Iron in PDB 5y5s: Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution

The structure of Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution, PDB code: 5y5s was solved by L.-J.Yu, M.Suga, Z.-Y.Wang-Otomo, J.-R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.92 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	145.280, 143.810, 210.280, 90.00, 90.74, 90.00
R / Rfree (%)	18.1 / 21.5

The structure of Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution also contains other interesting chemical elements:

Magnesium	(Mg)	37 atoms
Calcium	(Ca)	16 atoms

The binding sites of Iron atom in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution (pdb code 5y5s). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution, PDB code: 5y5s:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:58.9 occ:1.00 FE C:HEC501 0.0 58.9 1.0 ND C:HEC501 2.0 60.6 1.0 NA C:HEC501 2.0 60.4 1.0 NE2 C:HIS111 2.0 61.4 1.0 NC C:HEC501 2.1 55.0 1.0 NB C:HEC501 2.1 58.1 1.0 SD C:MET94 2.3 60.6 1.0 C4D C:HEC501 2.9 61.5 1.0 C1D C:HEC501 2.9 58.7 1.0 CE1 C:HIS111 3.0 58.0 1.0 C1A C:HEC501 3.0 63.9 1.0 C4A C:HEC501 3.0 63.2 1.0 C4C C:HEC501 3.1 59.0 1.0 CD2 C:HIS111 3.1 58.6 1.0 C1B C:HEC501 3.1 59.6 1.0 C4B C:HEC501 3.1 57.7 1.0 C1C C:HEC501 3.1 57.9 1.0 CE C:MET94 3.4 55.2 1.0 CHA C:HEC501 3.4 64.0 1.0 CHD C:HEC501 3.4 58.0 1.0 CG C:MET94 3.4 57.4 1.0 CHB C:HEC501 3.5 65.6 1.0 CHC C:HEC501 3.5 56.3 1.0 ND1 C:HIS111 4.1 61.0 1.0 CG C:HIS111 4.2 62.5 1.0 C2A C:HEC501 4.2 63.3 1.0 C3D C:HEC501 4.2 57.4 1.0 C2D C:HEC501 4.2 53.6 1.0 C3A C:HEC501 4.2 63.9 1.0 CB C:MET94 4.3 57.5 1.0 C3C C:HEC501 4.3 58.5 1.0 C2B C:HEC501 4.3 60.3 1.0 C2C C:HEC501 4.3 55.5 1.0 C3B C:HEC501 4.3 65.4 1.0

Iron binding site 2 out of 5 in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe502 b:46.5 occ:1.00 FE C:HEC502 0.0 46.5 1.0 ND C:HEC502 2.0 42.1 1.0 NA C:HEC502 2.0 44.5 1.0 NE2 C:HIS156 2.1 49.1 1.0 NC C:HEC502 2.1 42.2 1.0 NB C:HEC502 2.1 44.6 1.0 SD C:MET130 2.3 48.1 1.0 CE1 C:HIS156 2.9 47.6 1.0 C4D C:HEC502 3.0 42.2 1.0 C1D C:HEC502 3.0 41.1 1.0 C1A C:HEC502 3.0 48.0 1.0 C4C C:HEC502 3.1 45.1 1.0 C1B C:HEC502 3.1 49.0 1.0 C4A C:HEC502 3.1 46.0 1.0 C4B C:HEC502 3.1 49.2 1.0 C1C C:HEC502 3.1 48.3 1.0 CD2 C:HIS156 3.2 44.0 1.0 CG C:MET130 3.3 46.0 1.0 CHA C:HEC502 3.4 44.6 1.0 CHD C:HEC502 3.4 46.6 1.0 CE C:MET130 3.4 44.2 1.0 CHB C:HEC502 3.5 48.3 1.0 CHC C:HEC502 3.5 45.1 1.0 ND1 C:HIS156 4.1 46.7 1.0 CB C:MET130 4.2 45.3 1.0 C2A C:HEC502 4.2 48.6 1.0 C2D C:HEC502 4.2 42.3 1.0 C3D C:HEC502 4.2 45.3 1.0 C3A C:HEC502 4.2 46.2 1.0 CG C:HIS156 4.2 48.0 1.0 C3C C:HEC502 4.3 48.5 1.0 C2C C:HEC502 4.3 43.8 1.0 C2B C:HEC502 4.3 47.2 1.0 C3B C:HEC502 4.3 49.2 1.0

