Magnesium in PDB 7ddq: Structure of Rc-LH1-Pufx From Rhodobacter Veldkampii

The structure of Structure of Rc-LH1-Pufx From Rhodobacter Veldkampii also contains other interesting chemical elements:

Iron

(Fe)

1 atom

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 34;

Binding sites:

The binding sites of Magnesium atom in the Structure of Rc-LH1-Pufx From Rhodobacter Veldkampii (pdb code 7ddq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 34 binding sites of Magnesium where determined in the Structure of Rc-LH1-Pufx From Rhodobacter Veldkampii, PDB code: 7ddq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 34 in the Structure of Rc-LH1-Pufx From Rhodobacter Veldkampii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Rc-LH1-Pufx From Rhodobacter Veldkampii within 5.0Å range: probe atom residue distance (Å) B Occ o:Mg100 b:12.0 occ:1.00 MG o:BCL100 0.0 12.0 1.0 ND o:BCL100 2.0 12.0 1.0 NB o:BCL100 2.1 12.0 1.0 NC o:BCL100 2.1 12.0 1.0 NA o:BCL100 2.2 12.0 1.0 NE2 o:HIS32 2.9 8.5 1.0 C4D o:BCL100 3.0 12.0 1.0 C1B o:BCL100 3.1 12.0 1.0 C4B o:BCL100 3.1 12.0 1.0 C1C o:BCL100 3.1 12.0 1.0 C4A o:BCL100 3.1 12.0 1.0 C1D o:BCL100 3.1 12.0 1.0 C4C o:BCL100 3.1 12.0 1.0 C1A o:BCL100 3.2 12.0 1.0 CHC o:BCL100 3.4 12.0 1.0 CHB o:BCL100 3.4 12.0 1.0 CHA o:BCL100 3.4 12.0 1.0 CHD o:BCL100 3.5 12.0 1.0 CE1 o:HIS32 3.8 8.5 1.0 CBB N:BCL202 3.8 11.9 1.0 CD2 o:HIS32 3.9 8.5 1.0 CMB N:BCL202 4.1 11.9 1.0 C3D o:BCL100 4.2 12.0 1.0 C2D o:BCL100 4.3 12.0 1.0 C2B o:BCL100 4.3 12.0 1.0 C3B o:BCL100 4.3 12.0 1.0 C3A o:BCL100 4.4 12.0 1.0 C2C o:BCL100 4.4 12.0 1.0 C3C o:BCL100 4.4 12.0 1.0 C2A o:BCL100 4.5 12.0 1.0 C2B N:BCL202 4.6 11.9 1.0 CAB N:BCL202 4.7 11.9 1.0 C3B N:BCL202 4.9 11.9 1.0 CBD o:BCL100 4.9 12.0 1.0 CMD O:BCL101 4.9 14.3 1.0 CMA o:BCL100 4.9 12.0 1.0 ND1 o:HIS32 5.0 8.5 1.0

