Iron in PDB 8wdv: Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By CA2+-Deae

The structure of Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By CA2+-Deae also contains other interesting chemical elements:

Magnesium	(Mg)	37 atoms
Calcium	(Ca)	8 atoms

The binding sites of Iron atom in the Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By CA2+-Deae (pdb code 8wdv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By CA2+-Deae, PDB code: 8wdv:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By CA2+-Deae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By CA2+-Deae within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:72.8 occ:1.00 FE C:HEM401 0.0 72.8 1.0 ND C:HEM401 1.9 51.6 1.0 NA C:HEM401 2.0 52.0 1.0 NC C:HEM401 2.1 49.1 1.0 NE2 C:HIS111 2.1 52.5 1.0 NB C:HEM401 2.1 49.7 1.0 SD C:MET94 2.6 55.9 1.0 C4D C:HEM401 2.9 45.6 1.0 C1D C:HEM401 2.9 47.8 1.0 C1A C:HEM401 3.0 48.8 1.0 CE1 C:HIS111 3.0 50.2 1.0 C4C C:HEM401 3.0 44.2 1.0 C4A C:HEM401 3.0 48.8 1.0 C1B C:HEM401 3.1 48.1 1.0 C4B C:HEM401 3.1 47.5 1.0 CD2 C:HIS111 3.1 51.2 1.0 C1C C:HEM401 3.1 46.4 1.0 CHA C:HEM401 3.3 48.0 1.0 CHD C:HEM401 3.4 45.3 1.0 CHB C:HEM401 3.5 49.2 1.0 CHC C:HEM401 3.5 46.7 1.0 CG C:MET94 3.6 44.9 1.0 CE C:MET94 3.7 44.6 1.0 C3D C:HEM401 4.1 46.2 1.0 C2D C:HEM401 4.1 46.5 1.0 C2A C:HEM401 4.2 49.8 1.0 ND1 C:HIS111 4.2 52.6 1.0 C3A C:HEM401 4.2 49.6 1.0 CG C:HIS111 4.2 50.8 1.0 C3C C:HEM401 4.3 48.1 1.0 C2C C:HEM401 4.3 47.1 1.0 C2B C:HEM401 4.3 50.4 1.0 C3B C:HEM401 4.3 53.1 1.0 CB C:MET94 4.3 44.0 1.0

Iron binding site 2 out of 5 in the Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By CA2+-Deae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By CA2+-Deae within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe402 b:52.0 occ:1.00 FE C:HEM402 0.0 52.0 1.0 ND C:HEM402 1.9 42.2 1.0 NA C:HEM402 2.0 39.9 1.0 NC C:HEM402 2.1 35.2 1.0 NB C:HEM402 2.1 36.3 1.0 NE2 C:HIS156 2.1 27.9 1.0 SD C:MET130 2.5 40.6 1.0 C4D C:HEM402 2.9 28.8 1.0 C1D C:HEM402 2.9 33.0 1.0 C1A C:HEM402 3.0 34.2 1.0 C4C C:HEM402 3.0 28.7 1.0 CE1 C:HIS156 3.0 24.7 1.0 C4A C:HEM402 3.0 34.3 1.0 C1B C:HEM402 3.1 33.0 1.0 C4B C:HEM402 3.1 28.1 1.0 C1C C:HEM402 3.1 31.8 1.0 CD2 C:HIS156 3.2 28.6 1.0 CHA C:HEM402 3.3 30.7 1.0 CG C:MET130 3.3 31.5 1.0 CHD C:HEM402 3.4 33.0 1.0 CHB C:HEM402 3.5 35.0 1.0 CHC C:HEM402 3.5 31.4 1.0 CE C:MET130 3.6 29.9 1.0 C3D C:HEM402 4.1 36.1 1.0 C2D C:HEM402 4.1 36.0 1.0 C2A C:HEM402 4.2 35.8 1.0 CB C:MET130 4.2 32.1 1.0 ND1 C:HIS156 4.2 31.2 1.0 C3A C:HEM402 4.2 33.8 1.0 C3C C:HEM402 4.3 31.9 1.0 CG C:HIS156 4.3 25.4 1.0 C2C C:HEM402 4.3 29.9 1.0 C2B C:HEM402 4.3 34.6 1.0 C3B C:HEM402 4.3 33.9 1.0 CG C:PRO162 4.9 29.7 1.0

Iron binding site 3 out of 5 in the Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By CA2+-Deae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By CA2+-Deae within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe403 b:39.9 occ:1.00 FE C:HEM403 0.0 39.9 1.0 ND C:HEM403 1.9 26.3 1.0 NE2 C:HIS251 2.0 24.8 1.0 NA C:HEM403 2.0 27.6 1.0 NC C:HEM403 2.1 28.6 1.0 NB C:HEM403 2.1 21.2 1.0 SD C:MET236 2.3 23.9 1.0 CD2 C:HIS251 2.8 15.8 1.0 C4D C:HEM403 2.9 17.7 1.0 C1D C:HEM403 2.9 14.9 1.0 C1A C:HEM403 3.0 23.1 1.0 CE1 C:HIS251 3.0 18.2 1.0 C4C C:HEM403 3.0 20.4 1.0 C4A C:HEM403 3.0 12.3 1.0 C4B C:HEM403 3.1 10.6 1.0 C1B C:HEM403 3.1 14.6 1.0 C1C C:HEM403 3.1 15.7 1.0 CHA C:HEM403 3.3 15.8 1.0 CG C:MET236 3.4 13.2 1.0 CHD C:HEM403 3.4 17.0 1.0 CE C:MET236 3.4 13.5 1.0 CHB C:HEM403 3.5 17.7 1.0 CHC C:HEM403 3.5 13.3 1.0 CG C:HIS251 4.0 20.2 1.0 ND1 C:HIS251 4.1 18.4 1.0 C3D C:HEM403 4.1 22.6 1.0 C2D C:HEM403 4.1 22.3 1.0 C2A C:HEM403 4.2 24.2 1.0 C3A C:HEM403 4.2 25.3 1.0 CB C:MET236 4.2 16.9 1.0 C3C C:HEM403 4.3 24.4 1.0 C2C C:HEM403 4.3 21.0 1.0 C2B C:HEM403 4.3 16.8 1.0 C3B C:HEM403 4.3 21.0 1.0

