Iron in PDB 5awi: Domain-Swapped Cytochrome CB562 Dimer

The structure of Domain-Swapped Cytochrome CB562 Dimer, PDB code: 5awi was solved by T.Miyamoto, M.Kuribayashi, S.Nagao, Y.Shomura, Y.Higuchi, S.Hirota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.31 / 1.85
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	94.608, 94.608, 94.608, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 20.5

The structure of Domain-Swapped Cytochrome CB562 Dimer also contains other interesting chemical elements:

Zinc

(Zn)

7 atoms

The binding sites of Iron atom in the Domain-Swapped Cytochrome CB562 Dimer (pdb code 5awi). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Domain-Swapped Cytochrome CB562 Dimer, PDB code: 5awi:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Domain-Swapped Cytochrome CB562 Dimer


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Domain-Swapped Cytochrome CB562 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:24.5 occ:1.00 FE A:HEC201 0.0 24.5 1.0 ND A:HEC201 1.9 23.8 1.0 NA A:HEC201 2.0 24.2 1.0 NC A:HEC201 2.1 25.0 1.0 NB A:HEC201 2.1 26.0 1.0 NE2 A:HIS102 2.2 27.1 1.0 SD B:MET7 2.3 23.4 1.0 C4D A:HEC201 2.9 23.9 1.0 C1D A:HEC201 2.9 24.1 1.0 C1A A:HEC201 3.0 23.7 1.0 C4A A:HEC201 3.0 24.9 1.0 C4B A:HEC201 3.0 26.8 1.0 C1B A:HEC201 3.1 26.5 1.0 C4C A:HEC201 3.1 25.0 1.0 C1C A:HEC201 3.1 25.9 1.0 CD2 A:HIS102 3.1 27.5 1.0 CE1 A:HIS102 3.2 27.8 1.0 CE B:MET7 3.3 22.9 1.0 CHA A:HEC201 3.4 23.1 1.0 CHD A:HEC201 3.4 24.4 1.0 CG B:MET7 3.4 23.3 1.0 CHB A:HEC201 3.4 25.6 1.0 CHC A:HEC201 3.5 26.3 1.0 CB B:MET7 4.1 24.0 1.0 C2D A:HEC201 4.2 24.2 1.0 C3D A:HEC201 4.2 23.9 1.0 C2A A:HEC201 4.2 24.2 1.0 C3A A:HEC201 4.2 24.6 1.0 C2B A:HEC201 4.3 27.8 1.0 C3C A:HEC201 4.3 25.6 1.0 C2C A:HEC201 4.3 25.9 1.0 C3B A:HEC201 4.3 28.1 1.0 CG A:HIS102 4.3 29.1 1.0 ND1 A:HIS102 4.3 29.0 1.0 NH2 A:ARG106 4.9 31.2 1.0 CA B:MET7 5.0 24.5 1.0

Iron binding site 2 out of 2 in the Domain-Swapped Cytochrome CB562 Dimer


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Domain-Swapped Cytochrome CB562 Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe208 b:24.1 occ:1.00 FE A:HEC208 0.0 24.1 1.0 ND A:HEC208 1.9 23.6 1.0 NA A:HEC208 2.0 24.5 1.0 NC A:HEC208 2.1 23.8 1.0 NB A:HEC208 2.1 24.6 1.0 NE2 B:HIS102 2.1 26.8 1.0 SD A:MET7 2.3 23.9 1.0 C1D A:HEC208 2.9 23.7 1.0 C4D A:HEC208 3.0 24.1 1.0 C1A A:HEC208 3.0 24.4 1.0 C4A A:HEC208 3.0 24.9 1.0 CD2 B:HIS102 3.0 27.4 1.0 C4B A:HEC208 3.0 25.5 1.0 C4C A:HEC208 3.1 24.0 1.0 C1B A:HEC208 3.1 25.4 1.0 C1C A:HEC208 3.1 24.5 1.0 CE1 B:HIS102 3.2 27.4 1.0 CHA A:HEC208 3.4 23.9 1.0 CHD A:HEC208 3.4 23.5 1.0 CE A:MET7 3.4 24.2 1.0 CHB A:HEC208 3.4 25.3 1.0 CHC A:HEC208 3.4 24.8 1.0 CG A:MET7 3.5 24.4 1.0 CB A:MET7 4.2 24.3 1.0 CG B:HIS102 4.2 28.7 1.0 C3A A:HEC208 4.2 25.1 1.0 C2A A:HEC208 4.2 24.6 1.0 C2D A:HEC208 4.2 23.9 1.0 ND1 B:HIS102 4.2 28.0 1.0 C3D A:HEC208 4.2 24.3 1.0 C2C A:HEC208 4.3 24.2 1.0 C2B A:HEC208 4.3 26.3 1.0 C3C A:HEC208 4.3 23.9 1.0 C3B A:HEC208 4.3 26.5 1.0 NH2 B:ARG106 4.9 32.2 1.0

T.Miyamoto, M.Kuribayashi, S.Nagao, Y.Shomura, Y.Higuchi, S.Hirota. Domain-Swapped Cytochrome CB562 Dimer and Its Nanocage Encapsulating A Zn-SO4 Cluster in the Internal Cavity Chem Sci 2015.
ISSN: ESSN 2041-6539
DOI: 10.1039/C5SC02428E