Magnesium in PDB 8zk2: Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum

The structure of Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum 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 - 50; Page 6, Binding sites: 51 - 55;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum (pdb code 8zk2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 55 binding sites of Magnesium where determined in the Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum, PDB code: 8zk2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 55 in the Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum


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 Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg505 b:28.1 occ:1.00 O C:GLY271 2.2 21.2 1.0 OD1 C:ASP65 2.3 34.2 1.0 CG C:ASP65 3.1 34.2 1.0 OD2 C:ASP65 3.3 34.2 1.0 OE1 C:GLU63 3.3 27.4 1.0 C C:GLY271 3.4 21.2 1.0 N C:VAL272 4.2 21.6 1.0 CA C:VAL272 4.3 21.6 1.0 CA C:GLY271 4.3 21.2 1.0 CD C:GLU63 4.4 27.4 1.0 O C:VAL64 4.5 29.7 1.0 CB C:ASP65 4.5 34.2 1.0 CG1 C:VAL272 4.9 21.6 1.0 CG C:GLU63 5.0 27.4 1.0

Magnesium binding site 2 out of 55 in the Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum


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 Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg506 b:24.5 occ:1.00 OD2 C:ASP214 2.1 30.2 1.0 OD1 C:ASP194 2.1 31.5 1.0 O C:ASN222 2.2 25.9 1.0 OD1 C:ASP223 2.5 28.1 1.0 CG C:ASP214 3.2 30.2 1.0 CG C:ASP194 3.3 31.5 1.0 C C:ASN222 3.4 25.9 1.0 CB C:ASP193 3.6 34.6 1.0 CB C:ASP214 3.7 30.2 1.0 CG C:ASP223 3.8 28.1 1.0 CA C:ASP223 4.0 28.1 1.0 N C:ASP194 4.0 31.5 1.0 N C:ASP223 4.1 28.1 1.0 CB C:ASP194 4.2 31.5 1.0 OD1 C:ASP214 4.2 30.2 1.0 OD2 C:ASP194 4.2 31.5 1.0 OD2 C:ASP193 4.3 34.6 1.0 C C:ASP193 4.4 34.6 1.0 CB C:ASN222 4.4 25.9 1.0 CA C:ASP193 4.4 34.6 1.0 CG C:ASP193 4.4 34.6 1.0 CA C:ASN222 4.5 25.9 1.0 CB C:ASP223 4.5 28.1 1.0 OD2 C:ASP223 4.7 28.1 1.0 CA C:ASP194 4.7 31.5 1.0 N C:ASP193 4.8 34.6 1.0 CG C:ASN222 4.8 25.9 1.0 OG C:SER212 4.8 27.9 1.0 OD1 C:ASN222 4.9 25.9 1.0

Magnesium binding site 3 out of 55 in the Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum


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 Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg507 b:28.7 occ:1.00 O C:ASP194 2.2 31.5 1.0 OD1 C:ASP196 2.3 33.1 1.0 OD1 C:ASN192 2.4 37.4 1.0 OD2 C:ASP223 2.5 28.1 1.0 C C:ASP194 3.4 31.5 1.0 CG C:ASP196 3.4 33.1 1.0 CG C:ASN192 3.6 37.4 1.0 CG C:ASP223 3.6 28.1 1.0 N C:ASP196 4.0 33.1 1.0 OD2 C:ASP196 4.0 33.1 1.0 CB C:ASP194 4.1 31.5 1.0 CA C:ASP194 4.1 31.5 1.0 C C:ALA195 4.2 32.5 1.0 ND2 C:ASN192 4.2 37.4 1.0 N C:ASP194 4.3 31.5 1.0 CA C:ASP196 4.3 33.1 1.0 OD1 C:ASP223 4.3 28.1 1.0 N C:ALA195 4.4 32.5 1.0 CB C:ASP196 4.5 33.1 1.0 CB C:ASP223 4.5 28.1 1.0 CA C:GLY207 4.5 24.1 1.0 O C:ALA195 4.5 32.5 1.0 OD1 C:ASN222 4.6 25.9 1.0 CA C:ALA195 4.6 32.5 1.0 CA C:ASN192 4.7 37.4 1.0 CB C:ASN192 4.7 37.4 1.0 C C:ASN192 4.8 37.4 1.0

Magnesium binding site 4 out of 55 in the Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum


