Magnesium in PDB 5yq7: Cryo-Em Structure of the Rc-Lh Core Complex From Roseiflexus Castenholzii

The structure of Cryo-Em Structure of the Rc-Lh Core Complex From Roseiflexus Castenholzii also contains other interesting chemical elements:

Iron

(Fe)

5 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 48;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of the Rc-Lh Core Complex From Roseiflexus Castenholzii (pdb code 5yq7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 48 binding sites of Magnesium where determined in the Cryo-Em Structure of the Rc-Lh Core Complex From Roseiflexus Castenholzii, PDB code: 5yq7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 48 in the Cryo-Em Structure of the Rc-Lh Core Complex From Roseiflexus Castenholzii


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 Rc-Lh Core Complex From Roseiflexus Castenholzii within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg101 b:0.5 occ:1.00 MG E:BCL101 0.0 0.5 1.0 ND E:BCL101 2.0 0.5 1.0 NB E:BCL101 2.1 0.5 1.0 NC E:BCL101 2.1 0.5 1.0 NA E:BCL101 2.2 0.5 1.0 NE2 E:HIS44 2.3 0.8 1.0 C4D E:BCL101 3.0 0.5 1.0 C4B E:BCL101 3.0 0.5 1.0 CD2 E:HIS44 3.1 0.8 1.0 C1B E:BCL101 3.1 0.5 1.0 C1C E:BCL101 3.1 0.5 1.0 C4A E:BCL101 3.1 0.5 1.0 C1D E:BCL101 3.1 0.5 1.0 C4C E:BCL101 3.1 0.5 1.0 C1A E:BCL101 3.2 0.5 1.0 CE1 E:HIS44 3.4 0.8 1.0 CHC E:BCL101 3.4 0.5 1.0 CHB E:BCL101 3.4 0.5 1.0 CHA E:BCL101 3.4 0.5 1.0 CHD E:BCL101 3.5 0.5 1.0 C3D E:BCL101 4.2 0.5 1.0 C2B E:BCL101 4.2 0.5 1.0 C3B E:BCL101 4.2 0.5 1.0 CG E:HIS44 4.3 0.8 1.0 C2D E:BCL101 4.3 0.5 1.0 ND1 E:HIS44 4.4 0.8 1.0 C2C E:BCL101 4.4 0.5 1.0 C3A E:BCL101 4.4 0.5 1.0 C3C E:BCL101 4.4 0.5 1.0 C2A E:BCL101 4.5 0.5 1.0 CMD D:BCL101 4.7 0.9 1.0 CBD E:BCL101 4.9 0.5 1.0

Magnesium binding site 2 out of 48 in the Cryo-Em Structure of the Rc-Lh Core Complex From Roseiflexus Castenholzii


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 Rc-Lh Core Complex From Roseiflexus Castenholzii within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg102 b:0.2 occ:1.00 MG E:BCL102 0.0 0.2 1.0 ND E:BCL102 2.0 0.2 1.0 NB E:BCL102 2.1 0.2 1.0 NC E:BCL102 2.1 0.2 1.0 NA E:BCL102 2.2 0.2 1.0 NE2 E:HIS26 2.3 0.4 1.0 CE1 E:HIS26 2.9 0.4 1.0 C4D E:BCL102 3.0 0.2 1.0 C4B E:BCL102 3.1 0.2 1.0 C1B E:BCL102 3.1 0.2 1.0 C1C E:BCL102 3.1 0.2 1.0 C1D E:BCL102 3.1 0.2 1.0 C4A E:BCL102 3.1 0.2 1.0 C4C E:BCL102 3.2 0.2 1.0 C1A E:BCL102 3.2 0.2 1.0 CHC E:BCL102 3.4 0.2 1.0 CHB E:BCL102 3.4 0.2 1.0 CHA E:BCL102 3.4 0.2 1.0 CHD E:BCL102 3.5 0.2 1.0 CD2 E:HIS26 3.5 0.4 1.0 ND1 E:HIS26 4.1 0.4 1.0 C3D E:BCL102 4.2 0.2 1.0 C2B E:BCL102 4.3 0.2 1.0 C2D E:BCL102 4.3 0.2 1.0 C3B E:BCL102 4.3 0.2 1.0 C2C E:BCL102 4.4 0.2 1.0 C3C E:BCL102 4.4 0.2 1.0 C3A E:BCL102 4.5 0.2 1.0 CG E:HIS26 4.5 0.4 1.0 C2A E:BCL102 4.5 0.2 1.0 CBD E:BCL102 4.9 0.2 1.0 OAA 9:KGD101 5.0 0.2 1.0 CBA E:BCL102 5.0 0.2 1.0

