Magnesium in PDB 9k3q: 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

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 9k3q). 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: 9k3q:
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:87.3 occ:1.00 MG 1:07D1001 0.0 87.3 1.0 NE2 1:HIS39 1.9 80.8 1.0 NB 1:07D1001 2.0 75.9 1.0 NA 1:07D1001 2.1 77.3 1.0 NC 1:07D1001 2.1 71.4 1.0 ND 1:07D1001 2.1 82.0 1.0 CD2 1:HIS39 2.7 72.6 1.0 C4D 1:07D1001 3.0 73.3 1.0 CE1 1:HIS39 3.0 80.5 1.0 C4B 1:07D1001 3.0 79.0 1.0 C4A 1:07D1001 3.1 77.2 1.0 C1B 1:07D1001 3.1 75.3 1.0 C1A 1:07D1001 3.1 78.0 1.0 C4C 1:07D1001 3.1 73.0 1.0 C1C 1:07D1001 3.1 74.6 1.0 C1D 1:07D1001 3.2 80.6 1.0 CHB 1:07D1001 3.4 78.6 1.0 CHC 1:07D1001 3.4 79.0 1.0 CHA 1:07D1001 3.5 74.2 1.0 CHD 1:07D1001 3.5 79.7 1.0 CG 1:HIS39 3.9 72.4 1.0 ND1 1:HIS39 4.0 80.0 1.0 C3B 1:07D1001 4.1 77.7 1.0 C2B 1:07D1001 4.2 74.0 1.0 C2A 1:07D1001 4.2 76.9 1.0 C3D 1:07D1001 4.2 74.2 1.0 C3A 1:07D1001 4.2 75.5 1.0 C3C 1:07D1001 4.2 73.3 1.0 C2C 1:07D1001 4.3 79.4 1.0 C2D 1:07D1001 4.4 72.8 1.0 CMB X:07D1001 4.6 78.5 1.0 CBD 1:07D1001 4.9 74.5 1.0 CBB X:07D1001 5.0 80.4 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:67.8 occ:1.00 MG 2:07D1001 0.0 67.8 1.0 NE2 2:HIS29 1.9 52.9 1.0 NB 2:07D1001 2.0 79.5 1.0 NA 2:07D1001 2.1 76.8 1.0 NC 2:07D1001 2.1 77.2 1.0 ND 2:07D1001 2.1 73.9 1.0 CE1 2:HIS29 2.8 59.2 1.0 CD2 2:HIS29 2.9 53.9 1.0 C4D 2:07D1001 3.0 73.3 1.0 C1B 2:07D1001 3.0 77.4 1.0 C4A 2:07D1001 3.1 77.7 1.0 C4B 2:07D1001 3.1 72.2 1.0 C1A 2:07D1001 3.1 73.8 1.0 C4C 2:07D1001 3.1 75.7 1.0 C1C 2:07D1001 3.1 74.9 1.0 C1D 2:07D1001 3.2 74.7 1.0 CHB 2:07D1001 3.4 78.5 1.0 CHC 2:07D1001 3.5 70.0 1.0 CHA 2:07D1001 3.5 74.0 1.0 CHD 2:07D1001 3.5 75.1 1.0 ND1 2:HIS29 3.9 57.1 1.0 CG 2:HIS29 3.9 52.5 1.0 C2B 2:07D1001 4.1 73.3 1.0 C3B 2:07D1001 4.2 71.4 1.0 C2A 2:07D1001 4.2 69.0 1.0 C3D 2:07D1001 4.2 73.4 1.0 C3A 2:07D1001 4.2 71.1 1.0 C3C 2:07D1001 4.3 72.8 1.0 C2C 2:07D1001 4.3 79.7 1.0 C2D 2:07D1001 4.4 71.1 1.0 CMD 3:07D102 4.5 68.6 1.0 CBB 5:07D102 4.7 69.8 1.0 C35 5:CRT101 4.8 86.0 1.0 CBD 2:07D1001 4.9 76.7 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:81.6 occ:1.00 MG 3:07D102 0.0 81.6 1.0 NE2 3:HIS39 1.9 74.5 1.0 NB 3:07D102 2.0 73.0 1.0 NA 3:07D102 2.1 82.3 1.0 NC 3:07D102 2.1 71.6 1.0 ND 3:07D102 2.1 77.6 1.0 CD2 3:HIS39 2.7 69.7 1.0 C4D 3:07D102 3.0 74.5 1.0 CE1 3:HIS39 