C4B 4:07D1001 3.0 5.2 1.0 C1C 4:07D1001 3.0 5.1 1.0 C4A 4:07D1001 3.1 5.3 1.0 C1A 4:07D1001 3.1 5.5 1.0 C1D 4:07D1001 3.2 4.8 1.0 C4C 4:07D1001 3.3 5.2 1.0 CHC 4:07D1001 3.3 5.2 1.0 CHB 4:07D1001 3.4 5.0 1.0 CHA 4:07D1001 3.4 5.8 1.0 CHD 4:07D1001 3.6 5.1 1.0 ND1 4:HIS29 4.0 4.4 1.0 CG 4:HIS29 4.1 4.7 1.0 C3D 4:07D1001 4.1 4.5 1.0 CBB 7:07D102 4.2 10.8 1.0 C2B 4:07D1001 4.2 4.2 1.0 C14 7:07D102 4.3 12.9 1.0 C3B 4:07D1001 4.3 4.6 1.0 C2D 4:07D1001 4.3 4.4 1.0 CMD 5:07D102 4.4 7.6 1.0 C2C 4:07D1001 4.4 5.7 1.0 C3A 4:07D1001 4.4 5.8 1.0 C2A 4:07D1001 4.5 6.0 1.0 C3C 4:07D1001 4.5 5.2 1.0 CMB 7:07D102 4.8 9.9 1.0 CBD 4:07D1001 4.9 5.2 1.0

Magnesium binding site 5 out of 37 in the Cryo-Em Structure of the Rhodospirillum Rubrum Rc-LH1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of the Rhodospirillum Rubrum Rc-LH1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ 5:Mg102 b:8.3 occ:1.00 MG 5:07D102 0.0 8.3 1.0 NE2 5:HIS39 1.9 4.4 1.0 NB 5:07D102 2.1 5.5 1.0 ND 5:07D102 2.1 4.0 1.0 NA 5:07D102 2.2 8.3 1.0 NC 5:07D102 2.2 4.1 1.0 CE1 5:HIS39 2.8 5.1 1.0 C4D 5:07D102 3.0 5.4 1.0 CD2 5:HIS39 3.0 4.9 1.0 C1B 5:07D102 3.0 6.0 1.0 C1C 5:07D102 3.0 3.6 1.0 C4B 5:07D102 3.0 4.2 1.0 C4A 5:07D102 3.1 9.0 1.0 C1A 5:07D102 3.1 8.6 1.0 C1D 5:07D102 3.2 3.3 1.0 C4C 5:07D102 3.3 4.3 1.0 CHC 5:07D102 3.3 4.5 1.0 CHB 5:07D102 3.4 8.0 1.0 CHA 5:07D102 3.4 5.5 1.0 CHD 5:07D102 3.6 4.4 1.0 ND1 5:HIS39 3.9 3.5 1.0 CG 5:HIS39 4.1 6.2 1.0 CMB 2:07D1001 4.1 6.2 1.0 CBB 2:07D1001 4.1 6.3 1.0 C3D 5:07D102 4.1 6.0 1.0 C2B 5:07D102 4.2 5.2 1.0 C2D 5:07D102 4.3 4.7 1.0 C3B 5:07D102 4.3 3.8 1.0 C2C 5:07D102 4.4 3.2 1.0 C3A 5:07D102 4.4 11.8 1.0 C2A 5:07D102 4.4 11.6 1.0 C3C 5:07D102 4.5 4.2 1.0 CAB 2:07D1001 4.7 6.6 1.0 C2B 2:07D1001 4.8 6.0 1.0 CBD 5:07D102 4.9 3.3 1.0

Magnesium binding site 6 out of 37 in the Cryo-Em Structure of the Rhodospirillum Rubrum Rc-LH1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of the Rhodospirillum Rubrum Rc-LH1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ 6:Mg1001 b:10.1 occ:1.00 MG 6:07D1001 0.0 10.1 1.0 NE2 6:HIS29 1.9 6.4 1.0 NB 6:07D1001 2.1 8.1 1.0 ND 6:07D1001 2.1 7.5 1.0 NA 6:07D1001 2.2 8.2 1.0 NC 6:07D1001 2.2 6.7 1.0 CE1 6:HIS29 2.8 6.8 1.0 C4D 6:07D1001 3.0 7.2 1.0 CD2 6:HIS29 3.0 6.6 1.0 C1B 6:07D1001 3.0 8.3 1.0 C4B 6:07D1001 3.0 7.6 1.0 C1C 6:07D1001 3.0 6.9 1.0 C4A 6:07D1001 3.1 7.8 1.0 C1A 6:07D1001 3.1 8.8 1.0 C1D 6:07D1001 3.2 7.0 1.0 C4C 6:07D1001 3.3 6.3 1.0 CHC 6:07D1001 3.3 7.5 1.0 CHB 6:07D1001 3.4 8.1 1.0 CHA 6:07D1001 3.4 8.1 1.0 CHD 6:07D1001 3.6 7.0 1.0 ND1 6:HIS29 4.0 7.5 1.0 CG 6:HIS29 4.1 6.8 1.0 C3D 6:07D1001 4.1 7.2 1.0 C2B 6:07D1001 4.2 7.7 1.0 C3B 6:07D1001 4.3 7.6 1.0 C2D 6:07D1001 4.3 6.8 1.0 CBB 9:07D102 4.3 13.2 1.0 CMD 7:07D102 4.4 6.5 1.0 C2C 6:07D1001 4.4 6.3 1.0 C3A 6:07D1001 4.4 9.1 1.0 C2A 6:07D1001 4.5 10.1 1.0 C3C 6:07D1001 4.5 6.7 1.0 C12 9:07D102 4.8 20.1 1.0 CBD 6:07D1001 4.9 8.4 1.0