Magnesium binding site 3 out of 48 in the Cryo-Em Structure of the Rc-Lh Core Complex From Roseiflexus Castenholzii


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 Rc-Lh Core Complex From Roseiflexus Castenholzii within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:0.1 occ:1.00 MG B:BCL101 0.0 0.1 1.0 CE1 B:HIS44 1.9 0.7 1.0 ND B:BCL101 2.0 0.1 1.0 NB B:BCL101 2.1 0.1 1.0 NC B:BCL101 2.1 0.1 1.0 NA B:BCL101 2.2 0.1 1.0 NE2 B:HIS44 2.3 0.7 1.0 C4D B:BCL101 3.0 0.1 1.0 C4B B:BCL101 3.0 0.1 1.0 C1B B:BCL101 3.1 0.1 1.0 C1C B:BCL101 3.1 0.1 1.0 C1D B:BCL101 3.1 0.1 1.0 C4A B:BCL101 3.1 0.1 1.0 C4C B:BCL101 3.2 0.1 1.0 ND1 B:HIS44 3.2 0.7 1.0 C1A B:BCL101 3.2 0.1 1.0 CHC B:BCL101 3.4 0.1 1.0 CHB B:BCL101 3.4 0.1 1.0 CHA B:BCL101 3.4 0.1 1.0 CHD B:BCL101 3.5 0.1 1.0 CD2 B:HIS44 3.6 0.7 1.0 CG B:HIS44 4.0 0.7 1.0 C3D B:BCL101 4.2 0.1 1.0 C3B B:BCL101 4.2 0.1 1.0 C2B B:BCL101 4.2 0.1 1.0 C2D B:BCL101 4.3 0.1 1.0 C2C B:BCL101 4.4 0.1 1.0 C3A B:BCL101 4.4 0.1 1.0 C3C B:BCL101 4.4 0.1 1.0 C2A B:BCL101 4.5 0.1 1.0 CMB 9:BCL103 4.6 0.2 1.0 CBD B:BCL101 4.9 0.1 1.0 CMD A:BCL102 5.0 0.1 1.0

Magnesium binding site 4 out of 48 in the Cryo-Em Structure of the Rc-Lh Core Complex From Roseiflexus Castenholzii


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 Rc-Lh Core Complex From Roseiflexus Castenholzii within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:0.2 occ:1.00 MG B:BCL102 0.0 0.2 1.0 ND B:BCL102 2.0 0.2 1.0 NB B:BCL102 2.1 0.2 1.0 NC B:BCL102 2.1 0.2 1.0 NA B:BCL102 2.2 0.2 1.0 NE2 B:HIS26 2.3 0.8 1.0 CE1 B:HIS26 2.6 0.8 1.0 C4D B:BCL102 3.0 0.2 1.0 C4B B:BCL102 3.1 0.2 1.0 C1B B:BCL102 3.1 0.2 1.0 C1C B:BCL102 3.1 0.2 1.0 C4A B:BCL102 3.1 0.2 1.0 C1D B:BCL102 3.1 0.2 1.0 C4C B:BCL102 3.2 0.2 1.0 C1A B:BCL102 3.2 0.2 1.0 CHC B:BCL102 3.4 0.2 1.0 CHB B:BCL102 3.4 0.2 1.0 CHA B:BCL102 3.4 0.2 1.0 CHD B:BCL102 3.5 0.2 1.0 CD2 B:HIS26 3.5 0.8 1.0 ND1 B:HIS26 3.8 0.8 1.0 C3D B:BCL102 4.2 0.2 1.0 C2B B:BCL102 4.3 0.2 1.0 CG B:HIS26 4.3 0.8 1.0 C3B B:BCL102 4.3 0.2 1.0 C2D B:BCL102 4.3 0.2 1.0 C2C B:BCL102 4.4 0.2 1.0 C3C B:BCL102 4.4 0.2 1.0 C3A B:BCL102 4.4 0.2 1.0 C2A B:BCL102 4.5 0.2 1.0 CBD B:BCL102 4.9 0.2 1.0 CBA B:BCL102 5.0 0.2 1.0

Magnesium binding site 5 out of 48 in the Cryo-Em Structure of the Rc-Lh Core Complex From Roseiflexus Castenholzii


