Iron in PDB 8ydm: Cryo-Em Structure of Carc-Lh Complex From Chloroflexus Aurantiacus

The structure of Cryo-Em Structure of Carc-Lh Complex From Chloroflexus Aurantiacus also contains other interesting chemical elements:

Magnesium	(Mg)	24 atoms
Manganese	(Mn)	1 atom

The binding sites of Iron atom in the Cryo-Em Structure of Carc-Lh Complex From Chloroflexus Aurantiacus (pdb code 8ydm). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Cryo-Em Structure of Carc-Lh Complex From Chloroflexus Aurantiacus, PDB code: 8ydm:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Cryo-Em Structure of Carc-Lh Complex From Chloroflexus Aurantiacus


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 Carc-Lh Complex From Chloroflexus Aurantiacus within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:47.8 occ:1.00 FE C:HEM501 0.0 47.8 1.0 ND C:HEM501 2.0 47.8 1.0 NA C:HEM501 2.0 47.8 1.0 NC C:HEM501 2.0 47.8 1.0 NB C:HEM501 2.0 47.8 1.0 NE2 C:HIS135 2.1 70.2 1.0 CD2 C:HIS135 2.6 65.6 1.0 SD C:MET119 2.6 63.5 1.0 C1A C:HEM501 2.9 47.8 1.0 C4D C:HEM501 3.0 47.8 1.0 C4C C:HEM501 3.0 47.8 1.0 C1D C:HEM501 3.0 47.8 1.0 C1B C:HEM501 3.0 47.8 1.0 C4B C:HEM501 3.0 47.8 1.0 C1C C:HEM501 3.1 47.8 1.0 C4A C:HEM501 3.1 47.8 1.0 CHA C:HEM501 3.3 47.8 1.0 CHD C:HEM501 3.4 47.8 1.0 CE1 C:HIS135 3.4 70.7 1.0 CHC C:HEM501 3.5 47.8 1.0 CHB C:HEM501 3.5 47.8 1.0 CG C:MET119 3.7 57.0 1.0 CG C:HIS135 3.9 67.1 1.0 CE C:MET119 4.0 69.4 1.0 C2A C:HEM501 4.2 47.8 1.0 C3C C:HEM501 4.2 47.8 1.0 C3D C:HEM501 4.2 47.8 1.0 C2D C:HEM501 4.2 47.8 1.0 C3A C:HEM501 4.2 47.8 1.0 C2C C:HEM501 4.2 47.8 1.0 C2B C:HEM501 4.2 47.8 1.0 ND1 C:HIS135 4.2 70.5 1.0 C3B C:HEM501 4.3 47.8 1.0 CB C:MET119 4.7 54.3 1.0

Iron binding site 2 out of 4 in the Cryo-Em Structure of Carc-Lh Complex From Chloroflexus Aurantiacus


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 Carc-Lh Complex From Chloroflexus Aurantiacus within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe502 b:33.6 occ:1.00 FE C:HEM502 0.0 33.6 1.0 ND C:HEM502 2.0 33.6 1.0 NA C:HEM502 2.0 33.6 1.0 NC C:HEM502 2.0 33.6 1.0 NB C:HEM502 2.0 33.6 1.0 SD C:MET154 2.3 73.8 1.0 CE C:MET154 2.4 64.2 1.0 NE2 C:HIS183 2.7 59.7 1.0 C4D C:HEM502 2.9 33.6 1.0 C1A C:HEM502 2.9 33.6 1.0 C4C C:HEM502 3.0 33.6 1.0 C1D C:HEM502 3.0 33.6 1.0 C1B C:HEM502 3.0 33.6 1.0 C4B C:HEM502 3.0 33.6 1.0 C1C C:HEM502 3.1 33.6 1.0 C4A C:HEM502 3.1 33.6 1.0 CHA C:HEM502 3.3 33.6 1.0 CHD C:HEM502 3.4 33.6 1.0 CHB C:HEM502 3.5 33.6 1.0 CHC C:HEM502 3.5 33.6 1.0 CE1 C:HIS183 3.5 61.7 1.0 CD2 C:HIS183 3.6 61.9 1.0 CG C:MET154 3.8 57.7 1.0 C2A C:HEM502 4.2 33.6 1.0 C3C C:HEM502 4.2 33.6 1.0 CB C:MET154 4.2 53.4 1.0 C3D C:HEM502 4.2 33.6 1.0 C2D C:HEM502 4.2 33.6 1.0 C2C C:HEM502 4.2 33.6 1.0 C3A C:HEM502 4.2 33.6 1.0 C2B C:HEM502 4.2 33.6 1.0 C3B C:HEM502 4.3 33.6 1.0 ND1 C:HIS183 4.6 61.4 1.0 CG C:HIS183 4.6 57.2 1.0

