Iron 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:

Magnesium

(Mg)

55 atoms

The binding sites of Iron 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 Iron atom.
In total 5 binding sites of Iron where determined in the Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum, PDB code: 8zk2:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe501 b:46.9 occ:1.00 FE C:HEC501 0.0 46.9 1.0 NE2 C:HIS134 2.1 50.2 1.0 NA C:HEC501 2.1 46.9 1.0 NC C:HEC501 2.1 46.9 1.0 NB C:HEC501 2.1 46.9 1.0 ND C:HEC501 2.1 46.9 1.0 SD C:MET117 2.3 42.9 1.0 CD2 C:HIS134 3.0 50.2 1.0 C1D C:HEC501 3.1 46.9 1.0 CE1 C:HIS134 3.1 50.2 1.0 C4C C:HEC501 3.1 46.9 1.0 C1B C:HEC501 3.1 46.9 1.0 C4A C:HEC501 3.1 46.9 1.0 C1A C:HEC501 3.1 46.9 1.0 C4D C:HEC501 3.1 46.9 1.0 C4B C:HEC501 3.1 46.9 1.0 C1C C:HEC501 3.1 46.9 1.0 CHD C:HEC501 3.4 46.9 1.0 CHB C:HEC501 3.4 46.9 1.0 CHA C:HEC501 3.4 46.9 1.0 CHC C:HEC501 3.5 46.9 1.0 CG C:MET117 3.5 42.9 1.0 CE C:MET117 3.9 42.9 1.0 ND1 C:HIS134 4.2 50.2 1.0 CG C:HIS134 4.2 50.2 1.0 CB C:MET117 4.2 42.9 1.0 C2B C:HEC501 4.3 46.9 1.0 C3B C:HEC501 4.3 46.9 1.0 C2D C:HEC501 4.3 46.9 1.0 C3A C:HEC501 4.3 46.9 1.0 C3D C:HEC501 4.3 46.9 1.0 C2A C:HEC501 4.3 46.9 1.0 C3C C:HEC501 4.3 46.9 1.0 C2C C:HEC501 4.3 46.9 1.0 CA C:MET117 5.0 42.9 1.0

Iron binding site 2 out of 5 in the Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe502 b:34.0 occ:1.00 FE C:HEC502 0.0 34.0 1.0 NC C:HEC502 2.1 34.0 1.0 NE2 C:HIS179 2.1 32.4 1.0 NB C:HEC502 2.1 34.0 1.0 NA C:HEC502 2.2 34.0 1.0 ND C:HEC502 2.2 34.0 1.0 CE C:MET153 2.3 34.7 1.0 SD C:MET153 2.4 34.7 1.0 CG C:MET153 2.7 34.7 1.0 CE1 C:HIS179 2.8 32.4 1.0 C1C C:HEC502 3.1 34.0 1.0 C4C C:HEC502 3.1 34.0 1.0 C4B C:HEC502 3.1 34.0 1.0 C1B C:HEC502 3.1 34.0 1.0 C1D C:HEC502 3.2 34.0 1.0 C4A C:HEC502 3.2 34.0 1.0 C1A C:HEC502 3.2 34.0 1.0 C4D C:HEC502 3.2 34.0 1.0 CD2 C:HIS179 3.3 32.4 1.0 CHC C:HEC502 3.4 34.0 1.0 CHD C:HEC502 3.5 34.0 1.0 CHB C:HEC502 3.5 34.0 1.0 CHA C:HEC502 3.6 34.0 1.0 CB C:MET153 3.8 34.7 1.0 ND1 C:HIS179 4.1 32.4 1.0 C2C C:HEC502 4.3 34.0 1.0 CG C:HIS179 4.3 32.4 1.0 C3B C:HEC502 4.3 34.0 1.0 C3C C:HEC502 4.3 34.0 1.0 C2B C:HEC502 4.3 34.0 1.0 C3A C:HEC502 4.4 34.0 1.0 C2D C:HEC502 4.4 34.0 1.0 C2A C:HEC502 4.4 34.0 1.0 C3D C:HEC502 4.4 34.0 1.0 CA C:MET153 4.8 34.7 1.0 CE C:MET156 4.9 33.3 1.0