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 Rc-Lh Core Complex From Roseiflexus Castenholzii within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg101 b:0.9 occ:1.00 MG 0:BCL101 0.0 0.9 1.0 ND 0:BCL101 2.0 0.9 1.0 NB 0:BCL101 2.1 0.9 1.0 NC 0:BCL101 2.1 0.9 1.0 NA 0:BCL101 2.2 0.9 1.0 NE2 0:HIS44 2.3 0.4 1.0 CD2 0:HIS44 3.0 0.4 1.0 C4D 0:BCL101 3.0 0.9 1.0 C4B 0:BCL101 3.0 0.9 1.0 C1B 0:BCL101 3.1 0.9 1.0 C1C 0:BCL101 3.1 0.9 1.0 C4A 0:BCL101 3.1 0.9 1.0 C1D 0:BCL101 3.1 0.9 1.0 C4C 0:BCL101 3.2 0.9 1.0 C1A 0:BCL101 3.2 0.9 1.0 CHC 0:BCL101 3.4 0.9 1.0 CHB 0:BCL101 3.4 0.9 1.0 CHA 0:BCL101 3.4 0.9 1.0 CE1 0:HIS44 3.4 0.4 1.0 CHD 0:BCL101 3.5 0.9 1.0 CMB 7:BCL101 3.9 0.1 1.0 C3D 0:BCL101 4.2 0.9 1.0 C3B 0:BCL101 4.2 0.9 1.0 C2B 0:BCL101 4.2 0.9 1.0 CG 0:HIS44 4.2 0.4 1.0 C2D 0:BCL101 4.3 0.9 1.0 C2C 0:BCL101 4.4 0.9 1.0 ND1 0:HIS44 4.4 0.4 1.0 C3C 0:BCL101 4.4 0.9 1.0 C3A 0:BCL101 4.4 0.9 1.0 C2A 0:BCL101 4.5 0.9 1.0 CBB 7:BCL101 4.6 0.1 1.0 CMD 9:BCL103 4.7 0.2 1.0 C2B 7:BCL101 4.9 0.1 1.0 CBD 0:BCL101 4.9 0.9 1.0

Magnesium binding site 6 out of 48 in the Cryo-Em Structure of the Rc-Lh Core Complex From Roseiflexus Castenholzii


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 Rc-Lh Core Complex From Roseiflexus Castenholzii within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg102 b:0.5 occ:1.00 MG 0:BCL102 0.0 0.5 1.0 ND 0:BCL102 2.0 0.5 1.0 NB 0:BCL102 2.1 0.5 1.0 NC 0:BCL102 2.1 0.5 1.0 NA 0:BCL102 2.2 0.5 1.0 NE2 0:HIS26 2.3 0.5 1.0 C4D 0:BCL102 3.0 0.5 1.0 C4B 0:BCL102 3.1 0.5 1.0 C1B 0:BCL102 3.1 0.5 1.0 C1C 0:BCL102 3.1 0.5 1.0 C1D 0:BCL102 3.1 0.5 1.0 C4A 0:BCL102 3.1 0.5 1.0 CD2 0:HIS26 3.1 0.5 1.0 C4C 0:BCL102 3.2 0.5 1.0 C1A 0:BCL102 3.2 0.5 1.0 CE1 0:HIS26 3.3 0.5 1.0 CHC 0:BCL102 3.4 0.5 1.0 CHB 0:BCL102 3.4 0.5 1.0 CHA 0:BCL102 3.4 0.5 1.0 CHD 0:BCL102 3.5 0.5 1.0 C3D 0:BCL102 4.2 0.5 1.0 C2B 0:BCL102 4.3 0.5 1.0 C2D 0:BCL102 4.3 0.5 1.0 C3B 0:BCL102 4.3 0.5 1.0 CG 0:HIS26 4.3 0.5 1.0 ND1 0:HIS26 4.4 0.5 1.0 C2C 0:BCL102 4.4 0.5 1.0 C3A 0:BCL102 4.4 0.5 1.0 C3C 0:BCL102 4.5 0.5 1.0 C2A 0:BCL102 4.5 0.5 1.0 CBD 0:BCL102 4.9 0.5 1.0

Magnesium binding site 7 out of 48 in the Cryo-Em Structure of the Rc-Lh Core Complex From Roseiflexus Castenholzii