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 Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg401 b:32.8 occ:1.00 MG L:BCL401 0.0 32.8 1.0 NA L:BCL401 2.0 32.8 1.0 NC L:BCL401 2.0 32.8 1.0 ND L:BCL401 2.0 32.8 1.0 NB L:BCL401 2.0 32.8 1.0 NE2 L:HIS155 2.6 24.2 1.0 C4D L:BCL401 2.9 32.8 1.0 C1A L:BCL401 2.9 32.8 1.0 C4A L:BCL401 3.0 32.8 1.0 C4C L:BCL401 3.0 32.8 1.0 C1B L:BCL401 3.0 32.8 1.0 C1C L:BCL401 3.0 32.8 1.0 C4B L:BCL401 3.1 32.8 1.0 C1D L:BCL401 3.2 32.8 1.0 CHA L:BCL401 3.3 32.8 1.0 CHB L:BCL401 3.3 32.8 1.0 CHC L:BCL401 3.4 32.8 1.0 CE1 L:HIS155 3.4 24.2 1.0 CHD L:BCL401 3.5 32.8 1.0 CD2 L:HIS155 3.6 24.2 1.0 OBB L:BPH403 4.0 32.8 1.0 C3D L:BCL401 4.1 32.8 1.0 C2A L:BCL401 4.2 32.8 1.0 C3A L:BCL401 4.3 32.8 1.0 CE2 M:TYR211 4.3 25.9 1.0 C3C L:BCL401 4.3 32.8 1.0 C2C L:BCL401 4.3 32.8 1.0 C2B L:BCL401 4.3 32.8 1.0 C3B L:BCL401 4.3 32.8 1.0 C2D L:BCL401 4.4 32.8 1.0 CBC L:BCL401 4.5 32.8 1.0 CBA L:BCL401 4.6 32.8 1.0 ND1 L:HIS155 4.6 24.2 1.0 CG L:HIS155 4.7 24.2 1.0 CBD L:BCL401 4.8 32.8 1.0 CD2 M:TYR211 4.8 25.9 1.0 CAC L:BCL401 5.0 32.8 1.0 CAA L:BCL401 5.0 32.8 1.0

Magnesium binding site 5 out of 55 in the Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum


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 Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg402 b:32.8 occ:1.00 MG L:BCL402 0.0 32.8 1.0 NA L:BCL402 2.0 32.8 1.0 NC L:BCL402 2.0 32.8 1.0 ND L:BCL402 2.0 32.8 1.0 NB L:BCL402 2.0 32.8 1.0 NE2 L:HIS175 2.3 24.0 1.0 C4D L:BCL402 2.9 32.8 1.0 C4A L:BCL402 2.9 32.8 1.0 C1A L:BCL402 3.0 32.8 1.0 C4C L:BCL402 3.0 32.8 1.0 C1C L:BCL402 3.0 32.8 1.0 C1B L:BCL402 3.0 32.8 1.0 CE1 L:HIS175 3.0 24.0 1.0 C4B L:BCL402 3.1 32.8 1.0 C1D L:BCL402 3.1 32.8 1.0 CHB L:BCL402 3.3 32.8 1.0 CHC L:BCL402 3.4 32.8 1.0 CHA L:BCL402 3.4 32.8 1.0 CBB M:BCL403 3.5 32.8 1.0 CD2 L:HIS175 3.5 24.0 1.0 CAB M:BCL403 3.5 32.8 1.0 CHD L:BCL402 3.5 32.8 1.0 OBB M:BCL403 3.6 32.8 1.0 C3D L:BCL402 4.1 32.8 1.0 C3B M:BCL403 4.1 32.8 1.0 C3A L:BCL402 4.2 32.8 1.0 ND1 L:HIS175 4.3 24.0 1.0 C2A L:BCL402 4.3 32.8 1.0 C2C L:BCL402 4.3 32.8 1.0 C3C L:BCL402 4.3 32.8 1.0 C2B L:BCL402 4.3 32.8 1.0 C2D L:BCL402 4.4 32.8 1.0 C3B L:BCL402 4.4 32.8 1.0 CG L:HIS175 4.5 24.0 1.0 CMA L:BCL402 4.7 32.8 1.0 C4B M:BCL403 4.8 32.8 1.0 C2B M:BCL403 4.9 32.8 1.0 CBD L:BCL402 4.9 32.8 1.0 CD2 L:PHE169 5.0 23.1 1.0

Magnesium binding site 6 out of 55 in the Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum


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 Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg402 b:32.8 occ:1.00 MG M:BCL402 0.0 32.8 1.0 NA M:BCL402 2.0 32.8 1.0 NC M:BCL402 2.0 32.8 1.0 ND M:BCL402 2.0 32.8 1.0 NB M:BCL402 2.0 32.8 1.0 NE2 M:HIS183 2.6 23.6 1.0 C4D M:BCL402 2.9 32.8 1.0 C1A M:BCL402 2.9 32.8 1.0 C4A M:BCL402 3.0 32.8 1.0 C4C M:BCL402 3.0 32.8 1.0 C1C M:BCL402 3.0 32.8 1.0 C1B M:BCL402 3.0 32.8 1.0 C4B M:BCL402 3.1 32.8 1.0 C1D M:BCL402 3.2 32.8 1.0 CD2 M:HIS183 3.2 23.6 1.0 CHB M:BCL402 3.3 32.8 1.0 CHA M:BCL402 3.3 32.8 1.0 CHC M:BCL402 3.4 32.8 1.0 CHD M:BCL402 3.5 32.8 1.0 CE1 M:HIS183 3.8 23.6 1.0 C3D M:BCL402 4.1 32.8 1.0 OBB M:BPH404 4.2 32.8 1.0 C2A M:BCL402 4.2 32.8 1.0 C3A M:BCL402 4.3 32.8 1.0 C2C M:BCL402 4.3 32.8 1.0 C3C M:BCL402 4.3 32.8 1.0 C2B M:BCL402 4.4 32.8 1.0 C2D M:BCL402 4.4 32.8 1.0 C3B M:BCL402 4.4 32.8 1.0 CG M:HIS183 4.4 23.6 1.0 ND1 M:HIS183 4.7 23.6 1.0 CBD M:BCL402 4.8 32.8 1.0 CAA M:BCL402 4.9 32.8 1.0 CMA M:BCL402 5.0 32.8 1.0 CE2 L:PHE183 5.0 25.7 1.0

Magnesium binding site 7 out of 55 in the Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum


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 Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg403 b:32.8 occ:1.00 MG M:BCL403 0.0 32.8 1.0 NA M:BCL403 2.0 32.8 1.0 NC M:BCL403 2.0 32.8 1.0 ND M:BCL403 2.0 32.8 1.0 NB M:BCL403 2.0 32.8 1.0 NE2 M:HIS203 2.5 25.8 1.0 C4D M:BCL403 2.9 32.8 1.0 C1A M:BCL403 2.9 32.8 1.0 C4A M:BCL403 2.9 32.8 1.0 C1C M:BCL403 3.0 32.8 1.0 C1B M:BCL403 3.0 32.8 1.0 C4C M:BCL403 3.0 32.8 1.0 C4B M:BCL403 3.1 32.8 1.0 C1D M:BCL403 3.2 32.8 1.0 CE1 M:HIS203 3.2 25.8 1.0 CBB L:BCL402 3.2 32.8 1.0 CHB M:BCL403 3.3 32.8 1.0 CAB L:BCL402 3.3 32.8 1.0 CHA M:BCL403 3.3 32.8 1.0 CHC M:BCL403 3.4 32.8 1.0 OBB L:BCL402 3.5 32.8 1.0 CHD M:BCL403 3.5 32.8 1.0 CD2 M:HIS203 3.6 25.8 1.0 C3B L:BCL402 4.0 32.8 1.0 C3D M:BCL403 4.1 32.8 1.0 C2A M:BCL403 4.2 32.8 1.0 C3A M:BCL403 4.2 32.8 1.0 C2C M:BCL403 4.3 32.8 1.0 C3C M:BCL403 4.3 32.8 1.0 C2B M:BCL403 4.3 32.8 1.0 C3B M:BCL403 4.4 32.8 1.0 C2D M:BCL403 4.4 32.8 1.0 ND1 M:HIS203 4.4 25.8 1.0 CG M:HIS203 4.7 25.8 1.0 CBD M:BCL403 4.7 32.8 1.0 C4B L:BCL402 4.7 32.8 1.0 C2B L:BCL402 4.8 32.8 1.0 CD1 M:ILE207 4.9 26.3 1.0 CMC M:BCL403 4.9 32.8 1.0

Magnesium binding site 8 out of 55 in the Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum


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 Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg307 b:31.6 occ:1.00 OD1 H:ASP4 2.6 34.3 1.0 O13 R:PGV104 3.3 36.2 1.0 O H:MET1 3.4 41.2 1.0 O H:ILE2 3.6 37.7 1.0 CG H:ASP4 3.7 34.3 1.0 C H:MET1 3.8 41.2 1.0 C H:ILE2 4.1 37.7 1.0 O R:GLY38 4.1 30.4 1.0 O H:ASP4 4.1 34.3 1.0 OD2 H:ASP4 4.2 34.3 1.0 OD2 R:ASP40 4.2 30.2 1.0 N H:ILE2 4.2 37.7 1.0 CA H:ILE2 4.2 37.7 1.0 O11 R:PGV104 4.3 36.2 1.0 CB H:MET1 4.4 41.2 1.0 OD1 R:ASP40 4.4 30.2 1.0 P R:PGV104 4.4 36.2 1.0 CG R:ASP40 4.6 30.2 1.0 N H:ASP4 4.6 34.3 1.0 CA H:MET1 4.6 41.2 1.0 CB H:ASP4 4.9 34.3 1.0 C03 R:PGV104 4.9 36.2 1.0

Magnesium binding site 9 out of 55 in the Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum


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 Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:32.8 occ:1.00 MG B:BCL101 0.0 32.8 1.0 NA B:BCL101 2.0 32.8 1.0 NC B:BCL101 2.0 32.8 1.0 ND B:BCL101 2.0 32.8 1.0 NB B:BCL101 2.0 32.8 1.0 NE2 B:HIS40 2.2 31.5 1.0 C4D B:BCL101 2.9 32.8 1.0 CE1 B:HIS40 2.9 31.5 1.0 C4A B:BCL101 3.0 32.8 1.0 C1A B:BCL101 3.0 32.8 1.0 C4C B:BCL101 3.0 32.8 1.0 C1C B:BCL101 3.0 32.8 1.0 C1B B:BCL101 3.0 32.8 1.0 C4B B:BCL101 3.1 32.8 1.0 C1D B:BCL101 3.1 32.8 1.0 CHB B:BCL101 3.3 32.8 1.0 CD2 B:HIS40 3.4 31.5 1.0 CHC B:BCL101 3.4 32.8 1.0 CHA B:BCL101 3.4 32.8 1.0 CHD B:BCL101 3.5 32.8 1.0 CMB Z:BCL101 3.9 36.5 1.0 C3D B:BCL101 4.1 32.8 1.0 ND1 B:HIS40 4.2 31.5 1.0 CBB Z:BCL101 4.2 36.5 1.0 C3A B:BCL101 4.3 32.8 1.0 C2A B:BCL101 4.3 32.8 1.0 C3C B:BCL101 4.3 32.8 1.0 C2C B:BCL101 4.3 32.8 1.0 C2D B:BCL101 4.3 32.8 1.0 C2B B:BCL101 4.3 32.8 1.0 C3B B:BCL101 4.4 32.8 1.0 CG B:HIS40 4.4 31.5 1.0 CG2 A:ILE32 4.4 30.3 1.0 C2B Z:BCL101 4.5 36.5 1.0 CAB Z:BCL101 4.6 36.5 1.0 CD1 A:ILE32 4.6 30.3 1.0 C3B Z:BCL101 4.8 36.5 1.0 CBD B:BCL101 4.9 32.8 1.0 CMA B:BCL101 5.0 32.8 1.0

Magnesium binding site 10 out of 55 in the Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum


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 Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:33.0 occ:1.00 MG A:BCL101 0.0 33.0 1.0 NA A:BCL101 2.0 33.0 1.0 NC A:BCL101 2.0 33.0 1.0 ND A:BCL101 2.0 33.0 1.0 NB A:BCL101 2.0 33.0 1.0 NE2 A:HIS33 2.4 30.8 1.0 C4D A:BCL101 2.9 33.0 1.0 C1A A:BCL101 2.9 33.0 1.0 C4A A:BCL101 3.0 33.0 1.0 C1C A:BCL101 3.0 33.0 1.0 C4C A:BCL101 3.0 33.0 1.0 C1B A:BCL101 3.0 33.0 1.0 C4B A:BCL101 3.1 33.0 1.0 C1D A:BCL101 3.2 33.0 1.0 CE1 A:HIS33 3.2 30.8 1.0 CHB A:BCL101 3.3 33.0 1.0 CHA A:BCL101 3.4 33.0 1.0 CHC A:BCL101 3.4 33.0 1.0 CD2 A:HIS33 3.5 30.8 1.0 CHD A:BCL101 3.5 33.0 1.0 C3D A:BCL101 4.1 33.0 1.0 C2A A:BCL101 4.2 33.0 1.0 C3A A:BCL101 4.3 33.0 1.0 C2C A:BCL101 4.3 33.0 1.0 C3C A:BCL101 4.3 33.0 1.0 C2B A:BCL101 4.3 33.0 1.0 C3B A:BCL101 4.3 33.0 1.0 C2D A:BCL101 4.4 33.0 1.0 CMD B:BCL101 4.4 32.8 1.0 ND1 A:HIS33 4.4 30.8 1.0 CBB D:BCL101 4.5 32.8 1.0 CG A:HIS33 4.6 30.8 1.0 CMB D:BCL101 4.7 32.8 1.0 CBD A:BCL101 4.8 33.0 1.0

X.P.Wang, G.L.Wang, Y.Fu, A.Minamino, M.J.Zou, F.Ma, B.Xu, Z.Y.Wang-Otomo, Y.Kimura, M.T.Madigan, J.Overmann, L.J.Yu. Insights Into the Divergence of the Photosynthetic LH1 Complex Obtained From Structural Analysis of the Unusual Photocomplexes of Roseospirillum Parvum. Commun Biol V. 7 1658 2024.
ISSN: ESSN 2399-3642
PubMed: 39702771
DOI: 10.1038/S42003-024-07354-4