Magnesium binding site 2 out of 34 in the Structure of Rc-LH1-Pufx From Rhodobacter Veldkampii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Rc-LH1-Pufx From Rhodobacter Veldkampii within 5.0Å range: probe atom residue distance (Å) B Occ N:Mg202 b:11.9 occ:1.00 MG N:BCL202 0.0 11.9 1.0 ND N:BCL202 2.0 11.9 1.0 NB N:BCL202 2.1 11.9 1.0 NC N:BCL202 2.1 11.9 1.0 NA N:BCL202 2.2 11.9 1.0 NE2 N:HIS38 2.7 9.6 1.0 C4D N:BCL202 3.0 11.9 1.0 C4B N:BCL202 3.1 11.9 1.0 C1B N:BCL202 3.1 11.9 1.0 C1C N:BCL202 3.1 11.9 1.0 C4A N:BCL202 3.1 11.9 1.0 C1D N:BCL202 3.1 11.9 1.0 C4C N:BCL202 3.1 11.9 1.0 C1A N:BCL202 3.2 11.9 1.0 CD2 N:HIS38 3.2 9.6 1.0 CHC N:BCL202 3.4 11.9 1.0 CHB N:BCL202 3.4 11.9 1.0 CHA N:BCL202 3.4 11.9 1.0 CHD N:BCL202 3.5 11.9 1.0 CBB o:BCL100 3.8 12.0 1.0 CE1 N:HIS38 3.8 9.6 1.0 C3D N:BCL202 4.2 11.9 1.0 C2B N:BCL202 4.3 11.9 1.0 C2D N:BCL202 4.3 11.9 1.0 C3B N:BCL202 4.3 11.9 1.0 CMB o:BCL100 4.4 12.0 1.0 C2C N:BCL202 4.4 11.9 1.0 C3C N:BCL202 4.4 11.9 1.0 C3A N:BCL202 4.4 11.9 1.0 C2A N:BCL202 4.5 11.9 1.0 CG N:HIS38 4.5 9.6 1.0 CAB o:BCL100 4.6 12.0 1.0 C10 N:BCL202 4.7 11.9 1.0 ND1 N:HIS38 4.8 9.6 1.0 C2B o:BCL100 4.8 12.0 1.0 CMD n:BCL100 4.8 11.2 1.0 C3B o:BCL100 4.9 12.0 1.0 CBD N:BCL202 4.9 11.9 1.0

Magnesium binding site 3 out of 34 in the Structure of Rc-LH1-Pufx From Rhodobacter Veldkampii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Rc-LH1-Pufx From Rhodobacter Veldkampii within 5.0Å range: probe atom residue distance (Å) B Occ t:Mg101 b:31.2 occ:1.00 MG t:BCL101 0.0 31.2 1.0 ND t:BCL101 2.0 31.2 1.0 NB t:BCL101 2.1 31.2 1.0 NC t:BCL101 2.1 31.2 1.0 NA t:BCL101 2.2 31.2 1.0 NE2 t:HIS32 2.8 30.6 1.0 C4D t:BCL101 3.0 31.2 1.0 C4B t:BCL101 3.1 31.2 1.0 C1B t:BCL101 3.1 31.2 1.0 C1C t:BCL101 3.1 31.2 1.0 C4A t:BCL101 3.1 31.2 1.0 C1D t:BCL101 3.1 31.2 1.0 C4C t:BCL101 3.1 31.2 1.0 C1A t:BCL101 3.2 31.2 1.0 CHC t:BCL101 3.4 31.2 1.0 CD2 t:HIS32 3.4 30.6 1.0 CHB t:BCL101 3.4 31.2 1.0 CHA t:BCL101 3.4 31.2 1.0 CHD t:BCL101 3.5 31.2 1.0 CE1 t:HIS32 3.9 30.6 1.0 C3D t:BCL101 4.2 31.2 1.0 C2B t:BCL101 4.2 31.2 1.0 C3B t:BCL101 4.3 31.2 1.0 C2D t:BCL101 4.3 31.2 1.0 C2C t:BCL101 4.4 31.2 1.0 C3C t:BCL101 4.4 31.2 1.0 C3A t:BCL101 4.5 31.2 1.0 C2A t:BCL101 4.5 31.2 1.0 CBB S:BCL101 4.6 25.2 1.0 CMB S:BCL101 4.6 25.2 1.0 CG t:HIS32 4.6 30.6 1.0 CMD t:BCL103 4.7 40.8 1.0 CBD t:BCL101 4.9 31.2 1.0 ND1 t:HIS32 4.9 30.6 1.0