3.0 74.0 1.0 C4B 3:07D102 3.0 74.6 1.0 C4A 3:07D102 3.1 76.0 1.0 C1B 3:07D102 3.1 73.7 1.0 C1A 3:07D102 3.1 80.4 1.0 C4C 3:07D102 3.1 70.5 1.0 C1C 3:07D102 3.1 69.3 1.0 C1D 3:07D102 3.2 76.3 1.0 CHB 3:07D102 3.4 75.2 1.0 CHC 3:07D102 3.5 73.3 1.0 CHA 3:07D102 3.5 75.6 1.0 CHD 3:07D102 3.5 74.8 1.0 CG 3:HIS39 3.9 67.6 1.0 ND1 3:HIS39 4.0 77.2 1.0 C3B 3:07D102 4.1 76.3 1.0 C2B 3:07D102 4.2 74.0 1.0 C2A 3:07D102 4.2 75.8 1.0 C3D 3:07D102 4.2 71.8 1.0 C3A 3:07D102 4.2 72.4 1.0 C3C 3:07D102 4.2 70.4 1.0 C2C 3:07D102 4.3 72.5 1.0 C2D 3:07D102 4.3 69.3 1.0 CMB Z:07D1001 4.6 75.5 1.0 CBD 3:07D102 4.9 72.7 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:81.3 occ:1.00 MG 4:07D1001 0.0 81.3 1.0 NE2 4:HIS29 1.9 47.2 1.0 NA 4:07D1001 2.1 72.0 1.0 NC 4:07D1001 2.1 71.0 1.0 NB 4:07D1001 2.1 67.2 1.0 ND 4:07D1001 2.1 73.9 1.0 CD2 4:HIS29 2.9 51.4 1.0 CE1 4:HIS29 2.9 46.5 1.0 C4D 4:07D1001 3.0 69.2 1.0 C4A 4:07D1001 3.0 64.8 1.0 C1B 4:07D1001 3.1 66.8 1.0 C4B 4:07D1001 3.1 63.8 1.0 C1A 4:07D1001 3.1 64.6 1.0 C4C 4:07D1001 3.1 65.8 1.0 C1C 4:07D1001 3.1 68.5 1.0 C1D 4:07D1001 3.2 68.8 1.0 CHB 4:07D1001 3.4 66.9 1.0 CHC 4:07D1001 3.4 65.9 1.0 CHA 4:07D1001 3.5 64.8 1.0 CHD 4:07D1001 3.5 68.6 1.0 ND1 4:HIS29 4.0 54.6 1.0 CG 4:HIS29 4.0 54.4 1.0 C3B 4:07D1001 4.2 64.2 1.0 C2B 4:07D1001 4.2 63.9 1.0 C3A 4:07D1001 4.2 59.1 1.0 C3D 4:07D1001 4.2 63.8 1.0 C2A 4:07D1001 4.2 60.0 1.0 C3C 4:07D1001 4.2 60.3 1.0 C2C 4:07D1001 4.3 67.4 1.0 C2D 4:07D1001 4.4 63.1 1.0 CMD 5:07D102 4.5 66.0 1.0 C14 7:07D102 4.7 67.4 1.0 CBD 4:07D1001 4.9 68.8 1.0 C35 7:CRT101 5.0 70.8 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:70.8 occ:1.00 MG 5:07D102 0.0 70.8 1.0 NE2 5:HIS39 1.9 53.0 1.0 NB 5:07D102 2.0 75.3 1.0 ND 5:07D102 2.0 68.2 1.0 NA 5:07D102 2.1 77.3 1.0 NC 5:07D102 2.1 73.1 1.0 CD2 5:HIS39 2.8 55.5 1.0 C1B 5:07D102 3.0 72.0 1.0 C4D 5:07D102 3.0 68.6 1.0 CE1 5:HIS39 3.0 61.6 1.0 C4A 5:07D102 3.1 70.7 1.0 C4B 5:07D102 3.1 71.3 1.0 C1A 5:07D102 3.1 77.7 1.0 C4C 5:07D102 3.1 66.8 1.0 C1C 5:07D102 3.1 71.0 1.0 C1D 5:07D102 3.2 64.9 1.0 CHB 5:07D102 3.4 68.4 1.0 CHC 5:07D102 3.4 69.0 1.0 CHA 5:07D102 3.5 71.3 1.0 CHD 5:07D102 3.5 63.5 1.0 CG 5:HIS39 3.9 52.5 1.0 ND1 5:HIS39 4.0 66.4 1.0 C2B 5:07D102 4.1 70.8 1.0 C2A 5:07D102 4.2 76.6 1.0 C3D 5:07D102 4.2 69.0 1.0 C3C 5:07D102 4.2 66.1 1.0 C3B 5:07D102 4.2 73.6 1.0 C3A 5:07D102 4.2 64.1 1.0 C2C 5:07D102 4.3 71.0 1.0 C2D 