Iron in PDB 6dyd: Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3

The structure of Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3, PDB code: 6dyd 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)	37.28 / 1.72
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	32.569, 87.770, 37.460, 90.00, 95.56, 90.00
R / Rfree (%)	19.6 / 24.7

The structure of Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3 also contains other interesting chemical elements:

Copper	(Cu)	1 atom
Calcium	(Ca)	5 atoms

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

Iron binding site 1 out of 2 in the Cu(II)-Bound 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 Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:17.4 occ:1.00 FE A:HEC203 0.0 17.4 1.0 ND A:HEC203 2.0 13.5 1.0 NB A:HEC203 2.0 12.1 1.0 NA A:HEC203 2.0 16.1 1.0 NE2 A:HIS102 2.0 17.6 1.0 NC A:HEC203 2.1 18.4 1.0 SD A:MET7 2.3 16.9 1.0 CD2 A:HIS102 3.0 18.0 1.0 C4D A:HEC203 3.0 18.3 1.0 C1B A:HEC203 3.0 18.5 1.0 C4A A:HEC203 3.0 16.3 1.0 CE1 A:HIS102 3.0 16.7 1.0 C1A A:HEC203 3.1 19.5 1.0 C1D A:HEC203 3.1 15.3 1.0 C4B A:HEC203 3.1 17.0 1.0 C1C A:HEC203 3.1 15.3 1.0 C4C A:HEC203 3.1 15.9 1.0 CHA A:HEC203 3.4 20.3 1.0 CHB A:HEC203 3.4 19.4 1.0 CG A:MET7 3.4 14.2 1.0 CHC A:HEC203 3.5 14.3 1.0 CHD A:HEC203 3.5 17.3 1.0 CE A:MET7 3.5 17.0 1.0 ND1 A:HIS102 4.1 18.8 1.0 CG A:HIS102 4.2 20.3 1.0 CB A:MET7 4.2 19.7 1.0 C3A A:HEC203 4.2 21.1 1.0 C3D A:HEC203 4.3 21.2 1.0 C2A A:HEC203 4.3 24.2 1.0 C2B A:HEC203 4.3 16.2 1.0 C2D A:HEC203 4.3 17.2 1.0 C3B A:HEC203 4.3 15.8 1.0 C2C A:HEC203 4.3 16.3 1.0 C3C A:HEC203 4.3 14.6 1.0 CA A:MET7 5.0 18.7 1.0

Iron binding site 2 out of 2 in the Cu(II)-Bound 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 Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe204 b:25.0 occ:1.00 FE C:HEC204 0.0 25.0 1.0 NB C:HEC204 2.0 26.6 1.0 NA C:HEC204 2.0 26.0 1.0 NC C:HEC204 2.1 22.0 1.0 ND C:HEC204 2.1 25.1 1.0 NE2 C:HIS102 2.1 25.3 1.0 SD C:MET7 2.4 24.2 1.0 C4B C:HEC204 3.0 22.3 1.0 C1B C:HEC204 3.0 25.1 1.0 C4A C:HEC204 3.0 24.7 1.0 C1C C:HEC204 3.1 25.7 1.0 C4D C:HEC204 3.1 25.4 1.0 C1A C:HEC204 3.1 31.9 1.0 C1D C:HEC204 3.1 21.6 1.0 CD2 C:HIS102 3.1 22.5 1.0 CE1 C:HIS102 3.1 25.4 1.0 C4C C:HEC204 3.1 20.4 1.0 CE C:MET7 3.3 27.7 1.0 CHC C:HEC204 3.4 20.2 1.0 CHB C:HEC204 3.4 24.1 1.0 CHA C:HEC204 3.4 30.0 1.0 CHD C:HEC204 3.5 21.0 1.0 CG C:MET7 3.5 26.1 1.0 ND1 C:HIS102 4.2 22.7 1.0 C3B C:HEC204 4.2 23.9 1.0 C2B C:HEC204 4.2 26.0 1.0 CG C:HIS102 4.2 25.6 1.0 CB C:MET7 4.3 26.5 1.0 C3A C:HEC204 4.3 27.8 1.0 C2A C:HEC204 4.3 26.4 1.0 C2C C:HEC204 4.3 18.1 1.0 C2D C:HEC204 4.3 25.3 1.0 C3D C:HEC204 4.3 27.5 1.0 C3C C:HEC204 4.3 17.1 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