Iron binding site 3 out of 5 in the Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe503 b:32.8 occ:1.00 FE C:HEC503 0.0 32.8 1.0 NE2 C:HIS278 2.1 23.2 1.0 NC C:HEC503 2.1 32.8 1.0 NA C:HEC503 2.1 32.8 1.0 NB C:HEC503 2.1 32.8 1.0 ND C:HEC503 2.1 32.8 1.0 SD C:MET263 2.3 23.4 1.0 CE C:MET263 2.8 23.4 1.0 CD2 C:HIS278 3.0 23.2 1.0 C1D C:HEC503 3.1 32.8 1.0 CE1 C:HIS278 3.1 23.2 1.0 C4C C:HEC503 3.1 32.8 1.0 C4A C:HEC503 3.1 32.8 1.0 C1B C:HEC503 3.1 32.8 1.0 C4D C:HEC503 3.1 32.8 1.0 C1C C:HEC503 3.1 32.8 1.0 C4B C:HEC503 3.1 32.8 1.0 C1A C:HEC503 3.1 32.8 1.0 CG C:MET263 3.3 23.4 1.0 CHD C:HEC503 3.4 32.8 1.0 CHB C:HEC503 3.5 32.8 1.0 CHA C:HEC503 3.5 32.8 1.0 CHC C:HEC503 3.5 32.8 1.0 CG C:HIS278 4.1 23.2 1.0 ND1 C:HIS278 4.1 23.2 1.0 CB C:MET263 4.2 23.4 1.0 C2D C:HEC503 4.3 32.8 1.0 C2B C:HEC503 4.3 32.8 1.0 C3D C:HEC503 4.3 32.8 1.0 C3A C:HEC503 4.3 32.8 1.0 C3B C:HEC503 4.3 32.8 1.0 C2C C:HEC503 4.3 32.8 1.0 C3C C:HEC503 4.3 32.8 1.0 C2A C:HEC503 4.3 32.8 1.0

Iron binding site 4 out of 5 in the Cryo-Em Structure of Photosynthetic LH1-Rc Core Complex of Roseospirillum Parvum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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 C:Fe504 b:32.8 occ:1.00 FE C:HEC504 0.0 32.8 1.0 NA C:HEC504 2.0 32.8 1.0 NE2 C:HIS167 2.0 27.2 1.0 NE2 C:HIS338 2.0 25.5 1.0 NC C:HEC504 2.1 32.8 1.0 NB C:HEC504 2.1 32.8 1.0 ND C:HEC504 2.1 32.8 1.0 CE1 C:HIS338 2.8 25.5 1.0 CE1 C:HIS167 2.8 27.2 1.0 C1A C:HEC504 3.1 32.8 1.0 C4C C:HEC504 3.1 32.8 1.0 C1D C:HEC504 3.1 32.8 1.0 C4A C:HEC504 3.1 32.8 1.0 C4D C:HEC504 3.1 32.8 1.0 C1C C:HEC504 3.1 32.8 1.0 C4B C:HEC504 3.1 32.8 1.0 C1B C:HEC504 3.1 32.8 1.0 CD2 C:HIS167 3.2 27.2 1.0 CD2 C:HIS338 3.2 25.5 1.0 CHA C:HEC504 3.4 32.8 1.0 CHD C:HEC504 3.4 32.8 1.0 CHC C:HEC504 3.5 32.8 1.0 CHB C:HEC504 3.5 32.8 1.0 ND1 C:HIS167 4.0 27.2 1.0 ND1 C:HIS338 4.0 25.5 1.0 CG C:HIS167 4.2 27.2 1.0 CG C:HIS338 4.2 25.5 1.0 C2A C:HEC504 4.3 32.8 1.0 C3A C:HEC504 4.3 32.8 1.0 C3C C:HEC504 4.3 32.8 1.0 C2C C:HEC504 4.3 32.8 1.0 C3B C:HEC504 4.3 32.8 1.0 C2B C:HEC504 4.3 32.8 1.0 C2D C:HEC504 4.3 32.8 1.0 C3D C:HEC504 4.3 32.8 1.0 CD C:PRO344 4.9 26.2 1.0

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


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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 M:Fe401 b:40.2 occ:1.00 NE2 L:HIS192 2.1 32.1 1.0 NE2 M:HIS220 2.1 27.1 1.0 NE2 L:HIS232 2.2 32.4 1.0 OE2 M:GLU235 2.2 33.3 1.0 OE1 M:GLU235 2.2 33.3 1.0 NE2 M:HIS267 2.4 28.3 1.0 CD M:GLU235 2.5 33.3 1.0 CD2 M:HIS220 3.0 27.1 1.0 CE1 L:HIS192 3.0 32.1 1.0 CE1 L:HIS232 3.1 32.4 1.0 CD2 L:HIS232 3.1 32.4 1.0 CD2 L:HIS192 3.2 32.1 1.0 CE1 M:HIS220 3.2 27.1 1.0 CE1 M:HIS267 3.3 28.3 1.0 CD2 M:HIS267 3.4 28.3 1.0 CG M:GLU235 4.0 33.3 1.0 ND1 L:HIS192 4.2 32.1 1.0 CG M:HIS220 4.2 27.1 1.0 ND1 L:HIS232 4.2 32.4 1.0 CG L:HIS232 4.3 32.4 1.0 ND1 M:HIS220 4.3 27.1 1.0 CG L:HIS192 4.3 32.1 1.0 ND1 M:HIS267 4.4 28.3 1.0 CG1 M:ILE224 4.4 27.4 1.0 CG M:HIS267 4.5 28.3 1.0 CG1 L:ILE196 4.5 30.1 1.0 C25 L:PGV410 4.7 42.6 1.0 CD1 L:ILE196 4.7 30.1 1.0 CB M:GLU235 4.8 33.3 1.0 C26 L:PGV410 4.9 42.6 1.0 CD1 M:ILE224 4.9 27.4 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