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 Rc-Lh Core Complex From Roseiflexus Castenholzii within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg1001 b:98.9 occ:1.00 MG L:BCL1001 0.0 98.9 1.0 CE1 L:HIS192 1.5 95.8 1.0 ND L:BCL1001 2.0 98.9 1.0 NB L:BCL1001 2.1 98.9 1.0 NC L:BCL1001 2.1 98.9 1.0 NA L:BCL1001 2.2 98.9 1.0 NE2 L:HIS192 2.4 95.8 1.0 ND1 L:HIS192 2.7 95.8 1.0 C4D L:BCL1001 3.0 98.9 1.0 C4B L:BCL1001 3.1 98.9 1.0 C1B L:BCL1001 3.1 98.9 1.0 C1C L:BCL1001 3.1 98.9 1.0 C1D L:BCL1001 3.1 98.9 1.0 C4A L:BCL1001 3.1 98.9 1.0 C4C L:BCL1001 3.1 98.9 1.0 C1A L:BCL1001 3.2 98.9 1.0 CHC L:BCL1001 3.4 98.9 1.0 CHB L:BCL1001 3.4 98.9 1.0 CHA L:BCL1001 3.4 98.9 1.0 CHD L:BCL1001 3.5 98.9 1.0 CD2 L:HIS192 3.6 95.8 1.0 CG L:HIS192 3.7 95.8 1.0 C3D L:BCL1001 4.2 98.9 1.0 C2B L:BCL1001 4.2 98.9 1.0 O1A L:BCL1001 4.3 98.9 1.0 C3B L:BCL1001 4.3 98.9 1.0 C2D L:BCL1001 4.3 98.9 1.0 C3C L:BCL1001 4.4 98.9 1.0 C2C L:BCL1001 4.4 98.9 1.0 C3A L:BCL1001 4.5 98.9 1.0 C2A L:BCL1001 4.5 98.9 1.0 CBB L:BPH1003 4.8 0.0 1.0 CBD L:BCL1001 4.9 98.9 1.0

Magnesium binding site 8 out of 48 in the Cryo-Em Structure of the Rc-Lh Core Complex From Roseiflexus Castenholzii


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 Rc-Lh Core Complex From Roseiflexus Castenholzii within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg1002 b:95.2 occ:1.00 MG L:BCL1002 0.0 95.2 1.0 ND L:BCL1002 2.0 95.2 1.0 NB L:BCL1002 2.1 95.2 1.0 NC L:BCL1002 2.1 95.2 1.0 NA L:BCL1002 2.2 95.2 1.0 NE2 L:HIS212 2.3 97.5 1.0 C4D L:BCL1002 3.0 95.2 1.0 C4B L:BCL1002 3.1 95.2 1.0 C1B L:BCL1002 3.1 95.2 1.0 C1C L:BCL1002 3.1 95.2 1.0 C1D L:BCL1002 3.1 95.2 1.0 C4A L:BCL1002 3.1 95.2 1.0 CE1 L:HIS212 3.2 97.5 1.0 C4C L:BCL1002 3.2 95.2 1.0 C1A L:BCL1002 3.2 95.2 1.0 CHC L:BCL1002 3.4 95.2 1.0 CHB L:BCL1002 3.4 95.2 1.0 CD2 L:HIS212 3.4 97.5 1.0 CHA L:BCL1002 3.4 95.2 1.0 CHD L:BCL1002 3.5 95.2 1.0 CBB M:BCL702 3.7 92.1 1.0 C3D L:BCL1002 4.2 95.2 1.0 C2D L:BCL1002 4.3 95.2 1.0 C2B L:BCL1002 4.3 95.2 1.0 C3B L:BCL1002 4.3 95.2 1.0 ND1 L:HIS212 4.3 97.5 1.0 C2C L:BCL1002 4.4 95.2 1.0 C3A L:BCL1002 4.5 95.2 1.0 C3C L:BCL1002 4.5 95.2 1.0 C2A L:BCL1002 4.5 95.2 1.0 CG L:HIS212 4.5 97.5 1.0 CAB M:BCL702 4.7 92.1 1.0 CE2 L:PHE206 4.7 89.5 1.0 CBD L:BCL1002 4.9 95.2 1.0

Magnesium binding site 9 out of 48 in the Cryo-Em Structure of the Rc-Lh Core Complex From Roseiflexus Castenholzii


