Iron in PDB 5yq7: Cryo-Em Structure of the Rc-Lh Core Complex From Roseiflexus Castenholzii

The structure of Cryo-Em Structure of the Rc-Lh Core Complex From Roseiflexus Castenholzii also contains other interesting chemical elements:

Magnesium

(Mg)

48 atoms

The binding sites of Iron atom in the Cryo-Em Structure of the Rc-Lh Core Complex From Roseiflexus Castenholzii (pdb code 5yq7). 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 the Rc-Lh Core Complex From Roseiflexus Castenholzii, PDB code: 5yq7:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the Cryo-Em Structure of the Rc-Lh Core Complex From Roseiflexus Castenholzii


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 the Rc-Lh Core Complex From Roseiflexus Castenholzii within 5.0Å range: probe atom residue distance (Å) B Occ L:Fe1005 b:0.6 occ:1.00 OE2 M:GLU557 1.8 0.2 1.0 NE2 L:HIS229 1.9 0.6 1.0 NE2 M:HIS542 2.0 0.9 1.0 NE2 M:HIS589 2.0 0.7 1.0 CD M:GLU557 2.3 0.2 1.0 OE1 M:GLU557 2.3 0.2 1.0 CD2 L:HIS229 2.8 0.6 1.0 CE1 M:HIS542 2.8 0.9 1.0 CD2 M:HIS542 2.9 0.9 1.0 CE1 M:HIS589 3.0 0.7 1.0 CD2 M:HIS589 3.0 0.7 1.0 CE1 L:HIS229 3.0 0.6 1.0 NE2 L:HIS264 3.3 0.3 1.0 CG M:GLU557 3.8 0.2 1.0 ND1 M:HIS542 3.8 0.9 1.0 CG M:HIS542 3.9 0.9 1.0 CG L:HIS229 4.0 0.6 1.0 CD2 L:HIS264 4.0 0.3 1.0 ND1 L:HIS229 4.1 0.6 1.0 ND1 M:HIS589 4.1 0.7 1.0 CG M:HIS589 4.1 0.7 1.0 CE1 L:HIS264 4.3 0.3 1.0 CD1 M:ILE546 4.5 0.6 1.0 CB M:GLU557 4.7 0.2 1.0 CG2 L:VAL233 4.8 0.8 1.0

Iron binding site 2 out of 5 in the Cryo-Em Structure of the Rc-Lh Core Complex From Roseiflexus Castenholzii


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 the Rc-Lh Core Complex From Roseiflexus Castenholzii within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:0.1 occ:1.00 FE C:HEM501 0.0 0.1 1.0 CD2 C:HIS122 1.9 0.5 1.0 ND C:HEM501 2.0 0.1 1.0 NC C:HEM501 2.0 0.1 1.0 NB C:HEM501 2.0 0.1 1.0 NA C:HEM501 2.0 0.1 1.0 SD C:MET106 2.1 0.6 1.0 NE2 C:HIS122 2.1 0.5 1.0 CE C:MET106 2.5 0.6 1.0 C1D C:HEM501 3.0 0.1 1.0 C4C C:HEM501 3.0 0.1 1.0 C1B C:HEM501 3.0 0.1 1.0 C4D C:HEM501 3.0 0.1 1.0 C4A C:HEM501 3.0 0.1 1.0 C1C C:HEM501 3.0 0.1 1.0 C4B C:HEM501 3.1 0.1 1.0 C1A C:HEM501 3.1 0.1 1.0 CG C:HIS122 3.1 0.5 1.0 CE1 C:HIS122 3.3 0.5 1.0 CHD C:HEM501 3.4 0.1 1.0 CHB C:HEM501 3.4 0.1 1.0 CHA C:HEM501 3.4 0.1 1.0 CHC C:HEM501 3.4 0.1 1.0 ND1 C:HIS122 3.7 0.5 1.0 CG C:MET106 3.8 0.6 1.0 CB C:HIS122 4.1 0.5 1.0 C2D C:HEM501 4.2 0.1 1.0 C3D C:HEM501 4.2 0.1 1.0 C3C C:HEM501 4.3 0.1 1.0 C2C C:HEM501 4.3 0.1 1.0 C2B C:HEM501 4.3 0.1 1.0 C3A C:HEM501 4.3 0.1 1.0 C3B C:HEM501 4.3 0.1 1.0 C2A C:HEM501 4.3 0.1 1.0 CB C:MET106 4.9 0.6 1.0

Iron binding site 3 out of 5 in the Cryo-Em Structure of the Rc-Lh Core Complex From Roseiflexus Castenholzii


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 the Rc-Lh Core Complex From Roseiflexus Castenholzii within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe502 b:0.6 occ:1.00 FE C:HEM502 0.0 0.6 1.0 ND C:HEM502 2.0 0.6 1.0 NA C:HEM502 2.0 0.6 1.0 NE2 C:HIS175 2.0 0.9 1.0 NB C:HEM502 2.0 0.6 1.0 NC C:HEM502 2.0 0.6 1.0 SD C:MET145 2.1 0.8 1.0 CE C:MET145 2.3 0.8 1.0 CE1 C:HIS175 2.5 0.9 1.0 C4D C:HEM502 3.0 0.6 1.0 C1A C:HEM502 3.0 0.6 1.0 C4A C:HEM502 3.0 0.6 1.0 C1D C:HEM502 3.0 0.6 1.0 C1B C:HEM502 3.0 0.6 1.0 C4C C:HEM502 3.0 0.6 1.0 C1C C:HEM502 3.1 0.6 1.0 C4B C:HEM502 3.1 0.6 1.0 CD2 C:HIS175 3.3 0.9 1.0 CHA C:HEM502 3.4 0.6 1.0 CHB C:HEM502 3.4 0.6 1.0 CHD C:HEM502 3.4 0.6 1.0 CHC C:HEM502 3.5 0.6 1.0 ND1 C:HIS175 3.7 0.9 1.0 CG C:MET145 3.8 0.8 1.0 CG C:HIS175 4.1 0.9 1.0 C3D C:HEM502 4.2 0.6 1.0 C2A C:HEM502 4.2 0.6 1.0 C3A C:HEM502 4.2 0.6 1.0 C2D C:HEM502 4.2 0.6 1.0 C2B C:HEM502 4.3 0.6 1.0 C3C C:HEM502 4.3 0.6 1.0 C2C C:HEM502 4.3 0.6 1.0 C3B C:HEM502 4.3 0.6 1.0 CB C:MET145 4.7 0.8 1.0

