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

The structure of Fe(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3, PDB code: 6dye 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)	32.45 / 2.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	32.994, 82.687, 38.779, 90.00, 100.39, 90.00
R / Rfree (%)	19.8 / 27

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

Calcium

(Ca)

1 atom

The binding sites of Iron atom in the Fe(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3 (pdb code 6dye). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Fe(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3, PDB code: 6dye:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Fe(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 Fe(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:16.2 occ:1.00 NE2 A:HIS97 2.0 15.4 1.0 O A:HOH326 2.0 8.5 1.0 NE2 A:HIS71 2.2 16.8 1.0 NE2 A:HIS67 2.2 16.0 1.0 NE2 B:HIS67 2.3 15.2 1.0 NE2 B:HIS71 2.4 15.8 1.0 CE1 A:HIS97 2.8 15.2 1.0 CE1 A:HIS71 3.0 19.1 1.0 CD2 B:HIS67 3.1 17.0 1.0 CD2 A:HIS97 3.1 13.2 1.0 CE1 A:HIS67 3.2 10.8 1.0 CD2 A:HIS67 3.2 15.7 1.0 CD2 B:HIS71 3.2 14.8 1.0 CD2 A:HIS71 3.3 18.5 1.0 CE1 B:HIS71 3.4 14.5 1.0 CE1 B:HIS67 3.5 20.8 1.0 ND1 A:HIS97 4.0 17.6 1.0 CG A:HIS97 4.1 17.1 1.0 ND1 A:HIS71 4.2 22.7 1.0 O B:HOH330 4.3 14.7 1.0 ND1 A:HIS67 4.3 9.1 1.0 CG B:HIS67 4.3 17.2 1.0 CG A:HIS67 4.3 13.5 1.0 CG A:HIS71 4.3 17.6 1.0 CG B:HIS71 4.4 13.0 1.0 ND1 B:HIS67 4.5 19.4 1.0 ND1 B:HIS71 4.5 13.9 1.0

Iron binding site 2 out of 3 in the Fe(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 Fe(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:14.6 occ:1.00 FE A:HEC202 0.0 14.6 1.0 NA A:HEC202 2.0 15.8 1.0 NC A:HEC202 2.0 11.1 1.0 ND A:HEC202 2.1 11.6 1.0 NB A:HEC202 2.1 12.8 1.0 NE2 A:HIS102 2.3 9.5 1.0 SD A:MET7 2.5 16.7 1.0 C4A A:HEC202 3.0 13.9 1.0 C4C A:HEC202 3.1 9.3 1.0 C1C A:HEC202 3.1 10.3 1.0 C1A A:HEC202 3.1 13.3 1.0 C1D A:HEC202 3.1 13.3 1.0 C1B A:HEC202 3.1 11.8 1.0 C4D A:HEC202 3.1 13.2 1.0 C4B A:HEC202 3.1 11.7 1.0 CD2 A:HIS102 3.2 14.9 1.0 CE1 A:HIS102 3.3 10.7 1.0 CE A:MET7 3.3 12.3 1.0 CHB A:HEC202 3.4 12.9 1.0 CHD A:HEC202 3.4 9.1 1.0 CHA A:HEC202 3.4 13.7 1.0 CHC A:HEC202 3.4 11.8 1.0 CG A:MET7 3.5 13.0 1.0 C3A A:HEC202 4.2 14.4 1.0 C2A A:HEC202 4.3 19.1 1.0 C2C A:HEC202 4.3 8.7 1.0 C3C A:HEC202 4.3 8.0 1.0 C2B A:HEC202 4.3 12.2 1.0 C2D A:HEC202 4.3 10.9 1.0 CG A:HIS102 4.3 12.6 1.0 C3B A:HEC202 4.3 9.5 1.0 C3D A:HEC202 4.3 12.6 1.0 ND1 A:HIS102 4.3 16.7 1.0 CB A:MET7 4.4 15.1 1.0 CA A:MET7 5.0 18.5 1.0

Iron binding site 3 out of 3 in the Fe(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 3 of Fe(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:9.6 occ:1.00 FE B:HEC201 0.0 9.6 1.0 NB B:HEC201 2.0 8.7 1.0 ND B:HEC201 2.1 8.4 1.0 NA B:HEC201 2.1 13.0 1.0 NC B:HEC201 2.1 10.4 1.0 NE2 B:HIS102 2.2 6.0 1.0 SD B:MET7 2.5 6.5 1.0 C4D B:HEC201 3.0 14.7 1.0 C1A B:HEC201 3.0 13.0 1.0 C4B B:HEC201 3.0 11.4 1.0 C1D B:HEC201 3.1 8.5 1.0 C1B B:HEC201 3.1 9.8 1.0 C1C B:HEC201 3.1 10.6 1.0 C4A B:HEC201 3.1 12.4 1.0 C4C B:HEC201 3.1 10.2 1.0 CD2 B:HIS102 3.2 11.2 1.0 CE1 B:HIS102 3.2 11.5 1.0 CE B:MET7 3.3 13.6 1.0 CHA B:HEC201 3.3 13.3 1.0 CG B:MET7 3.4 14.6 1.0 CHC B:HEC201 3.4 11.8 1.0 CHD B:HEC201 3.5 6.0 1.0 CHB B:HEC201 3.5 10.6 1.0 CB B:MET7 4.1 10.1 1.0 C3D B:HEC201 4.3 10.1 1.0 C2A B:HEC201 4.3 11.7 1.0 C3B B:HEC201 4.3 10.3 1.0 C2D B:HEC201 4.3 8.8 1.0 C2B B:HEC201 4.3 7.7 1.0 ND1 B:HIS102 4.3 10.8 1.0 C3A B:HEC201 4.3 13.2 1.0 CG B:HIS102 4.3 11.7 1.0 C2C B:HEC201 4.4 10.2 1.0 C3C B:HEC201 4.4 14.7 1.0 CA B:MET7 4.9 9.8 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