Magnesium binding site 4 out of 34 in the Structure of Rc-LH1-Pufx From Rhodobacter Veldkampii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Rc-LH1-Pufx From Rhodobacter Veldkampii within 5.0Å range: probe atom residue distance (Å) B Occ t:Mg103 b:40.8 occ:1.00 MG t:BCL103 0.0 40.8 1.0 ND t:BCL103 2.0 40.8 1.0 NB t:BCL103 2.1 40.8 1.0 NC t:BCL103 2.1 40.8 1.0 NA t:BCL103 2.2 40.8 1.0 NE2 T:HIS38 2.7 32.8 1.0 C4D t:BCL103 3.0 40.8 1.0 C4B t:BCL103 3.1 40.8 1.0 C1B t:BCL103 3.1 40.8 1.0 C1C t:BCL103 3.1 40.8 1.0 C4A t:BCL103 3.1 40.8 1.0 C1D t:BCL103 3.1 40.8 1.0 C4C t:BCL103 3.2 40.8 1.0 C1A t:BCL103 3.2 40.8 1.0 CD2 T:HIS38 3.3 32.8 1.0 CHC t:BCL103 3.4 40.8 1.0 CHB t:BCL103 3.4 40.8 1.0 CHA t:BCL103 3.4 40.8 1.0 CHD t:BCL103 3.5 40.8 1.0 CE1 T:HIS38 3.9 32.8 1.0 CMB u:BCL101 4.2 42.4 1.0 C3D t:BCL103 4.2 40.8 1.0 C2B t:BCL103 4.3 40.8 1.0 C3B t:BCL103 4.3 40.8 1.0 C2D t:BCL103 4.3 40.8 1.0 C10 t:BCL103 4.4 40.8 1.0 C2C t:BCL103 4.4 40.8 1.0 C2A t:BCL103 4.4 40.8 1.0 C3A t:BCL103 4.4 40.8 1.0 C3C t:BCL103 4.5 40.8 1.0 CG T:HIS38 4.5 32.8 1.0 CBB u:BCL101 4.6 42.4 1.0 ND1 T:HIS38 4.8 32.8 1.0 CAB u:BCL101 4.8 42.4 1.0 C2B u:BCL101 4.8 42.4 1.0 CBD t:BCL103 4.9 40.8 1.0 C8 t:BCL103 5.0 40.8 1.0

Magnesium binding site 5 out of 34 in the Structure of Rc-LH1-Pufx From Rhodobacter Veldkampii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Rc-LH1-Pufx From Rhodobacter Veldkampii within 5.0Å range: probe atom residue distance (Å) B Occ S:Mg101 b:25.2 occ:1.00 MG S:BCL101 0.0 25.2 1.0 ND S:BCL101 2.0 25.2 1.0 NB S:BCL101 2.1 25.2 1.0 NC S:BCL101 2.1 25.2 1.0 NA S:BCL101 2.2 25.2 1.0 NE2 S:HIS38 2.7 22.5 1.0 C4D S:BCL101 3.0 25.2 1.0 C4B S:BCL101 3.1 25.2 1.0 C1B S:BCL101 3.1 25.2 1.0 C1C S:BCL101 3.1 25.2 1.0 C4A S:BCL101 3.1 25.2 1.0 C1D S:BCL101 3.1 25.2 1.0 C4C S:BCL101 3.1 25.2 1.0 CD2 S:HIS38 3.2 22.5 1.0 C1A S:BCL101 3.2 25.2 1.0 CHC S:BCL101 3.4 25.2 1.0 CHB S:BCL101 3.4 25.2 1.0 CHA S:BCL101 3.4 25.2 1.0 CHD S:BCL101 3.5 25.2 1.0 CBB t:BCL101 3.9 31.2 1.0 CE1 S:HIS38 4.0 22.5 1.0 C3D S:BCL101 4.2 25.2 1.0 C2B S:BCL101 4.3 25.2 1.0 C3B S:BCL101 4.3 25.2 1.0 C2D S:BCL101 4.3 25.2 1.0 CMB t:BCL101 4.3 31.2 1.0 C2C S:BCL101 4.4 25.2 1.0 C2A S:BCL101 4.4 25.2 1.0 C3A S:BCL101 4.4 25.2 1.0 C3C S:BCL101 4.4 25.2 1.0 CG S:HIS38 4.5 22.5 1.0 C11 S:BCL101 4.7 25.2 1.0 CAB t:BCL101 4.7 31.2 1.0 ND1 S:HIS38 4.8 22.5 1.0 C2B t:BCL101 4.9 31.2 1.0 CBD S:BCL101 4.9 25.2 1.0 C3B t:BCL101 5.0 31.2 1.0

