Iron in PDB 7nkz: Cryo-Em Structure of the Cytochrome Bd Oxidase From M. Tuberculosis at 2.5 A Resolution

The binding sites of Iron atom in the Cryo-Em Structure of the Cytochrome Bd Oxidase From M. Tuberculosis at 2.5 A Resolution (pdb code 7nkz). 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 Cytochrome Bd Oxidase From M. Tuberculosis at 2.5 A Resolution, PDB code: 7nkz:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Cryo-Em Structure of the Cytochrome Bd Oxidase From M. Tuberculosis at 2.5 A Resolution


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 Cytochrome Bd Oxidase From M. Tuberculosis at 2.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe703 b:33.3 occ:1.00 FE A:HDD703 0.0 33.3 1.0 ND A:HDD703 1.8 33.3 1.0 NA A:HDD703 2.1 33.3 1.0 NC A:HDD703 2.1 33.3 1.0 NB A:HDD703 2.1 33.3 1.0 NE2 A:HIS18 2.7 29.4 1.0 C4D A:HDD703 2.8 33.3 1.0 C1D A:HDD703 2.8 33.3 1.0 C4C A:HDD703 3.0 33.3 1.0 C1A A:HDD703 3.0 33.3 1.0 C1B A:HDD703 3.1 33.3 1.0 C4B A:HDD703 3.1 33.3 1.0 C4A A:HDD703 3.1 33.3 1.0 C1C A:HDD703 3.1 33.3 1.0 CHA A:HDD703 3.3 33.3 1.0 CHD A:HDD703 3.3 33.3 1.0 O1 A:OXY701 3.3 38.1 1.0 CHC A:HDD703 3.5 33.3 1.0 CHB A:HDD703 3.5 33.3 1.0 CE1 A:HIS18 3.6 29.4 1.0 CD2 A:HIS18 3.6 29.4 1.0 O2 A:OXY701 3.9 38.1 1.0 C3D A:HDD703 4.1 33.3 1.0 C2D A:HDD703 4.1 33.3 1.0 C3C A:HDD703 4.3 33.3 1.0 C2A A:HDD703 4.4 33.3 1.0 CZ A:PHE103 4.4 38.1 1.0 C2B A:HDD703 4.4 33.3 1.0 C3B A:HDD703 4.4 33.3 1.0 C3A A:HDD703 4.4 33.3 1.0 C2C A:HDD703 4.4 33.3 1.0 CG2 A:VAL22 4.6 29.6 1.0 ND1 A:HIS18 4.7 29.4 1.0 OND A:HDD703 4.8 33.3 1.0 CG A:HIS18 4.8 29.4 1.0 CE1 A:PHE103 4.8 38.1 1.0 CAD A:HDD703 4.9 33.3 1.0 O1D A:HDD703 5.0 33.3 1.0

Iron binding site 2 out of 3 in the Cryo-Em Structure of the Cytochrome Bd Oxidase From M. Tuberculosis at 2.5 A Resolution


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 Cytochrome Bd Oxidase From M. Tuberculosis at 2.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe704 b:36.1 occ:1.00 FE A:HEB704 0.0 36.1 1.0 NA A:HEB704 2.1 36.1 1.0 NB A:HEB704 2.2 36.1 1.0 NC A:HEB704 2.2 36.1 1.0 ND A:HEB704 2.3 36.1 1.0 OE2 A:GLU396 2.7 37.1 1.0 C1A A:HEB704 3.2 36.1 1.0 C1C A:HEB704 3.2 36.1 1.0 C1B A:HEB704 3.3 36.1 1.0 C4A A:HEB704 3.3 36.1 1.0 C4B A:HEB704 3.3 36.1 1.0 C4C A:HEB704 3.3 36.1 1.0 C4D A:HEB704 3.4 36.1 1.0 C1D A:HEB704 3.4 36.1 1.0 CD A:GLU396 3.5 37.1 1.0 CG A:GLU396 3.6 37.1 1.0 CHC A:HEB704 3.7 36.1 1.0 CE1 A:PHE11 3.7 35.9 1.0 CHB A:HEB704 3.7 36.1 1.0 CHA A:HEB704 3.7 36.1 1.0 CHD A:HEB704 3.8 36.1 1.0 CD1 A:PHE11 4.0 35.9 1.0 CG2 A:THR15 4.2 33.0 1.0 C2A A:HEB704 4.2 36.1 1.0 C2C A:HEB704 4.2 36.1 1.0 C2B A:HEB704 4.2 36.1 1.0 C3A A:HEB704 4.3 36.1 1.0 C3B A:HEB704 4.3 36.1 1.0 C3C A:HEB704 4.4 36.1 1.0 C2D A:HEB704 4.4 36.1 1.0 C3D A:HEB704 4.6 36.1 1.0 OE1 A:GLU396 4.6 37.1 1.0 CB A:GLU396 4.6 37.1 1.0 NH2 A:ARG399 4.6 37.2 1.0 CZ A:PHE11 4.8 35.9 1.0 ND2 A:ASN147 4.9 34.3 1.0 OG1 A:THR15 4.9 33.0 1.0

Iron binding site 3 out of 3 in the Cryo-Em Structure of the Cytochrome Bd Oxidase From M. Tuberculosis at 2.5 A Resolution


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 Cytochrome Bd Oxidase From M. Tuberculosis at 2.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe705 b:40.2 occ:1.00 FE A:HEB705 0.0 40.2 1.0 NA A:HEB705 2.1 40.2 1.0 NB A:HEB705 2.2 40.2 1.0 NC A:HEB705 2.2 40.2 1.0 ND A:HEB705 2.3 40.2 1.0 SD A:MET344 2.3 44.3 1.0 NE2 A:HIS185 2.6 36.4 1.0 C1A A:HEB705 3.2 40.2 1.0 C1C A:HEB705 3.2 40.2 1.0 C1B A:HEB705 3.3 40.2 1.0 C4A A:HEB705 3.3 40.2 1.0 C4B A:HEB705 3.3 40.2 1.0 C4C A:HEB705 3.3 40.2 1.0 C4D A:HEB705 3.4 40.2 1.0 C1D A:HEB705 3.4 40.2 1.0 CD2 A:HIS185 3.4 36.4 1.0 CE1 A:HIS185 3.6 36.4 1.0 CG A:MET344 3.6 44.3 1.0 CHB A:HEB705 3.7 40.2 1.0 CHC A:HEB705 3.7 40.2 1.0 CHA A:HEB705 3.7 40.2 1.0 CHD A:HEB705 3.8 40.2 1.0 CE A:MET344 3.8 44.3 1.0 C2A A:HEB705 4.2 40.2 1.0 C2C A:HEB705 4.2 40.2 1.0 C2B A:HEB705 4.2 40.2 1.0 C3A A:HEB705 4.3 40.2 1.0 C3B A:HEB705 4.3 40.2 1.0 C3C A:HEB705 4.4 40.2 1.0 C2D A:HEB705 4.4 40.2 1.0 C3D A:HEB705 4.6 40.2 1.0 CG A:HIS185 4.6 36.4 1.0 ND1 A:HIS185 4.7 36.4 1.0 CB A:MET344 4.9 44.3 1.0

S.Safarian, H.K.Opel-Reading, D.Wu, A.R.Mehdipour, K.Hards, L.K.Harold, M.Radloff, I.Stewart, S.Welsch, G.Hummer, G.M.Cook, K.L.Krause, H.Michel. The Cryo-Em Structure of the Bd Oxidase From M. Tuberculosis Reveals A Unique Structural Framework and Enables Rational Drug Design to Combat Tb Nat Commun 2021.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-021-25537-Z