Iron in PDB 8wdu: Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By Sucrose Density

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

Calcium	(Ca)	6 atoms
Magnesium	(Mg)	37 atoms

The binding sites of Iron atom in the Photosynthetic LH1-Rc Complex From the Purple Sulfur Bacterium Allochromatium Vinosum Purified By Sucrose Density (pdb code 8wdu). 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 Sucrose Density, PDB code: 8wdu:
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 Sucrose Density


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 Sucrose Density within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:64.0 occ:1.00 FE C:HEM401 0.0 64.0 1.0 ND C:HEM401 1.9 54.6 1.0 NA C:HEM401 2.0 52.1 1.0 NC C:HEM401 2.1 52.2 1.0 NE2 C:HIS111 2.1 50.3 1.0 NB C:HEM401 2.1 51.4 1.0 SD C:MET94 2.7 46.9 1.0 C4D C:HEM401 2.9 51.0 1.0 C1D C:HEM401 2.9 47.2 1.0 C1A C:HEM401 3.0 51.1 1.0 CE1 C:HIS111 3.0 47.5 1.0 C4C C:HEM401 3.0 45.3 1.0 C4A C:HEM401 3.1 52.5 1.0 C1B C:HEM401 3.1 47.0 1.0 C4B C:HEM401 3.1 48.0 1.0 CD2 C:HIS111 3.1 47.8 1.0 C1C C:HEM401 3.1 49.5 1.0 CHA C:HEM401 3.3 49.2 1.0 CHD C:HEM401 3.4 45.7 1.0 CG C:MET94 3.4 44.7 1.0 CHB C:HEM401 3.5 46.3 1.0 CHC C:HEM401 3.5 46.1 1.0 CE C:MET94 3.6 41.5 1.0 C3D C:HEM401 4.1 48.1 1.0 C2D C:HEM401 4.1 46.0 1.0 ND1 C:HIS111 4.2 48.8 1.0 C2A C:HEM401 4.2 53.8 1.0 C3A C:HEM401 4.2 53.0 1.0 CG C:HIS111 4.2 46.5 1.0 C3C C:HEM401 4.3 50.2 1.0 CB C:MET94 4.3 43.4 1.0 C2C C:HEM401 4.3 48.8 1.0 C2B C:HEM401 4.3 47.3 1.0 C3B C:HEM401 4.3 48.0 1.0

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


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 Sucrose Density within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe402 b:55.5 occ:1.00 FE C:HEM402 0.0 55.5 1.0 ND C:HEM402 1.9 47.0 1.0 NA C:HEM402 2.0 37.8 1.0 NE2 C:HIS156 2.0 25.1 1.0 NC C:HEM402 2.1 33.0 1.0 NB C:HEM402 2.1 34.0 1.0 SD C:MET130 2.5 48.1 1.0 C4D C:HEM402 2.9 34.1 1.0 C1D C:HEM402 2.9 28.7 1.0 CE1 C:HIS156 2.9 23.4 1.0 C1A C:HEM402 3.0 30.8 1.0 C4C C:HEM402 3.0 23.1 1.0 C4A C:HEM402 3.0 31.7 1.0 C1B C:HEM402 3.1 34.7 1.0 C4B C:HEM402 3.1 31.7 1.0 CD2 C:HIS156 3.1 22.5 1.0 C1C C:HEM402 3.1 27.0 1.0 CHA C:HEM402 3.3 30.1 1.0 CHD C:HEM402 3.4 27.2 1.0 CG C:MET130 3.4 29.9 1.0 CHB C:HEM402 3.5 30.2 1.0 CE C:MET130 3.5 35.1 1.0 CHC C:HEM402 3.5 33.6 1.0 ND1 C:HIS156 4.1 27.9 1.0 C3D C:HEM402 4.1 36.7 1.0 C2D C:HEM402 4.1 30.8 1.0 C2A C:HEM402 4.2 36.1 1.0 CG C:HIS156 4.2 25.0 1.0 CB C:MET130 4.2 29.2 1.0 C3A C:HEM402 4.2 34.8 1.0 C3C C:HEM402 4.3 31.8 1.0 C2C C:HEM402 4.3 34.0 1.0 C2B C:HEM402 4.3 31.9 1.0 C3B C:HEM402 4.3 32.0 1.0 CG C:PRO162 4.9 29.4 1.0