Magnesium binding site 6 out of 34 in the Structure of Rc-LH1-Pufx From Rhodobacter Veldkampii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Rc-LH1-Pufx From Rhodobacter Veldkampii within 5.0Å range: probe atom residue distance (Å) B Occ r:Mg101 b:22.4 occ:1.00 MG r:BCL101 0.0 22.4 1.0 ND r:BCL101 2.0 22.4 1.0 NB r:BCL101 2.1 22.4 1.0 NC r:BCL101 2.1 22.4 1.0 NA r:BCL101 2.2 22.4 1.0 NE2 r:HIS32 2.7 17.4 1.0 C4D r:BCL101 3.0 22.4 1.0 C4B r:BCL101 3.1 22.4 1.0 C1B r:BCL101 3.1 22.4 1.0 C1C r:BCL101 3.1 22.4 1.0 C4A r:BCL101 3.1 22.4 1.0 C1D r:BCL101 3.1 22.4 1.0 C4C r:BCL101 3.1 22.4 1.0 C1A r:BCL101 3.2 22.4 1.0 CD2 r:HIS32 3.4 17.4 1.0 CHC r:BCL101 3.4 22.4 1.0 CHB r:BCL101 3.4 22.4 1.0 CHA r:BCL101 3.4 22.4 1.0 CHD r:BCL101 3.5 22.4 1.0 CE1 r:HIS32 3.9 17.4 1.0 CBB O:BCL101 4.2 14.3 1.0 C3D r:BCL101 4.2 22.4 1.0 C2B r:BCL101 4.2 22.4 1.0 C3B r:BCL101 4.3 22.4 1.0 C2D r:BCL101 4.3 22.4 1.0 C2C r:BCL101 4.4 22.4 1.0 C3C r:BCL101 4.4 22.4 1.0 C3A r:BCL101 4.4 22.4 1.0 CMD R:BCL101 4.4 25.6 1.0 C2A r:BCL101 4.5 22.4 1.0 CG r:HIS32 4.6 17.4 1.0 CMB O:BCL101 4.7 14.3 1.0 ND1 r:HIS32 4.8 17.4 1.0 CBD r:BCL101 4.9 22.4 1.0

Magnesium binding site 7 out of 34 in the Structure of Rc-LH1-Pufx From Rhodobacter Veldkampii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Rc-LH1-Pufx From Rhodobacter Veldkampii within 5.0Å range: probe atom residue distance (Å) B Occ O:Mg101 b:14.3 occ:1.00 MG O:BCL101 0.0 14.3 1.0 ND O:BCL101 2.0 14.3 1.0 NB O:BCL101 2.1 14.3 1.0 NC O:BCL101 2.1 14.3 1.0 NA O:BCL101 2.2 14.3 1.0 NE2 O:HIS38 2.7 15.2 1.0 C4D O:BCL101 3.0 14.3 1.0 C4B O:BCL101 3.1 14.3 1.0 C1B O:BCL101 3.1 14.3 1.0 C1C O:BCL101 3.1 14.3 1.0 C4A O:BCL101 3.1 14.3 1.0 C1D O:BCL101 3.1 14.3 1.0 C4C O:BCL101 3.1 14.3 1.0 CD2 O:HIS38 3.2 15.2 1.0 C1A O:BCL101 3.2 14.3 1.0 CHC O:BCL101 3.4 14.3 1.0 CHB O:BCL101 3.4 14.3 1.0 CHA O:BCL101 3.4 14.3 1.0 CHD O:BCL101 3.5 14.3 1.0 CE1 O:HIS38 3.9 15.2 1.0 CBB r:BCL101 4.1 22.4 1.0 C3D O:BCL101 4.2 14.3 1.0 C2B O:BCL101 4.3 14.3 1.0 CMB r:BCL101 4.3 22.4 1.0 C3B O:BCL101 4.3 14.3 1.0 C2D O:BCL101 4.3 14.3 1.0 C2A O:BCL101 4.4 14.3 1.0 C2C O:BCL101 4.4 14.3 1.0 C3A O:BCL101 4.4 14.3 1.0 C3C O:BCL101 4.4 14.3 1.0 CG O:HIS38 4.5 15.2 1.0 C11 O:BCL101 4.8 14.3 1.0 ND1 O:HIS38 4.8 15.2 1.0 C2B r:BCL101 4.8 22.4 1.0 CAB r:BCL101 4.9 22.4 1.0 CBD O:BCL101 4.9 14.3 1.0 CAA O:BCL101 4.9 14.3 1.0

