Iron in PDB 6dyf: Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y

The structure of Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y, PDB code: 6dyf 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)	41.44 / 1.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	34.742, 82.882, 38.528, 90.00, 98.96, 90.00
R / Rfree (%)	14.7 / 16.5

The structure of Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Copper	(Cu)	1 atom

The binding sites of Iron atom in the Cu(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y (pdb code 6dyf). 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, CH3Y, PDB code: 6dyf:
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, CH3Y


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, CH3Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:14.1 occ:1.00 FE A:HEC201 0.0 14.1 1.0 NA A:HEC201 2.0 15.4 1.0 NB A:HEC201 2.0 14.3 1.0 ND A:HEC201 2.0 15.1 1.0 NE2 A:HIS102 2.0 15.2 1.0 NC A:HEC201 2.0 13.5 1.0 SD A:MET7 2.3 14.0 1.0 CE1 A:HIS102 3.0 15.2 1.0 CD2 A:HIS102 3.0 15.0 1.0 C1A A:HEC201 3.0 17.2 1.0 C4B A:HEC201 3.0 13.4 1.0 C4A A:HEC201 3.0 16.0 1.0 C1D A:HEC201 3.0 14.3 1.0 C1C A:HEC201 3.0 13.4 1.0 C1B A:HEC201 3.0 14.1 1.0 C4D A:HEC201 3.0 15.7 1.0 C4C A:HEC201 3.1 13.6 1.0 HE1 A:HIS102 3.2 18.3 1.0 HD2 A:HIS102 3.2 18.0 1.0 HG3 A:MET7 3.2 17.9 1.0 CE A:MET7 3.3 15.2 1.0 HE3 A:MET7 3.4 18.2 1.0 CHC A:HEC201 3.4 13.4 1.0 CHA A:HEC201 3.4 15.4 1.0 CG A:MET7 3.4 14.9 1.0 CHB A:HEC201 3.4 15.7 1.0 CHD A:HEC201 3.4 13.8 1.0 HE1 A:MET7 3.4 18.2 1.0 HB3 A:MET7 3.8 18.7 1.0 ND1 A:HIS102 4.1 15.8 1.0 CG A:HIS102 4.1 15.4 1.0 HG2 A:MET7 4.2 17.9 1.0 HE2 A:MET7 4.2 18.2 1.0 CB A:MET7 4.2 15.6 1.0 C2A A:HEC201 4.2 19.8 1.0 C2D A:HEC201 4.2 14.8 1.0 C3A A:HEC201 4.2 18.0 1.0 C3B A:HEC201 4.2 13.6 1.0 C2B A:HEC201 4.3 13.9 1.0 C2C A:HEC201 4.3 13.4 1.0 C3D A:HEC201 4.3 15.3 1.0 C3C A:HEC201 4.3 13.6 1.0 HHC A:HEC201 4.4 16.1 1.0 HHA A:HEC201 4.4 18.5 1.0 HHB A:HEC201 4.4 18.8 1.0 HHD A:HEC201 4.4 16.6 1.0 HA A:MET7 4.6 18.2 1.0 HD12 A:LEU10 4.7 18.1 1.0 HB3 A:CYS98 4.8 16.5 1.0 HD1 A:HIS102 4.9 18.9 1.0 HA A:CYS98 4.9 16.9 1.0 HB2 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, CH3Y


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, CH3Y within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:10.6 occ:1.00 FE B:HEC201 0.0 10.6 1.0 NB B:HEC201 2.0 11.2 1.0 NC B:HEC201 2.0 10.7 1.0 NA B:HEC201 2.0 11.5 1.0 ND B:HEC201 2.0 11.4 1.0 NE2 B:HIS102 2.0 11.2 1.0 SD B:MET7 2.3 10.9 1.0 CE1 B:HIS102 3.0 11.6 1.0 C1C B:HEC201 3.0 11.3 1.0 C4B B:HEC201 3.0 10.8 1.0 C4D B:HEC201 3.0 11.3 1.0 CD2 B:HIS102 3.0 11.0 1.0 C4A B:HEC201 3.0 11.7 1.0 C1D B:HEC201 3.0 11.3 1.0 C1A B:HEC201 3.0 11.4 1.0 C4C B:HEC201 3.0 11.1 1.0 C1B B:HEC201 3.0 11.4 1.0 HE1 B:HIS102 3.2 13.9 1.0 HD2 B:HIS102 3.2 13.2 1.0 HG3 B:MET7 3.3 13.8 1.0 CHC B:HEC201 3.4 11.2 1.0 CE B:MET7 3.4 13.6 1.0 CHB B:HEC201 3.4 11.5 1.0 CHA B:HEC201 3.4 11.3 1.0 CHD B:HEC201 3.4 10.9 1.0 HE3 B:MET7 3.4 16.3 1.0 CG B:MET7 3.4 11.5 1.0 HE1 B:MET7 3.5 16.3 1.0 HB3 B:MET7 3.9 13.5 1.0 ND1 B:HIS102 4.1 12.1 1.0 CG B:HIS102 4.2 11.8 1.0 HG2 B:MET7 4.2 13.8 1.0 C3D B:HEC201 4.2 11.7 1.0 C3B B:HEC201 4.2 11.3 1.0 HE2 B:MET7 4.2 16.3 1.0 C2A B:HEC201 4.3 12.1 1.0 C2C B:HEC201 4.3 11.3 1.0 C3A B:HEC201 4.3 12.1 1.0 C2B B:HEC201 4.3 11.5 1.0 C2D B:HEC201 4.3 11.9 1.0 CB B:MET7 4.3 11.2 1.0 HD2 B:ARG106 4.3 15.0 1.0 C3C B:HEC201 4.3 11.4 1.0 HHC B:HEC201 4.4 13.5 1.0 HHB B:HEC201 4.4 13.8 1.0 HHA B:HEC201 4.4 13.6 1.0 HHD B:HEC201 4.4 13.1 1.0 HA B:MET7 4.6 13.8 1.0 HD13 B:LEU10 4.7 15.8 1.0 HB3 B:CYS98 4.7 15.8 1.0 HD1 B:HIS102 4.9 14.5 1.0 HH21 B:ARG106 5.0 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