Iron in PDB 9fka: Cryo-Em Structure of the Reduced Cytochrome Bd Oxidase From M. Tuberculosis

The binding sites of Iron atom in the Cryo-Em Structure of the Reduced Cytochrome Bd Oxidase From M. Tuberculosis (pdb code 9fka). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Cryo-Em Structure of the Reduced Cytochrome Bd Oxidase From M. Tuberculosis, PDB code: 9fka:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Cryo-Em Structure of the Reduced Cytochrome Bd Oxidase From M. Tuberculosis


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 Reduced Cytochrome Bd Oxidase From M. Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe503 b:105.4 occ:1.00 FE A:HEM503 0.0 105.4 1.0 ND A:HEM503 1.8 79.9 1.0 NA A:HEM503 1.9 80.3 1.0 NB A:HEM503 2.0 77.6 1.0 NC A:HEM503 2.0 68.6 1.0 OE1 A:GLU396 2.6 82.8 1.0 C4D A:HEM503 2.7 77.9 1.0 C1D A:HEM503 2.8 73.0 1.0 C1A A:HEM503 2.9 80.6 1.0 C4C A:HEM503 2.9 69.3 1.0 C4B A:HEM503 2.9 72.5 1.0 C1B A:HEM503 3.0 76.6 1.0 C4A A:HEM503 3.0 77.8 1.0 C1C A:HEM503 3.0 68.2 1.0 CD A:GLU396 3.1 81.8 1.0 CHA A:HEM503 3.2 83.7 1.0 CHD A:HEM503 3.3 72.4 1.0 CHC A:HEM503 3.4 73.9 1.0 CG A:GLU396 3.4 73.5 1.0 CHB A:HEM503 3.4 77.5 1.0 C3D A:HEM503 3.9 70.0 1.0 C2D A:HEM503 4.0 69.8 1.0 C2A A:HEM503 4.0 75.9 1.0 C3C A:HEM503 4.1 67.6 1.0 OE2 A:GLU396 4.1 86.9 1.0 CE1 A:PHE11 4.1 81.2 1.0 C3A A:HEM503 4.1 77.3 1.0 C2C A:HEM503 4.1 66.3 1.0 C3B A:HEM503 4.1 66.8 1.0 C2B A:HEM503 4.2 73.2 1.0 CB A:GLU396 4.3 74.7 1.0 CD1 A:PHE11 4.3 78.3 1.0 NH2 A:ARG399 4.5 75.5 1.0 CG2 A:THR15 4.8 74.6 1.0 OG1 A:THR15 4.9 80.6 1.0

Iron binding site 2 out of 3 in the Cryo-Em Structure of the Reduced Cytochrome Bd Oxidase From M. Tuberculosis


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 Reduced Cytochrome Bd Oxidase From M. Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe504 b:86.8 occ:1.00 FE A:HEM504 0.0 86.8 1.0 ND A:HEM504 1.8 74.4 1.0 NA A:HEM504 1.9 75.0 1.0 NB A:HEM504 2.0 73.5 1.0 NC A:HEM504 2.1 83.6 1.0 C4D A:HEM504 2.7 76.1 1.0 C1D A:HEM504 2.8 71.7 1.0 CE A:MET344 2.8 90.0 1.0 C1A A:HEM504 2.8 71.6 1.0 SD A:MET344 2.9 94.6 1.0 C4B A:HEM504 2.9 70.8 1.0 C1B A:HEM504 2.9 73.8 1.0 C4A A:HEM504 2.9 79.9 1.0 C4C A:HEM504 3.0 75.0 1.0 NE2 A:HIS185 3.0 81.4 1.0 C1C A:HEM504 3.0 81.2 1.0 CHA A:HEM504 3.2 76.5 1.0 CHD A:HEM504 3.3 73.2 1.0 CHC A:HEM504 3.3 76.8 1.0 CHB A:HEM504 3.4 78.8 1.0 CD2 A:HIS185 3.5 72.0 1.0 CG A:MET344 3.8 87.9 1.0 C3D A:HEM504 3.9 75.8 1.0 C2D A:HEM504 3.9 72.0 1.0 C2A A:HEM504 4.0 66.8 1.0 CE1 A:HIS185 4.1 90.6 1.0 C3A A:HEM504 4.1 75.1 1.0 C2B A:HEM504 4.1 73.7 1.0 C3B A:HEM504 4.1 75.1 1.0 C2C A:HEM504 4.1 76.3 1.0 C3C A:HEM504 4.1 69.2 1.0 CG A:HIS185 4.7 75.6 1.0 CA A:GLY391 4.9 80.4 1.0 ND1 A:HIS185 5.0 88.0 1.0

Iron binding site 3 out of 3 in the Cryo-Em Structure of the Reduced Cytochrome Bd Oxidase From M. Tuberculosis


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 Reduced Cytochrome Bd Oxidase From M. Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe505 b:98.4 occ:1.00 FE A:HDD505 0.0 98.4 1.0 ND A:HDD505 1.8 79.7 1.0 NA A:HDD505 2.0 86.2 1.0 NC A:HDD505 2.0 76.8 1.0 NB A:HDD505 2.0 79.8 1.0 NE2 A:HIS18 2.7 79.2 1.0 C1D A:HDD505 2.8 74.8 1.0 C4D A:HDD505 2.8 79.2 1.0 C4C A:HDD505 2.9 77.3 1.0 C1A A:HDD505 2.9 77.7 1.0 C1C A:HDD505 3.0 72.5 1.0 C4A A:HDD505 3.0 84.5 1.0 C1B A:HDD505 3.0 77.3 1.0 C4B A:HDD505 3.0 75.2 1.0 CHD A:HDD505 3.2 74.9 1.0 CHA A:HDD505 3.2 78.6 1.0 CE1 A:HIS18 3.3 79.6 1.0 CHC A:HDD505 3.4 72.2 1.0 CHB A:HDD505 3.4 78.9 1.0 CD2 A:HIS18 3.7 75.8 1.0 C2D A:HDD505 4.0 78.8 1.0 C3D A:HDD505 4.0 77.5 1.0 C3C A:HDD505 4.2 75.1 1.0 C2A A:HDD505 4.2 75.5 1.0 C2C A:HDD505 4.2 70.7 1.0 C3A A:HDD505 4.2 77.5 1.0 C3B A:HDD505 4.3 72.9 1.0 C2B A:HDD505 4.3 75.2 1.0 ND1 A:HIS18 4.4 75.0 1.0 OND A:HDD505 4.5 89.6 1.0 CG2 A:VAL22 4.5 84.2 1.0 CG A:HIS18 4.7 70.0 1.0 CAD A:HDD505 4.8 79.3 1.0 CZ A:PHE103 4.8 89.3 1.0 OE2 A:GLU98 5.0 102.9 1.0

T.T.Van Der Velden, K.Kayastha, C.Y.J.Waterham, S.Brunle, L.J.C.Jeuken. Menaquinone-Specific Turnover By Mycobacterium Tuberculosis Cytochrome Bd Is Redox Regulated By the Q-Loop Disulfide Bond. J.Biol.Chem. V. 301 08094 2024.
ISSN: ESSN 1083-351X
PubMed: 39706268
DOI: 10.1016/J.JBC.2024.108094