Magnesium binding site 8 out of 34 in the Structure of Rc-LH1-Pufx From Rhodobacter Veldkampii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Rc-LH1-Pufx From Rhodobacter Veldkampii within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg101 b:16.6 occ:1.00 MG a:BCL101 0.0 16.6 1.0 ND a:BCL101 2.0 16.6 1.0 NB a:BCL101 2.1 16.6 1.0 NC a:BCL101 2.1 16.6 1.0 NA a:BCL101 2.2 16.6 1.0 NE2 a:HIS32 2.7 11.7 1.0 C4D a:BCL101 3.0 16.6 1.0 C4B a:BCL101 3.1 16.6 1.0 C1B a:BCL101 3.1 16.6 1.0 C1C a:BCL101 3.1 16.6 1.0 C1D a:BCL101 3.1 16.6 1.0 C4A a:BCL101 3.1 16.6 1.0 C4C a:BCL101 3.1 16.6 1.0 C1A a:BCL101 3.2 16.6 1.0 CD2 a:HIS32 3.4 11.7 1.0 CHC a:BCL101 3.4 16.6 1.0 CHB a:BCL101 3.4 16.6 1.0 CHA a:BCL101 3.4 16.6 1.0 CHD a:BCL101 3.5 16.6 1.0 CE1 a:HIS32 3.8 11.7 1.0 C3D a:BCL101 4.2 16.6 1.0 C2B a:BCL101 4.3 16.6 1.0 C2D a:BCL101 4.3 16.6 1.0 C3B a:BCL101 4.3 16.6 1.0 C2C a:BCL101 4.4 16.6 1.0 C3C a:BCL101 4.4 16.6 1.0 C3A a:BCL101 4.4 16.6 1.0 C2A a:BCL101 4.4 16.6 1.0 CMD A:BCL101 4.5 13.5 1.0 CG a:HIS32 4.6 11.7 1.0 ND1 a:HIS32 4.8 11.7 1.0 CBD a:BCL101 4.9 16.6 1.0

