Iron in PDB 6rko: Cryo-Em Structure of the E. Coli Cytochrome Bd-I Oxidase at 2.68 A Resolution

All present enzymatic activity of Cryo-Em Structure of the E. Coli Cytochrome Bd-I Oxidase at 2.68 A Resolution:
7.1.1.7;

The binding sites of Iron atom in the Cryo-Em Structure of the E. Coli Cytochrome Bd-I Oxidase at 2.68 A Resolution (pdb code 6rko). 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 E. Coli Cytochrome Bd-I Oxidase at 2.68 A Resolution, PDB code: 6rko:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Cryo-Em Structure of the E. Coli Cytochrome Bd-I Oxidase at 2.68 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 E. Coli Cytochrome Bd-I Oxidase at 2.68 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe603 b:0.4 occ:1.00 FE A:HDD603 0.0 0.4 1.0 ND A:HDD603 1.8 0.4 1.0 NA A:HDD603 2.1 0.4 1.0 NC A:HDD603 2.1 0.4 1.0 NB A:HDD603 2.1 0.4 1.0 NE2 A:HIS19 2.6 0.4 1.0 C4D A:HDD603 2.8 0.4 1.0 C1D A:HDD603 2.8 0.4 1.0 C4C A:HDD603 3.0 0.4 1.0 C1A A:HDD603 3.0 0.4 1.0 C1B A:HDD603 3.1 0.4 1.0 C4B A:HDD603 3.1 0.4 1.0 C4A A:HDD603 3.1 0.4 1.0 C1C A:HDD603 3.1 0.4 1.0 CHA A:HDD603 3.3 0.4 1.0 CHD A:HDD603 3.3 0.4 1.0 O1 A:OXY606 3.3 0.5 1.0 CHC A:HDD603 3.4 0.4 1.0 CHB A:HDD603 3.5 0.4 1.0 CD2 A:HIS19 3.5 0.4 1.0 CE1 A:HIS19 3.6 0.4 1.0 O2 A:OXY606 3.7 0.5 1.0 C3D A:HDD603 4.1 0.4 1.0 C2D A:HDD603 4.1 0.4 1.0 C3C A:HDD603 4.3 0.4 1.0 C2A A:HDD603 4.3 0.4 1.0 CZ A:PHE104 4.4 1.7 1.0 C2B A:HDD603 4.4 0.4 1.0 C3B A:HDD603 4.4 0.4 1.0 C3A A:HDD603 4.4 0.4 1.0 C2C A:HDD603 4.4 0.4 1.0 CG2 A:VAL23 4.4 2.1 1.0 OND A:HDD603 4.7 0.4 1.0 CE1 A:PHE104 4.7 1.7 1.0 CG A:HIS19 4.7 0.4 1.0 ND1 A:HIS19 4.7 0.4 1.0 CAD A:HDD603 4.7 0.4 1.0 CA A:GLY70 4.8 1.2 1.0