Magnesium binding site 7 out of 37 in the Cryo-Em Structure of the Rhodospirillum Rubrum Rc-LH1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of the Rhodospirillum Rubrum Rc-LH1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ 7:Mg102 b:9.2 occ:1.00 MG 7:07D102 0.0 9.2 1.0 NE2 7:HIS39 1.9 6.4 1.0 NB 7:07D102 2.1 8.1 1.0 ND 7:07D102 2.1 7.3 1.0 NA 7:07D102 2.2 8.9 1.0 NC 7:07D102 2.2 7.7 1.0 CE1 7:HIS39 2.8 8.0 1.0 C4D 7:07D102 3.0 6.8 1.0 CD2 7:HIS39 3.0 6.8 1.0 C1B 7:07D102 3.0 8.6 1.0 C4B 7:07D102 3.0 7.6 1.0 C1C 7:07D102 3.0 7.4 1.0 C4A 7:07D102 3.1 10.2 1.0 C1A 7:07D102 3.1 9.0 1.0 C1D 7:07D102 3.2 6.3 1.0 C4C 7:07D102 3.3 6.4 1.0 CHC 7:07D102 3.3 7.2 1.0 CHB 7:07D102 3.4 10.3 1.0 CHA 7:07D102 3.4 7.8 1.0 CHD 7:07D102 3.6 6.7 1.0 ND1 7:HIS39 4.0 8.9 1.0 CG 7:HIS39 4.1 8.1 1.0 C3D 7:07D102 4.1 5.8 1.0 CMB 4:07D1001 4.2 4.0 1.0 CBB 4:07D1001 4.2 3.9 1.0 C2B 7:07D102 4.2 8.4 1.0 C3B 7:07D102 4.3 7.8 1.0 C2D 7:07D102 4.3 6.0 1.0 C3A 7:07D102 4.4 12.0 1.0 C2C 7:07D102 4.4 7.4 1.0 C2A 7:07D102 4.5 10.7 1.0 C3C 7:07D102 4.5 7.7 1.0 CAB 4:07D1001 4.7 4.7 1.0 C2B 4:07D1001 4.8 4.2 1.0 CBD 7:07D102 4.9 7.5 1.0

Magnesium binding site 8 out of 37 in the Cryo-Em Structure of the Rhodospirillum Rubrum Rc-LH1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Structure of the Rhodospirillum Rubrum Rc-LH1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ 8:Mg1001 b:14.7 occ:1.00 MG 8:07D1001 0.0 14.7 1.0 NE2 8:HIS29 1.9 9.8 1.0 NB 8:07D1001 2.1 10.7 1.0 ND 8:07D1001 2.1 11.3 1.0 NA 8:07D1001 2.2 11.9 1.0 NC 8:07D1001 2.2 10.3 1.0 CE1 8:HIS29 2.8 10.6 1.0 C4D 8:07D1001 3.0 11.8 1.0 CD2 8:HIS29 3.0 9.7 1.0 C1B 8:07D1001 3.0 10.5 1.0 C4B 8:07D1001 3.0 10.4 1.0 C1C 8:07D1001 3.0 10.6 1.0 C4A 8:07D1001 3.1 12.0 1.0 C1A 8:07D1001 3.1 11.5 1.0 C1D 8:07D1001 3.2 10.5 1.0 C4C 8:07D1001 3.3 9.8 1.0 CHC 8:07D1001 3.3 10.6 1.0 CHB 8:07D1001 3.4 10.9 1.0 CHA 8:07D1001 3.4 12.4 1.0 CHD 8:07D1001 3.6 9.9 1.0 ND1 8:HIS29 4.0 10.6 1.0 CG 8:HIS29 4.1 10.2 1.0 C3D 8:07D1001 4.1 11.7 1.0 C2B 8:07D1001 4.2 11.7 1.0 C3B 8:07D1001 4.3 11.6 1.0 CBB I:07D102 4.3 12.0 1.0 C2D 8:07D1001 4.3 11.6 1.0 C2C 8:07D1001 4.4 11.4 1.0 C3A 8:07D1001 4.4 13.9 1.0 C2A 8:07D1001 4.5 12.5 1.0 C3C 8:07D1001 4.5 10.0 1.0 CMD 9:07D102 4.5 7.2 1.0 C14 I:07D102 4.6 17.9 1.0 CMB I:07D102 4.7 11.9 1.0 CBD 8:07D1001 4.9 11.0 1.0