Magnesium binding site 9 out of 34 in the Structure of Rc-LH1-Pufx From Rhodobacter Veldkampii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of Rc-LH1-Pufx From Rhodobacter Veldkampii within 5.0Å range: probe atom residue distance (Å) B Occ e:Mg100 b:10.1 occ:1.00 MG e:BCL100 0.0 10.1 1.0 ND e:BCL100 2.0 10.1 1.0 NB e:BCL100 2.1 10.1 1.0 NC e:BCL100 2.1 10.1 1.0 NA e:BCL100 2.2 10.1 1.0 NE2 e:HIS32 2.7 6.3 1.0 C4D e:BCL100 3.0 10.1 1.0 C4B e:BCL100 3.1 10.1 1.0 C1B e:BCL100 3.1 10.1 1.0 C1C e:BCL100 3.1 10.1 1.0 C4A e:BCL100 3.1 10.1 1.0 C1D e:BCL100 3.1 10.1 1.0 C4C e:BCL100 3.1 10.1 1.0 C1A e:BCL100 3.2 10.1 1.0 CHC e:BCL100 3.4 10.1 1.0 CHB e:BCL100 3.4 10.1 1.0 CD2 e:HIS32 3.4 6.3 1.0 CHA e:BCL100 3.4 10.1 1.0 CHD e:BCL100 3.5 10.1 1.0 CE1 e:HIS32 3.8 6.3 1.0 C3D e:BCL100 4.2 10.1 1.0 CBB D:BCL202 4.2 15.6 1.0 C2B e:BCL100 4.2 10.1 1.0 C2D e:BCL100 4.3 10.1 1.0 C3B e:BCL100 4.3 10.1 1.0 C2C e:BCL100 4.4 10.1 1.0 C3C e:BCL100 4.4 10.1 1.0 C3A e:BCL100 4.4 10.1 1.0 C2A e:BCL100 4.5 10.1 1.0 CMB D:BCL202 4.5 15.6 1.0 CMD E:BCL202 4.5 10.8 1.0 CG e:HIS32 4.7 6.3 1.0 ND1 e:HIS32 4.8 6.3 1.0 CBD e:BCL100 4.9 10.1 1.0

Magnesium binding site 10 out of 34 in the Structure of Rc-LH1-Pufx From Rhodobacter Veldkampii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of Rc-LH1-Pufx From Rhodobacter Veldkampii within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg202 b:15.6 occ:1.00 MG D:BCL202 0.0 15.6 1.0 ND D:BCL202 2.0 15.6 1.0 NB D:BCL202 2.1 15.6 1.0 NC D:BCL202 2.1 15.6 1.0 NA D:BCL202 2.2 15.6 1.0 NE2 D:HIS38 2.7 9.8 1.0 C4D D:BCL202 3.0 15.6 1.0 C4B D:BCL202 3.1 15.6 1.0 C1B D:BCL202 3.1 15.6 1.0 C1C D:BCL202 3.1 15.6 1.0 C4A D:BCL202 3.1 15.6 1.0 C4C D:BCL202 3.1 15.6 1.0 C1D D:BCL202 3.1 15.6 1.0 C1A D:BCL202 3.2 15.6 1.0 CD2 D:HIS38 3.3 9.8 1.0 CHC D:BCL202 3.4 15.6 1.0 CHB D:BCL202 3.4 15.6 1.0 CHA D:BCL202 3.4 15.6 1.0 CHD D:BCL202 3.5 15.6 1.0 CE1 D:HIS38 3.8 9.8 1.0 CBB e:BCL100 4.1 10.1 1.0 C3D D:BCL202 4.2 15.6 1.0 CMB e:BCL100 4.2 10.1 1.0 C2B D:BCL202 4.3 15.6 1.0 C2D D:BCL202 4.3 15.6 1.0 C3B D:BCL202 4.3 15.6 1.0 C2C D:BCL202 4.4 15.6 1.0 C3C D:BCL202 4.4 15.6 1.0 C2A D:BCL202 4.4 15.6 1.0 C3A D:BCL202 4.4 15.6 1.0 CG D:HIS38 4.6 9.8 1.0 C10 D:BCL202 4.6 15.6 1.0 CAB e:BCL100 4.7 10.1 1.0 C2B e:BCL100 4.7 10.1 1.0 ND1 D:HIS38 4.8 9.8 1.0 C3B e:BCL100 4.9 10.1 1.0 CBD D:BCL202 4.9 15.6 1.0

L.Bracun, A.Yamagata, B.M.Christianson, T.Terada, D.P.Canniffe, M.Shirouzu, L.N.Liu. Cryo-Em Structure of the Photosynthetic Rc-LH1-Pufx Supercomplex at 2.8-Angstrom Resolution. Sci Adv V. 7 2021.
ISSN: ESSN 2375-2548
PubMed: 34134992
DOI: 10.1126/SCIADV.ABF8864