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 Rc-Lh Core Complex From Roseiflexus Castenholzii within 5.0Å range: probe atom residue distance (Å) B Occ 8:Mg101 b:0.1 occ:1.00 MG 8:BCL101 0.0 0.1 1.0 ND 8:BCL101 2.0 0.1 1.0 NB 8:BCL101 2.1 0.1 1.0 NC 8:BCL101 2.1 0.1 1.0 NA 8:BCL101 2.2 0.1 1.0 NE2 8:HIS44 2.3 0.1 1.0 CD2 8:HIS44 2.8 0.1 1.0 C4D 8:BCL101 3.0 0.1 1.0 C4B 8:BCL101 3.0 0.1 1.0 C1B 8:BCL101 3.1 0.1 1.0 C1C 8:BCL101 3.1 0.1 1.0 C4A 8:BCL101 3.1 0.1 1.0 C1D 8:BCL101 3.1 0.1 1.0 C4C 8:BCL101 3.2 0.1 1.0 C1A 8:BCL101 3.2 0.1 1.0 CHC 8:BCL101 3.4 0.1 1.0 CHB 8:BCL101 3.4 0.1 1.0 CHA 8:BCL101 3.4 0.1 1.0 CHD 8:BCL101 3.5 0.1 1.0 CE1 8:HIS44 3.5 0.1 1.0 CG 8:HIS44 4.1 0.1 1.0 C3D 8:BCL101 4.2 0.1 1.0 C3B 8:BCL101 4.2 0.1 1.0 C2B 8:BCL101 4.2 0.1 1.0 C2D 8:BCL101 4.3 0.1 1.0 ND1 8:HIS44 4.4 0.1 1.0 CMB 5:BCL102 4.4 0.5 1.0 C2C 8:BCL101 4.4 0.1 1.0 C3A 8:BCL101 4.4 0.1 1.0 C3C 8:BCL101 4.5 0.1 1.0 C2A 8:BCL101 4.5 0.1 1.0 CBD 8:BCL101 4.9 0.1 1.0

Magnesium binding site 10 out of 48 in the Cryo-Em Structure of the Rc-Lh Core Complex From Roseiflexus Castenholzii


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 Rc-Lh Core Complex From Roseiflexus Castenholzii within 5.0Å range: probe atom residue distance (Å) B Occ 8:Mg102 b:0.3 occ:1.00 MG 8:BCL102 0.0 0.3 1.0 ND 8:BCL102 2.0 0.3 1.0 NB 8:BCL102 2.1 0.3 1.0 NC 8:BCL102 2.1 0.3 1.0 NA 8:BCL102 2.2 0.3 1.0 NE2 8:HIS26 2.3 0.5 1.0 CE1 8:HIS26 3.0 0.5 1.0 C4D 8:BCL102 3.0 0.3 1.0 C4B 8:BCL102 3.1 0.3 1.0 C1B 8:BCL102 3.1 0.3 1.0 C1C 8:BCL102 3.1 0.3 1.0 C1D 8:BCL102 3.1 0.3 1.0 C4A 8:BCL102 3.1 0.3 1.0 C4C 8:BCL102 3.2 0.3 1.0 C1A 8:BCL102 3.2 0.3 1.0 CHC 8:BCL102 3.4 0.3 1.0 CHB 8:BCL102 3.4 0.3 1.0 CHA 8:BCL102 3.4 0.3 1.0 CD2 8:HIS26 3.4 0.5 1.0 CHD 8:BCL102 3.5 0.3 1.0 ND1 8:HIS26 4.1 0.5 1.0 C3D 8:BCL102 4.2 0.3 1.0 C2D 8:BCL102 4.3 0.3 1.0 C2B 8:BCL102 4.3 0.3 1.0 C3B 8:BCL102 4.3 0.3 1.0 CG 8:HIS26 4.4 0.5 1.0 C2C 8:BCL102 4.4 0.3 1.0 C3C 8:BCL102 4.4 0.3 1.0 C3A 8:BCL102 4.4 0.3 1.0 C2A 8:BCL102 4.5 0.3 1.0 OAA 3:KGD101 4.6 1.0 1.0 CBD 8:BCL102 4.9 0.3 1.0

Y.Y.Xin, Y.Shi, T.X.Niu, Q.Q.Wang, W.Q.Niu, X.J.Huang, W.Ding, L.Yang, R.E.Blankenship, X.L.Xu, F.Sun. Cryo-Em Structure of the Rc-Lh Core Complex From An Early Branching Photosynthetic Prokaryote. Nat Commun V. 9 1568 2018.
ISSN: ESSN 2041-1723
PubMed: 29674684
DOI: 10.1038/S41467-018-03881-X