Iron binding site 4 out of 5 in the Cryo-Em Structure of the Rc-Lh Core Complex From Roseiflexus Castenholzii


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 the Rc-Lh Core Complex From Roseiflexus Castenholzii within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe503 b:95.2 occ:1.00 FE C:HEM503 0.0 95.2 1.0 CE1 C:HIS244 1.7 99.1 1.0 ND C:HEM503 2.0 95.2 1.0 NA C:HEM503 2.0 95.2 1.0 NB C:HEM503 2.0 95.2 1.0 NC C:HEM503 2.0 95.2 1.0 NE2 C:HIS244 2.0 99.1 1.0 SD C:MET229 2.1 95.8 1.0 CE C:MET229 2.8 95.8 1.0 ND1 C:HIS244 2.9 99.1 1.0 C1D C:HEM503 3.0 95.2 1.0 C4A C:HEM503 3.0 95.2 1.0 C4D C:HEM503 3.0 95.2 1.0 C4C C:HEM503 3.0 95.2 1.0 C1B C:HEM503 3.0 95.2 1.0 C1A C:HEM503 3.0 95.2 1.0 C1C C:HEM503 3.1 95.2 1.0 C4B C:HEM503 3.1 95.2 1.0 CD2 C:HIS244 3.3 99.1 1.0 CHD C:HEM503 3.4 95.2 1.0 CHB C:HEM503 3.4 95.2 1.0 CHA C:HEM503 3.4 95.2 1.0 CHC C:HEM503 3.5 95.2 1.0 CG C:MET229 3.6 95.8 1.0 CG C:HIS244 3.7 99.1 1.0 C2D C:HEM503 4.2 95.2 1.0 C3D C:HEM503 4.2 95.2 1.0 C3A C:HEM503 4.2 95.2 1.0 C2A C:HEM503 4.2 95.2 1.0 C3C C:HEM503 4.3 95.2 1.0 C2B C:HEM503 4.3 95.2 1.0 C2C C:HEM503 4.3 95.2 1.0 C3B C:HEM503 4.3 95.2 1.0 CB C:MET229 4.7 95.8 1.0

Iron binding site 5 out of 5 in the Cryo-Em Structure of the Rc-Lh Core Complex From Roseiflexus Castenholzii


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 the Rc-Lh Core Complex From Roseiflexus Castenholzii within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe504 b:0.9 occ:1.00 FE C:HEM504 0.0 0.9 1.0 ND C:HEM504 2.0 0.9 1.0 NA C:HEM504 2.0 0.9 1.0 NE2 C:HIS297 2.0 0.3 1.0 SD C:MET263 2.0 0.2 1.0 NB C:HEM504 2.0 0.9 1.0 NC C:HEM504 2.0 0.9 1.0 CE C:MET263 2.2 0.2 1.0 CE1 C:HIS297 2.2 0.3 1.0 C1D C:HEM504 3.0 0.9 1.0 C1B C:HEM504 3.0 0.9 1.0 C4D C:HEM504 3.0 0.9 1.0 C4A C:HEM504 3.0 0.9 1.0 C4C C:HEM504 3.0 0.9 1.0 C1A C:HEM504 3.0 0.9 1.0 C1C C:HEM504 3.1 0.9 1.0 C4B C:HEM504 3.1 0.9 1.0 CD2 C:HIS297 3.3 0.3 1.0 CHD C:HEM504 3.4 0.9 1.0 CHB C:HEM504 3.4 0.9 1.0 CHA C:HEM504 3.4 0.9 1.0 ND1 C:HIS297 3.5 0.3 1.0 CHC C:HEM504 3.5 0.9 1.0 CG C:MET263 3.7 0.2 1.0 CG C:HIS297 4.1 0.3 1.0 C2D C:HEM504 4.2 0.9 1.0 C3D C:HEM504 4.2 0.9 1.0 C3A C:HEM504 4.2 0.9 1.0 C2B C:HEM504 4.2 0.9 1.0 C2A C:HEM504 4.3 0.9 1.0 C3C C:HEM504 4.3 0.9 1.0 C3B C:HEM504 4.3 0.9 1.0 C2C C:HEM504 4.3 0.9 1.0 CB C:MET263 4.6 0.2 1.0 CD1 C:ILE302 4.7 0.4 1.0 CG1 C:ILE302 4.9 0.4 1.0

Y.Y.Xin, Y.Shi, T.X.Niu, Q.Q.Wang, W.Q.Niu, X.J.Huang, W.Ding, L.Yang, R.E.Blankenship, X.L.Xu, F.Sun. Cryo-Em Structure of the Rc-Lh Core Complex From An Early Branching Photosynthetic Prokaryote. Nat Commun V. 9 1568 2018.
ISSN: ESSN 2041-1723
PubMed: 29674684
DOI: 10.1038/S41467-018-03881-X