Iron in PDB 6dyb: Metal-Free Structure of the Engineered Cyt CB562 Variant, CH3

The structure of Metal-Free Structure of the Engineered Cyt CB562 Variant, CH3, PDB code: 6dyb was solved by F.A.Tezcan, J.Rittle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.23 / 2.75
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	73.008, 73.008, 143.994, 90.00, 90.00, 120.00
R / Rfree (%)	22.6 / 30.9

The structure of Metal-Free Structure of the Engineered Cyt CB562 Variant, CH3 also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Iron atom in the Metal-Free Structure of the Engineered Cyt CB562 Variant, CH3 (pdb code 6dyb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Metal-Free Structure of the Engineered Cyt CB562 Variant, CH3, PDB code: 6dyb:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Metal-Free Structure of the Engineered Cyt CB562 Variant, CH3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Metal-Free Structure of the Engineered Cyt CB562 Variant, CH3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:52.5 occ:1.00 FE A:HEC201 0.0 52.5 1.0 NC A:HEC201 1.9 42.1 1.0 ND A:HEC201 2.0 47.4 1.0 NA A:HEC201 2.0 39.0 1.0 NB A:HEC201 2.1 43.8 1.0 NE2 A:HIS102 2.2 43.8 1.0 SD A:MET7 2.5 42.7 1.0 C4C A:HEC201 2.9 45.1 1.0 C1D A:HEC201 2.9 44.4 1.0 C1C A:HEC201 3.0 44.0 1.0 C4A A:HEC201 3.0 41.7 1.0 C1B A:HEC201 3.1 42.8 1.0 C4D A:HEC201 3.1 42.3 1.0 C1A A:HEC201 3.1 40.3 1.0 CD2 A:HIS102 3.1 47.3 1.0 C4B A:HEC201 3.2 41.7 1.0 CE1 A:HIS102 3.2 46.4 1.0 CHD A:HEC201 3.3 46.9 1.0 CE A:MET7 3.4 37.7 1.0 CHB A:HEC201 3.4 43.8 1.0 CG A:MET7 3.4 38.4 1.0 CHA A:HEC201 3.5 43.9 1.0 CHC A:HEC201 3.5 42.1 1.0 CB A:MET7 4.1 42.3 1.0 C3C A:HEC201 4.2 47.2 1.0 C2D A:HEC201 4.2 41.2 1.0 C2C A:HEC201 4.2 45.8 1.0 C3A A:HEC201 4.3 39.5 1.0 C3D A:HEC201 4.3 42.6 1.0 ND1 A:HIS102 4.3 51.1 1.0 CG A:HIS102 4.3 45.8 1.0 C2A A:HEC201 4.3 38.4 1.0 C2B A:HEC201 4.3 41.3 1.0 C3B A:HEC201 4.4 45.5 1.0 CA A:MET7 5.0 42.1 1.0

Iron binding site 2 out of 2 in the Metal-Free Structure of the Engineered Cyt CB562 Variant, CH3


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Metal-Free Structure of the Engineered Cyt CB562 Variant, CH3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:96.3 occ:1.00 FE C:HEC201 0.0 96.3 1.0 NB C:HEC201 1.9 87.6 1.0 NC C:HEC201 2.0 84.1 1.0 NA C:HEC201 2.2 89.0 1.0 ND C:HEC201 2.2 89.8 1.0 NE2 C:HIS102 2.4 83.9 1.0 SD C:MET7 2.6 93.2 1.0 CE C:MET7 2.8 86.9 1.0 C4B C:HEC201 2.9 84.7 1.0 C1B C:HEC201 3.0 85.5 1.0 C1C C:HEC201 3.0 91.0 1.0 C4C C:HEC201 3.0 84.4 1.0 C1D C:HEC201 3.1 90.8 1.0 C4A C:HEC201 3.1 87.7 1.0 CD2 C:HIS102 3.1 86.8 1.0 C4D C:HEC201 3.2 91.2 1.0 C1A C:HEC201 3.2 91.1 1.0 CHC C:HEC201 3.3 84.1 1.0 CHB C:HEC201 3.4 84.9 1.0 CHD C:HEC201 3.4 92.3 1.0 CE1 C:HIS102 3.5 86.1 1.0 CHA C:HEC201 3.6 93.0 1.0 CG C:MET7 4.0 91.1 1.0 CB C:MET7 4.0 86.5 1.0 C3B C:HEC201 4.2 82.9 1.0 C2B C:HEC201 4.2 80.0 1.0 C2C C:HEC201 4.2 94.9 1.0 C3C C:HEC201 4.3 93.0 1.0 C2D C:HEC201 4.4 91.7 1.0 CG C:HIS102 4.4 90.8 1.0 C3A C:HEC201 4.4 84.3 1.0 C3D C:HEC201 4.4 96.5 1.0 C2A C:HEC201 4.4 88.7 1.0 ND1 C:HIS102 4.5 88.4 1.0

J.Rittle, M.J.Field, M.T.Green, F.A.Tezcan. An Efficient, Step-Economical Strategy For the Design of Functional Metalloproteins. Nat.Chem. V. 11 434 2019.
ISSN: ESSN 1755-4349
PubMed: 30778140
DOI: 10.1038/S41557-019-0218-9