5:07D102 4.3 65.5 1.0 CBB 2:07D1001 4.6 74.2 1.0 CBD 5:07D102 4.9 70.5 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:76.1 occ:1.00 MG 6:07D1001 0.0 76.1 1.0 NE2 6:HIS29 1.9 39.0 1.0 NB 6:07D1001 2.0 68.7 1.0 NC 6:07D1001 2.1 73.6 1.0 NA 6:07D1001 2.1 68.9 1.0 ND 6:07D1001 2.1 70.7 1.0 CE1 6:HIS29 2.7 42.7 1.0 C4D 6:07D1001 3.0 70.0 1.0 C1B 6:07D1001 3.0 69.6 1.0 CD2 6:HIS29 3.0 43.6 1.0 C4B 6:07D1001 3.1 62.2 1.0 C4A 6:07D1001 3.1 65.6 1.0 C1A 6:07D1001 3.1 64.2 1.0 C4C 6:07D1001 3.1 68.1 1.0 C1C 6:07D1001 3.1 64.6 1.0 C1D 6:07D1001 3.2 66.0 1.0 CHB 6:07D1001 3.4 66.6 1.0 CHC 6:07D1001 3.5 58.9 1.0 CHA 6:07D1001 3.5 64.0 1.0 CHD 6:07D1001 3.5 65.1 1.0 ND1 6:HIS29 3.8 51.1 1.0 CG 6:HIS29 4.0 42.1 1.0 C2B 6:07D1001 4.1 66.0 1.0 C3B 6:07D1001 4.1 62.8 1.0 C2A 6:07D1001 4.2 60.6 1.0 C3D 6:07D1001 4.2 65.0 1.0 C3A 6:07D1001 4.2 62.5 1.0 C3C 6:07D1001 4.2 64.5 1.0 C2C 6:07D1001 4.3 68.2 1.0 C2D 6:07D1001 4.4 63.3 1.0 CMD 7:07D102 4.6 54.9 1.0 C35 9:CRT101 4.9 75.5 1.0 CBD 6:07D1001 4.9 62.4 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:59.6 occ:1.00 MG 7:07D102 0.0 59.6 1.0 NE2 7:HIS39 1.9 63.4 1.0 NB 7:07D102 2.0 62.8 1.0 NA 7:07D102 2.1 74.0 1.0 NC 7:07D102 2.1 56.0 1.0 ND 7:07D102 2.1 64.6 1.0 CD2 7:HIS39 2.7 56.9 1.0 C4D 7:07D102 3.0 61.2 1.0 CE1 7:HIS39 3.0 69.9 1.0 C4B 7:07D102 3.1 66.6 1.0 C1B 7:07D102 3.1 61.0 1.0 C4A 7:07D102 3.1 64.1 1.0 C1A 7:07D102 3.1 68.0 1.0 C4C 7:07D102 3.1 58.0 1.0 C1C 7:07D102 3.1 61.4 1.0 C1D 7:07D102 3.2 63.4 1.0 CHC 7:07D102 3.5 62.6 1.0 CHB 7:07D102 3.5 60.7 1.0 CHA 7:07D102 3.5 63.2 1.0 CHD 7:07D102 3.5 60.9 1.0 CG 7:HIS39 3.9 54.6 1.0 ND1 7:HIS39 4.0 70.2 1.0 C3B 7:07D102 4.1 67.8 1.0 C2A 7:07D102 4.2 62.0 1.0 C2B 7:07D102 4.2 63.9 1.0 C3C 7:07D102 4.2 61.9 1.0 C3A 7:07D102 4.2 56.9 1.0 C3D 7:07D102 4.2 57.0 1.0 C2C 7:07D102 4.3 68.9 1.0 C2D 7:07D102 4.4 57.8 1.0 CMB 4:07D1001 4.7 66.4 1.0 CBD 7:07D102 4.9 59.2 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:65.4 occ:1.00 MG 8:07D1001 0.0 65.4 1.0 NE2 8:HIS29 1.9 44.9 1.0 NB 8:07D1001 2.0 63.2 1.0 NA 8:07D1001 2.1 64.1 1.0 NC 8:07D1001 2.1 63.0 1.0 ND 8:07D1001 2.1 61.7 1.0 CE1 8:HIS29 2.8 46.1 1.0 CD2 8:HIS29 2.9 39.6 1.0 C4D 8:07D1001 3.0 59.2 1.0 C1B 8:07D1001 3.0 62.7 1.0 C4B 8:07D1001 3.1 62.6 1.0 C4A 8:07D1001 3.1 61.3 1.0 C1A 8:07D1001 3.1 62.9 1.0 C4C 8:07D1001 3.1 61.2 1.0 C1C 8:07D1001 3.1 60.5 1.0 C1D 8:07D1001 3.2 60.9 1.0 