Iron binding site 2 out of 3 in the Cryo-Em Structure of the E. Coli Cytochrome Bd-I Oxidase at 2.68 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 E. Coli Cytochrome Bd-I Oxidase at 2.68 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe604 b:0.4 occ:1.00 FE A:HEB604 0.0 0.4 1.0 NA A:HEB604 2.1 0.4 1.0 NC A:HEB604 2.1 0.4 1.0 NB A:HEB604 2.1 0.4 1.0 ND A:HEB604 2.1 0.4 1.0 OE1 A:GLU445 2.2 0.9 1.0 CD A:GLU445 3.1 0.9 1.0 C1A A:HEB604 3.1 0.4 1.0 C4A A:HEB604 3.1 0.4 1.0 C4B A:HEB604 3.1 0.4 1.0 C1C A:HEB604 3.1 0.4 1.0 C1D A:HEB604 3.1 0.4 1.0 C4C A:HEB604 3.1 0.4 1.0 C4D A:HEB604 3.1 0.4 1.0 C1B A:HEB604 3.2 0.4 1.0 CHC A:HEB604 3.4 0.4 1.0 CHA A:HEB604 3.5 0.4 1.0 CHD A:HEB604 3.5 0.4 1.0 CHB A:HEB604 3.5 0.4 1.0 CG A:GLU445 3.6 0.9 1.0 CE2 A:PHE12 3.8 0.4 1.0 OE2 A:GLU445 4.0 0.9 1.0 CD2 A:PHE12 4.1 0.4 1.0 CB A:GLU445 4.2 0.9 1.0 NH1 A:ARG448 4.2 1.0 1.0 C2A A:HEB604 4.4 0.4 1.0 C3A A:HEB604 4.4 0.4 1.0 C3C A:HEB604 4.4 0.4 1.0 C3B A:HEB604 4.4 0.4 1.0 C2D A:HEB604 4.4 0.4 1.0 C2C A:HEB604 4.5 0.4 1.0 C3D A:HEB604 4.5 0.4 1.0 C2B A:HEB604 4.5 0.4 1.0 CB A:ALA16 4.8 0.4 1.0 ND2 A:ASN148 4.9 1.7 1.0 CZ A:PHE12 5.0 0.4 1.0

Iron binding site 3 out of 3 in the Cryo-Em Structure of the E. Coli Cytochrome Bd-I Oxidase at 2.68 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 E. Coli Cytochrome Bd-I Oxidase at 2.68 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe605 b:2.8 occ:1.00 FE A:HEB605 0.0 2.8 1.0 NA A:HEB605 2.1 2.8 1.0 NB A:HEB605 2.1 2.8 1.0 NC A:HEB605 2.2 2.8 1.0 ND A:HEB605 2.4 2.8 1.0 NE2 A:HIS186 2.4 1.9 1.0 SD A:MET393 2.7 2.8 1.0 C1B A:HEB605 3.2 2.8 1.0 C1A A:HEB605 3.2 2.8 1.0 C4A A:HEB605 3.2 2.8 1.0 C4B A:HEB605 3.2 2.8 1.0 C1C A:HEB605 3.2 2.8 1.0 CD2 A:HIS186 3.3 1.9 1.0 C4C A:HEB605 3.3 2.8 1.0 C4D A:HEB605 3.4 2.8 1.0 C1D A:HEB605 3.4 2.8 1.0 CE1 A:HIS186 3.5 1.9 1.0 CHB A:HEB605 3.6 2.8 1.0 CE A:MET393 3.6 2.8 1.0 CHC A:HEB605 3.6 2.8 1.0 CHA A:HEB605 3.7 2.8 1.0 CG A:MET393 3.7 2.8 1.0 CHD A:HEB605 3.8 2.8 1.0 C2B A:HEB605 4.1 2.8 1.0 C2A A:HEB605 4.1 2.8 1.0 C2C A:HEB605 4.2 2.8 1.0 C3A A:HEB605 4.2 2.8 1.0 C3B A:HEB605 4.2 2.8 1.0 C3C A:HEB605 4.4 2.8 1.0 C2D A:HEB605 4.4 2.8 1.0 CG A:HIS186 4.4 1.9 1.0 ND1 A:HIS186 4.5 1.9 1.0 OD2 A:ASP239 4.5 4.7 1.0 C3D A:HEB605 4.6 2.8 1.0

S.Safarian, A.Hahn, D.J.Mills, M.Radloff, M.L.Eisinger, A.Nikolaev, J.Meier-Credo, F.Melin, H.Miyoshi, R.B.Gennis, J.Sakamoto, J.D.Langer, P.Hellwig, W.Kuhlbrandt, H.Michel. Active Site Rearrangement and Structural Divergence in Prokaryotic Respiratory Oxidases. Science V. 366 100 2019.
ISSN: ESSN 1095-9203
PubMed: 31604309
DOI: 10.1126/SCIENCE.AAY0967