Iron binding site 4 out of 5 in the Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By CA2+-Deae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By CA2+-Deae within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe404 b:35.8 occ:1.00 FE C:HEM404 0.0 35.8 1.0 ND C:HEM404 1.9 31.5 1.0 NE2 C:HIS311 2.0 10.1 1.0 NA C:HEM404 2.0 22.9 1.0 NC C:HEM404 2.1 26.3 1.0 NE2 C:HIS144 2.1 26.2 1.0 NB C:HEM404 2.1 26.9 1.0 CE1 C:HIS311 2.9 12.6 1.0 C4D C:HEM404 2.9 20.6 1.0 C1D C:HEM404 2.9 18.8 1.0 C1A C:HEM404 3.0 17.1 1.0 CE1 C:HIS144 3.0 22.7 1.0 C4C C:HEM404 3.0 22.3 1.0 C4A C:HEM404 3.0 15.4 1.0 CD2 C:HIS311 3.1 16.6 1.0 C1B C:HEM404 3.1 15.5 1.0 C4B C:HEM404 3.1 18.9 1.0 C1C C:HEM404 3.1 17.4 1.0 CD2 C:HIS144 3.2 19.6 1.0 CHA C:HEM404 3.3 20.4 1.0 CHD C:HEM404 3.4 14.9 1.0 CHB C:HEM404 3.5 17.5 1.0 CHC C:HEM404 3.5 15.4 1.0 ND1 C:HIS311 4.0 20.3 1.0 C3D C:HEM404 4.1 24.2 1.0 C2D C:HEM404 4.1 25.4 1.0 ND1 C:HIS144 4.1 24.9 1.0 CG C:HIS311 4.2 21.8 1.0 C2A C:HEM404 4.2 23.8 1.0 C3A C:HEM404 4.2 23.2 1.0 CG C:HIS144 4.2 23.3 1.0 C3C C:HEM404 4.3 27.7 1.0 C2C C:HEM404 4.3 23.2 1.0 C2B C:HEM404 4.3 23.4 1.0 C3B C:HEM404 4.3 22.9 1.0 CB C:ALA272 4.5 14.2 1.0 CD C:PRO317 4.8 20.8 1.0 CG C:PRO317 5.0 20.1 1.0

Iron binding site 5 out of 5 in the Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By CA2+-Deae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By CA2+-Deae within 5.0Å range: probe atom residue distance (Å) B Occ M:Fe402 b:61.6 occ:1.00 OE2 M:GLU234 2.0 51.0 1.0 NE2 L:HIS196 2.1 38.4 1.0 OE1 M:GLU234 2.1 56.2 1.0 NE2 M:HIS219 2.1 32.6 1.0 NE2 L:HIS236 2.2 36.5 1.0 NE2 M:HIS266 2.2 33.2 1.0 CD M:GLU234 2.3 46.6 1.0 CE1 L:HIS196 2.9 32.3 1.0 CE1 M:HIS219 3.0 30.7 1.0 CE1 M:HIS266 3.1 29.1 1.0 CE1 L:HIS236 3.2 29.5 1.0 CD2 L:HIS196 3.2 30.2 1.0 CD2 M:HIS219 3.2 28.4 1.0 CD2 L:HIS236 3.2 27.0 1.0 CD2 M:HIS266 3.3 26.9 1.0 CG M:GLU234 3.8 40.7 1.0 ND1 L:HIS196 4.1 35.9 1.0 ND1 M:HIS219 4.2 25.5 1.0 CG L:HIS196 4.2 34.3 1.0 ND1 M:HIS266 4.3 25.1 1.0 ND1 L:HIS236 4.3 31.4 1.0 CG M:HIS219 4.3 24.9 1.0 CG L:HIS236 4.3 29.8 1.0 CG M:HIS266 4.4 26.0 1.0 CG1 M:ILE223 4.5 35.0 1.0 CG1 L:ILE200 4.5 43.9 1.0 O M:HOH519 4.6 47.8 1.0 CB M:GLU234 4.7 41.8 1.0 CD1 L:ILE200 4.8 42.0 1.0 CD1 M:ILE223 5.0 32.2 1.0

K.Tani, R.Kanno, A.Harada, Y.Kobayashi, A.Minamino, S.Takenaka, N.Nakamura, X.C.Ji, E.R.Purba, M.Hall, L.J.Yu, M.T.Madigan, A.Mizoguchi, K.Iwasaki, B.M.Humbel, Y.Kimura, Z.Y.Wang-Otomo. High-Resolution Structure and Biochemical Properties of the LH1-Rc Photocomplex From the Model Purple Sulfur Bacterium, Allochromatium Vinosum Commun Biol V. 7 176 2024.
ISSN: ESSN 2399-3642
DOI: 10.1038/S42003-024-05863-W