Iron binding site 3 out of 5 in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe503 b:35.1 occ:1.00 FE C:HEC503 0.0 35.1 1.0 ND C:HEC503 2.0 37.6 1.0 NA C:HEC503 2.0 35.4 1.0 NE2 C:HIS251 2.1 34.8 1.0 NB C:HEC503 2.1 34.9 1.0 NC C:HEC503 2.1 30.4 1.0 SD C:MET236 2.3 34.8 1.0 C1D C:HEC503 3.0 37.5 1.0 C4D C:HEC503 3.0 32.5 1.0 C1A C:HEC503 3.0 34.2 1.0 C4A C:HEC503 3.0 34.8 1.0 CE1 C:HIS251 3.0 38.5 1.0 C1B C:HEC503 3.0 34.4 1.0 C4C C:HEC503 3.0 36.6 1.0 CD2 C:HIS251 3.0 32.3 1.0 C4B C:HEC503 3.1 34.0 1.0 C1C C:HEC503 3.1 40.2 1.0 CG C:MET236 3.3 29.3 1.0 CHD C:HEC503 3.4 34.0 1.0 CHA C:HEC503 3.4 35.6 1.0 CHB C:HEC503 3.4 30.8 1.0 CE C:MET236 3.5 32.9 1.0 CHC C:HEC503 3.5 31.1 1.0 ND1 C:HIS251 4.2 36.3 1.0 CG C:HIS251 4.2 33.3 1.0 CB C:MET236 4.2 32.3 1.0 C3A C:HEC503 4.2 32.6 1.0 C2A C:HEC503 4.2 35.5 1.0 C2D C:HEC503 4.2 42.3 1.0 C3D C:HEC503 4.2 39.2 1.0 C2B C:HEC503 4.3 30.1 1.0 C3C C:HEC503 4.3 32.3 1.0 C2C C:HEC503 4.3 37.1 1.0 C3B C:HEC503 4.3 30.7 1.0

Iron binding site 4 out of 5 in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe504 b:40.1 occ:1.00 FE C:HEC504 0.0 40.1 1.0 ND C:HEC504 2.0 39.3 1.0 NA C:HEC504 2.0 38.5 1.0 NE2 C:HIS144 2.0 41.4 1.0 NE2 C:HIS311 2.1 43.3 1.0 NC C:HEC504 2.1 45.9 1.0 NB C:HEC504 2.1 36.9 1.0 CE1 C:HIS144 2.8 41.3 1.0 C1D C:HEC504 3.0 43.2 1.0 C4D C:HEC504 3.0 39.9 1.0 CE1 C:HIS311 3.0 36.6 1.0 C1A C:HEC504 3.0 40.1 1.0 C4B C:HEC504 3.1 42.0 1.0 C4C C:HEC504 3.1 45.7 1.0 C4A C:HEC504 3.1 45.0 1.0 C1B C:HEC504 3.1 41.4 1.0 CD2 C:HIS311 3.1 40.2 1.0 C1C C:HEC504 3.1 41.6 1.0 CD2 C:HIS144 3.2 38.3 1.0 CHD C:HEC504 3.4 41.2 1.0 CHA C:HEC504 3.4 37.6 1.0 CHC C:HEC504 3.5 40.2 1.0 CHB C:HEC504 3.5 38.7 1.0 ND1 C:HIS144 4.0 40.5 1.0 ND1 C:HIS311 4.1 37.5 1.0 CG C:HIS311 4.2 36.1 1.0 C2D C:HEC504 4.2 47.8 1.0 C3D C:HEC504 4.2 46.0 1.0 CG C:HIS144 4.2 42.3 1.0 C2A C:HEC504 4.2 40.9 1.0 C3A C:HEC504 4.2 40.1 1.0 C2C C:HEC504 4.3 39.5 1.0 C2B C:HEC504 4.3 34.2 1.0 C3C C:HEC504 4.3 44.4 1.0 C3B C:HEC504 4.3 36.8 1.0 CB C:ALA272 4.5 35.1 1.0

Iron binding site 5 out of 5 in the Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Photosynthetic LH1-Rc Super-Complex at 1.9 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ L:Fe310 b:39.4 occ:1.00 NE2 M:HIS219 2.2 38.2 1.0 NE2 L:HIS199 2.2 35.9 1.0 NE2 L:HIS239 2.2 38.5 1.0 NE2 M:HIS266 2.2 34.5 1.0 OE2 M:GLU234 2.2 39.4 1.0 OE1 M:GLU234 2.2 42.5 1.0 CD M:GLU234 2.5 43.7 1.0 CE1 M:HIS219 3.0 40.0 1.0 CE1 L:HIS239 3.0 34.3 1.0 CD2 L:HIS199 3.1 38.7 1.0 CE1 L:HIS199 3.1 35.1 1.0 CE1 M:HIS266 3.1 37.7 1.0 CD2 M:HIS266 3.2 36.9 1.0 CD2 L:HIS239 3.3 36.6 1.0 CD2 M:HIS219 3.3 40.4 1.0 CG M:GLU234 4.1 40.9 1.0 ND1 M:HIS219 4.2 37.9 1.0 ND1 L:HIS239 4.2 37.6 1.0 ND1 L:HIS199 4.2 33.6 1.0 ND1 M:HIS266 4.3 36.2 1.0 CG L:HIS199 4.3 35.6 1.0 CG M:HIS219 4.3 43.0 1.0 CG M:HIS266 4.3 35.3 1.0 CG L:HIS239 4.3 35.5 1.0 CG1 M:ILE223 4.5 40.5 1.0 CG1 L:ILE203 4.5 36.7 1.0 CD1 L:ILE203 4.9 39.5 1.0 O M:HOH577 4.9 43.7 1.0 CB M:GLU234 5.0 41.4 1.0

L.-J.Yu, M.Suga, Z.-Y.Wang-Otomo, J.R.Shen. Structure of Photosynthetic LH1-Rc Supercomplex at 1.9 Angstrom Resolution. Nature V. 556 209 2018.
ISSN: ESSN 1476-4687
PubMed: 29618814
DOI: 10.1038/S41586-018-0002-9