Iron binding site 3 out of 4 in the Cryo-Em Structure of Carc-Lh Complex From Chloroflexus Aurantiacus


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 Carc-Lh Complex From Chloroflexus Aurantiacus within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe503 b:16.2 occ:1.00 FE C:HEM503 0.0 16.2 1.0 ND C:HEM503 2.0 16.2 1.0 NA C:HEM503 2.0 16.2 1.0 NC C:HEM503 2.0 16.2 1.0 NB C:HEM503 2.0 16.2 1.0 NE2 C:HIS298 2.1 59.0 1.0 CG C:MET283 2.5 47.9 1.0 CD2 C:HIS298 2.6 51.0 1.0 C1A C:HEM503 2.9 16.2 1.0 C4D C:HEM503 2.9 16.2 1.0 C4C C:HEM503 2.9 16.2 1.0 C1D C:HEM503 3.0 16.2 1.0 C4B C:HEM503 3.0 16.2 1.0 C1B C:HEM503 3.0 16.2 1.0 C4A C:HEM503 3.1 16.2 1.0 C1C C:HEM503 3.1 16.2 1.0 CHA C:HEM503 3.3 16.2 1.0 SD C:MET283 3.3 65.3 1.0 CHD C:HEM503 3.4 16.2 1.0 CE1 C:HIS298 3.4 66.2 1.0 CHB C:HEM503 3.5 16.2 1.0 CHC C:HEM503 3.5 16.2 1.0 CB C:MET283 3.7 45.7 1.0 CE C:MET283 3.8 63.4 1.0 CG C:HIS298 3.9 53.0 1.0 C2A C:HEM503 4.1 16.2 1.0 C3C C:HEM503 4.2 16.2 1.0 C3D C:HEM503 4.2 16.2 1.0 C3A C:HEM503 4.2 16.2 1.0 C2D C:HEM503 4.2 16.2 1.0 C2B C:HEM503 4.2 16.2 1.0 ND1 C:HIS298 4.2 64.0 1.0 C2C C:HEM503 4.2 16.2 1.0 C3B C:HEM503 4.2 16.2 1.0

Iron binding site 4 out of 4 in the Cryo-Em Structure of Carc-Lh Complex From Chloroflexus Aurantiacus


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 Carc-Lh Complex From Chloroflexus Aurantiacus within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe504 b:20.7 occ:1.00 FE C:HEM504 0.0 20.7 1.0 SD C:MET330 1.8 79.9 1.0 ND C:HEM504 2.0 20.7 1.0 NA C:HEM504 2.0 20.7 1.0 NC C:HEM504 2.0 20.7 1.0 NB C:HEM504 2.0 20.7 1.0 NE2 C:HIS382 2.8 55.5 1.0 CE C:MET330 2.8 62.2 1.0 C4D C:HEM504 2.9 20.7 1.0 C1A C:HEM504 2.9 20.7 1.0 C4C C:HEM504 3.0 20.7 1.0 C1D C:HEM504 3.0 20.7 1.0 C1B C:HEM504 3.0 20.7 1.0 C4B C:HEM504 3.0 20.7 1.0 C1C C:HEM504 3.1 20.7 1.0 C4A C:HEM504 3.1 20.7 1.0 CHA C:HEM504 3.3 20.7 1.0 CHD C:HEM504 3.4 20.7 1.0 CHC C:HEM504 3.5 20.7 1.0 CHB C:HEM504 3.5 20.7 1.0 CG C:MET330 3.5 50.1 1.0 CD2 C:HIS382 3.7 52.2 1.0 CE1 C:HIS382 3.7 56.5 1.0 CB C:MET330 4.1 52.3 1.0 C2A C:HEM504 4.2 20.7 1.0 C3D C:HEM504 4.2 20.7 1.0 C3C C:HEM504 4.2 20.7 1.0 C2D C:HEM504 4.2 20.7 1.0 C3A C:HEM504 4.2 20.7 1.0 C2C C:HEM504 4.2 20.7 1.0 C2B C:HEM504 4.2 20.7 1.0 C3B C:HEM504 4.3 20.7 1.0 ND1 C:HIS382 4.8 62.7 1.0 CG C:HIS382 4.9 52.8 1.0

G.Huang, S.Dong, L.Ma, L.Li, J.Ju, M.J.Wang, J.P.Zhang, S.F.Sui, X.Qin. Cryo-Em Structure of A Minimal Reaction Center-Light-Harvesting Complex From the Phototrophic Bacterium Chloroflexus Aurantiacus. J Integr Plant Biol 2025.
ISSN: ESSN 1744-7909
PubMed: 39912559
DOI: 10.1111/JIPB.13853