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


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 Sucrose Density within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe403 b:41.8 occ:1.00 FE C:HEM403 0.0 41.8 1.0 ND C:HEM403 1.9 28.5 1.0 NA C:HEM403 2.0 29.3 1.0 NC C:HEM403 2.1 22.3 1.0 NB C:HEM403 2.1 26.8 1.0 NE2 C:HIS251 2.2 16.9 1.0 SD C:MET236 2.3 25.7 1.0 C4D C:HEM403 2.9 18.0 1.0 C1D C:HEM403 2.9 14.3 1.0 C1A C:HEM403 3.0 20.3 1.0 C4C C:HEM403 3.0 18.2 1.0 CD2 C:HIS251 3.0 4.6 1.0 C4A C:HEM403 3.0 16.3 1.0 C1B C:HEM403 3.1 14.1 1.0 C4B C:HEM403 3.1 15.5 1.0 C1C C:HEM403 3.1 22.1 1.0 CHA C:HEM403 3.3 18.6 1.0 CE1 C:HIS251 3.3 21.5 1.0 CHD C:HEM403 3.4 16.0 1.0 CG C:MET236 3.4 14.5 1.0 CE C:MET236 3.5 15.4 1.0 CHB C:HEM403 3.5 16.3 1.0 CHC C:HEM403 3.5 19.2 1.0 CB C:MET236 4.0 14.5 1.0 C3D C:HEM403 4.1 24.5 1.0 C2D C:HEM403 4.1 24.2 1.0 C2A C:HEM403 4.2 21.4 1.0 C3A C:HEM403 4.2 24.7 1.0 CG C:HIS251 4.2 16.3 1.0 C3C C:HEM403 4.3 33.1 1.0 C2C C:HEM403 4.3 21.4 1.0 C2B C:HEM403 4.3 17.7 1.0 C3B C:HEM403 4.3 24.6 1.0 ND1 C:HIS251 4.4 28.0 1.0

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


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 Sucrose Density within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe404 b:42.5 occ:1.00 FE C:HEM404 0.0 42.5 1.0 ND C:HEM404 1.9 33.5 1.0 NA C:HEM404 2.0 30.0 1.0 NE2 C:HIS144 2.0 24.7 1.0 NC C:HEM404 2.1 26.6 1.0 NB C:HEM404 2.1 29.1 1.0 NE2 C:HIS311 2.2 22.0 1.0 C4D C:HEM404 2.9 24.3 1.0 C1D C:HEM404 2.9 16.0 1.0 CE1 C:HIS144 2.9 20.1 1.0 C1A C:HEM404 3.0 17.1 1.0 C4C C:HEM404 3.0 17.9 1.0 C4A C:HEM404 3.1 21.8 1.0 CD2 C:HIS144 3.1 17.7 1.0 C1B C:HEM404 3.1 16.3 1.0 C4B C:HEM404 3.1 20.8 1.0 CE1 C:HIS311 3.1 18.0 1.0 C1C C:HEM404 3.1 20.5 1.0 CD2 C:HIS311 3.2 9.1 1.0 CHA C:HEM404 3.3 25.8 1.0 CHD C:HEM404 3.4 18.7 1.0 CHB C:HEM404 3.5 18.6 1.0 CHC C:HEM404 3.5 23.8 1.0 ND1 C:HIS144 4.1 20.0 1.0 C3D C:HEM404 4.1 29.8 1.0 C2D C:HEM404 4.1 25.3 1.0 CG C:HIS144 4.2 23.6 1.0 C2A C:HEM404 4.2 26.9 1.0 C3A C:HEM404 4.2 26.7 1.0 ND1 C:HIS311 4.2 18.8 1.0 C3C C:HEM404 4.3 29.7 1.0 C2C C:HEM404 4.3 22.2 1.0 CG C:HIS311 4.3 18.5 1.0 C2B C:HEM404 4.3 20.2 1.0 C3B C:HEM404 4.3 21.3 1.0 CB C:ALA272 4.5 24.2 1.0 CD C:PRO317 4.8 24.9 1.0 CG C:PRO317 5.0 27.4 1.0

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


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 Sucrose Density within 5.0Å range: probe atom residue distance (Å) B Occ M:Fe401 b:48.0 occ:1.00 NE2 L:HIS196 2.1 26.8 1.0 OE2 M:GLU234 2.1 45.1 1.0 OE1 M:GLU234 2.1 42.1 1.0 NE2 M:HIS219 2.2 21.0 1.0 NE2 M:HIS266 2.2 27.6 1.0 NE2 L:HIS236 2.2 26.8 1.0 CD M:GLU234 2.4 31.9 1.0 CE1 L:HIS196 2.9 23.9 1.0 CE1 M:HIS266 3.0 24.6 1.0 CE1 M:HIS219 3.1 24.3 1.0 CE1 L:HIS236 3.1 22.4 1.0 CD2 L:HIS196 3.2 20.6 1.0 CD2 M:HIS219 3.3 18.6 1.0 CD2 L:HIS236 3.3 22.2 1.0 CD2 M:HIS266 3.3 20.6 1.0 CG M:GLU234 3.9 30.8 1.0 ND1 L:HIS196 4.1 24.1 1.0 ND1 M:HIS266 4.2 22.0 1.0 ND1 M:HIS219 4.2 24.0 1.0 CG L:HIS196 4.3 24.0 1.0 ND1 L:HIS236 4.3 20.3 1.0 CG1 M:ILE223 4.3 26.5 1.0 CG M:HIS219 4.4 19.6 1.0 CG M:HIS266 4.4 21.8 1.0 CG L:HIS236 4.4 27.1 1.0 CG1 L:ILE200 4.5 30.9 1.0 O M:HOH544 4.7 42.9 1.0 CB M:GLU234 4.8 35.9 1.0 CD1 L:ILE200 4.9 25.2 1.0 CD1 M:ILE223 5.0 21.8 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