Magnesium binding site 9 out of 37 in the Cryo-Em Structure of the Rhodospirillum Rubrum Rc-LH1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cryo-Em Structure of the Rhodospirillum Rubrum Rc-LH1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ 9:Mg102 b:13.3 occ:1.00 MG 9:07D102 0.0 13.3 1.0 NE2 9:HIS39 1.9 4.3 1.0 NB 9:07D102 2.1 7.2 1.0 ND 9:07D102 2.1 5.7 1.0 NA 9:07D102 2.2 10.5 1.0 NC 9:07D102 2.2 7.1 1.0 CE1 9:HIS39 2.8 4.0 1.0 C4D 9:07D102 3.0 6.4 1.0 CD2 9:HIS39 3.0 4.3 1.0 C1B 9:07D102 3.0 10.4 1.0 C4B 9:07D102 3.0 7.5 1.0 C1C 9:07D102 3.0 6.8 1.0 C4A 9:07D102 3.1 12.3 1.0 C1A 9:07D102 3.1 8.9 1.0 C1D 9:07D102 3.2 6.1 1.0 C4C 9:07D102 3.3 7.5 1.0 CHC 9:07D102 3.3 6.4 1.0 CHB 9:07D102 3.4 12.3 1.0 CHA 9:07D102 3.4 8.3 1.0 CHD 9:07D102 3.6 7.2 1.0 ND1 9:HIS39 4.0 3.0 1.0 CG 9:HIS39 4.1 3.8 1.0 CBB 6:07D1001 4.1 8.1 1.0 C3D 9:07D102 4.1 6.0 1.0 C2B 9:07D102 4.2 14.2 1.0 CMB 6:07D1001 4.3 7.9 1.0 C3B 9:07D102 4.3 10.7 1.0 C2D 9:07D102 4.3 6.6 1.0 C2A 9:07D102 4.4 10.2 1.0 C2C 9:07D102 4.4 6.4 1.0 C3A 9:07D102 4.4 13.2 1.0 C3C 9:07D102 4.5 8.7 1.0 CAB 6:07D1001 4.7 8.0 1.0 CBD 9:07D102 4.9 6.1 1.0 C2B 6:07D1001 4.9 7.7 1.0 CD1 8:ILE28 5.0 11.8 1.0

Magnesium binding site 10 out of 37 in the Cryo-Em Structure of the Rhodospirillum Rubrum Rc-LH1 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryo-Em Structure of the Rhodospirillum Rubrum Rc-LH1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:4.1 occ:1.00 MG A:07D101 0.0 4.1 1.0 NE2 A:HIS29 1.9 3.4 1.0 NB A:07D101 2.1 3.9 1.0 ND A:07D101 2.1 4.7 1.0 NA A:07D101 2.2 4.8 1.0 NC A:07D101 2.2 3.8 1.0 CE1 A:HIS29 2.8 3.1 1.0 C4D A:07D101 3.0 4.6 1.0 CD2 A:HIS29 3.0 3.2 1.0 C1B A:07D101 3.0 3.3 1.0 C1C A:07D101 3.0 4.0 1.0 C4B A:07D101 3.0 3.9 1.0 C4A A:07D101 3.1 4.4 1.0 C1A A:07D101 3.1 5.6 1.0 C1D A:07D101 3.2 4.2 1.0 C4C A:07D101 3.3 4.2 1.0 CHC A:07D101 3.3 4.3 1.0 CHB A:07D101 3.4 3.5 1.0 CHA A:07D101 3.4 5.5 1.0 CHD A:07D101 3.6 4.2 1.0 ND1 A:HIS29 4.0 2.9 1.0 CG A:HIS29 4.1 3.1 1.0 C3D A:07D101 4.1 4.4 1.0 CBB Y:07D102 4.1 14.9 1.0 C2B A:07D101 4.2 3.5 1.0 C3B A:07D101 4.3 4.0 1.0 C2D A:07D101 4.3 4.2 1.0 C2C A:07D101 4.4 4.0 1.0 C3A A:07D101 4.4 6.1 1.0 CMD W:07D1001 4.5 10.0 1.0 C2A A:07D101 4.5 6.2 1.0 C3C A:07D101 4.5 4.5 1.0 CBD A:07D101 4.9 5.1 1.0 CMB Y:07D102 5.0 12.2 1.0

P.Qian, T.I.Croll, D.J.K.Swainsbury, P.Castro-Hartmann, N.W.Moriarty, K.Sader, C.N.Hunter. Cryo-Em Structure of the Rhodospirillum Rubrum Rc-LH1 Complex at 2.5 Angstrom. Biochem.J. V. 478 3253 2021.
ISSN: ESSN 1470-8728
PubMed: 34402504
DOI: 10.1042/BCJ20210511