CHC 8:07D1001 3.5 59.9 1.0 CHB 8:07D1001 3.5 61.4 1.0 CHA 8:07D1001 3.5 60.8 1.0 CHD 8:07D1001 3.5 58.2 1.0 ND1 8:HIS29 3.9 46.5 1.0 CG 8:HIS29 4.0 36.9 1.0 C2B 8:07D1001 4.1 61.8 1.0 C3B 8:07D1001 4.2 60.4 1.0 C2A 8:07D1001 4.2 54.0 1.0 C14 I:07D102 4.2 65.4 1.0 C3D 8:07D1001 4.2 62.5 1.0 C3A 8:07D1001 4.2 53.3 1.0 C3C 8:07D1001 4.2 61.4 1.0 C2C 8:07D1001 4.3 65.2 1.0 C2D 8:07D1001 4.4 59.2 1.0 CMD 9:07D102 4.6 60.3 1.0 C35 I:CRT101 4.9 62.7 1.0 CBD 8:07D1001 4.9 59.2 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:55.7 occ:1.00 MG 9:07D102 0.0 55.7 1.0 NE2 9:HIS39 1.9 55.1 1.0 NB 9:07D102 2.0 65.3 1.0 NA 9:07D102 2.1 67.1 1.0 NC 9:07D102 2.1 63.9 1.0 ND 9:07D102 2.1 70.3 1.0 CD2 9:HIS39 2.5 52.1 1.0 C4D 9:07D102 3.0 64.8 1.0 C1B 9:07D102 3.0 68.6 1.0 C4A 9:07D102 3.1 63.6 1.0 C4B 9:07D102 3.1 64.6 1.0 C1A 9:07D102 3.1 64.7 1.0 C4C 9:07D102 3.1 64.4 1.0 CE1 9:HIS39 3.1 66.2 1.0 C1C 9:07D102 3.1 62.1 1.0 C1D 9:07D102 3.2 63.3 1.0 CHB 9:07D102 3.4 64.7 1.0 CHC 9:07D102 3.5 61.9 1.0 CHA 9:07D102 3.5 61.8 1.0 CHD 9:07D102 3.5 63.8 1.0 CG 9:HIS39 3.8 57.4 1.0 ND1 9:HIS39 4.0 71.2 1.0 C2B 9:07D102 4.1 66.4 1.0 C3B 9:07D102 4.2 65.0 1.0 C2A 9:07D102 4.2 60.9 1.0 C3A 9:07D102 4.2 59.3 1.0 C3D 9:07D102 4.2 56.9 1.0 C3C 9:07D102 4.2 59.3 1.0 C2C 9:07D102 4.3 63.0 1.0 C2D 9:07D102 4.4 53.5 1.0 CBB 6:07D1001 4.6 68.1 1.0 CBD 9:07D102 4.9 55.0 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:91.9 occ:1.00 MG A:07D101 0.0 91.9 1.0 NE2 A:HIS29 1.9 58.9 1.0 NB A:07D101 2.1 75.9 1.0 NA A:07D101 2.1 83.4 1.0 NC A:07D101 2.1 80.2 1.0 ND A:07D101 2.1 80.0 1.0 CD2 A:HIS29 2.8 55.5 1.0 CE1 A:HIS29 2.9 59.2 1.0 C4D A:07D101 3.0 77.4 1.0 C4A A:07D101 3.1 81.1 1.0 C1B A:07D101 3.1 78.3 1.0 C4B A:07D101 3.1 72.4 1.0 C1C A:07D101 3.1 76.0 1.0 C1A A:07D101 3.1 78.6 1.0 C4C A:07D101 3.1 75.6 1.0 C1D A:07D101 3.2 75.3 1.0 CHC A:07D101 3.4 73.7 1.0 CHB A:07D101 3.4 79.8 1.0 CHA A:07D101 3.5 75.8 1.0 CHD A:07D101 3.5 73.7 1.0 CG A:HIS29 4.0 52.3 1.0 ND1 A:HIS29 4.0 59.4 1.0 C2B A:07D101 4.1 80.0 1.0 C2A A:07D101 4.2 78.3 1.0 C3B A:07D101 4.2 77.9 1.0 C3A A:07D101 4.2 76.3 1.0 C3D A:07D101 4.2 78.4 1.0 C2C A:07D101 4.3 80.3 1.0 C3C A:07D101 4.3 75.7 1.0 C2D A:07D101 4.3 76.6 1.0 CBB Y:07D102 4.5 80.3 1.0 CMD W:07D1002 4.5 68.8 1.0 CBD A:07D101 4.9 77.9 1.0

Z.K.Liu, P.Wang, L.N.Liu. Cryo-Em Structure of the Rhodospirillum Rubrum Rc-LH1 Complex To Be Published.