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

The structure of Co(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3, PDB code: 6dyc 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)	38.52 / 1.33
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	33.239, 83.290, 39.170, 90.00, 100.49, 90.00
R / Rfree (%)	17.6 / 19.2

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

Cobalt	(Co)	1 atom
Calcium	(Ca)	1 atom

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

Iron binding site 1 out of 2 in the Co(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 Co(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:11.5 occ:1.00 FE A:HEC202 0.0 11.5 1.0 NE2 A:HIS102 2.0 12.2 1.0 NA A:HEC202 2.0 12.6 1.0 NB A:HEC202 2.0 10.9 1.0 NC A:HEC202 2.0 10.4 1.0 ND A:HEC202 2.1 12.3 1.0 SD A:MET7 2.3 12.0 1.0 CD2 A:HIS102 3.0 12.3 1.0 CE1 A:HIS102 3.0 12.9 1.0 C1A A:HEC202 3.0 13.9 1.0 C4B A:HEC202 3.0 11.3 1.0 C1C A:HEC202 3.0 11.2 1.0 C1D A:HEC202 3.0 11.5 1.0 C4A A:HEC202 3.1 13.9 1.0 C1B A:HEC202 3.1 11.6 1.0 C4C A:HEC202 3.1 11.1 1.0 C4D A:HEC202 3.1 12.0 1.0 HD2 A:HIS102 3.2 14.7 1.0 HE1 A:HIS102 3.2 15.5 1.0 HG3 A:MET7 3.3 16.6 1.0 CE A:MET7 3.4 15.3 1.0 HE3 A:MET7 3.4 18.4 1.0 CHC A:HEC202 3.4 10.6 1.0 CHA A:HEC202 3.4 13.3 1.0 CHB A:HEC202 3.4 12.9 1.0 CHD A:HEC202 3.4 11.6 1.0 CG A:MET7 3.4 13.8 1.0 HE1 A:MET7 3.5 18.4 1.0 HB3 A:MET7 3.8 16.6 1.0 ND1 A:HIS102 4.1 12.7 1.0 CG A:HIS102 4.1 12.3 1.0 HG2 A:MET7 4.2 16.6 1.0 HE2 A:MET7 4.2 18.4 1.0 CB A:MET7 4.2 13.8 1.0 C2A A:HEC202 4.2 15.0 1.0 C3B A:HEC202 4.3 11.0 1.0 C3A A:HEC202 4.3 14.4 1.0 C2D A:HEC202 4.3 15.2 1.0 C2C A:HEC202 4.3 11.2 1.0 C2B A:HEC202 4.3 11.0 1.0 C3C A:HEC202 4.3 10.7 1.0 C3D A:HEC202 4.3 14.7 1.0 HHC A:HEC202 4.4 12.8 1.0 HHA A:HEC202 4.4 15.9 1.0 HHB A:HEC202 4.4 15.5 1.0 HHD A:HEC202 4.4 13.9 1.0 HD12 A:LEU10 4.6 18.2 1.0 HA A:MET7 4.6 16.5 1.0 HB3 A:CYS98 4.7 14.1 1.0 HD2 A:ARG106 4.8 20.2 1.0 HD1 A:HIS102 4.9 15.2 1.0 HB2 A:MET7 5.0 16.6 1.0

Iron binding site 2 out of 2 in the Co(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 Co(II)-Bound Structure of the Engineered Cyt CB562 Variant, CH3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:10.9 occ:1.00 FE B:HEC201 0.0 10.9 1.0 NA B:HEC201 2.0 10.2 1.0 NE2 B:HIS102 2.0 10.6 1.0 ND B:HEC201 2.0 12.5 1.0 NB B:HEC201 2.0 12.4 1.0 NC B:HEC201 2.0 10.9 1.0 SD B:MET7 2.3 12.1 1.0 CE1 B:HIS102 3.0 12.1 1.0 CD2 B:HIS102 3.0 10.4 1.0 C4A B:HEC201 3.0 11.8 1.0 C1D B:HEC201 3.0 11.3 1.0 C4B B:HEC201 3.0 10.9 1.0 C4D B:HEC201 3.0 10.1 1.0 C1B B:HEC201 3.0 10.0 1.0 C1C B:HEC201 3.1 11.0 1.0 C1A B:HEC201 3.1 10.8 1.0 C4C B:HEC201 3.1 11.6 1.0 HD2 B:HIS102 3.2 12.5 1.0 HE1 B:HIS102 3.2 14.5 1.0 HG3 B:MET7 3.3 14.9 1.0 CE B:MET7 3.3 21.4 1.0 CHB B:HEC201 3.4 11.4 1.0 HE3 B:MET7 3.4 25.7 1.0 CHC B:HEC201 3.4 10.9 1.0 CG B:MET7 3.4 12.4 1.0 CHA B:HEC201 3.4 10.2 1.0 HE1 B:MET7 3.4 25.7 1.0 CHD B:HEC201 3.5 10.6 1.0 HB3 B:MET7 3.8 16.0 1.0 ND1 B:HIS102 4.1 12.2 1.0 CG B:HIS102 4.1 9.8 1.0 HG2 B:MET7 4.2 14.9 1.0 CB B:MET7 4.2 13.3 1.0 HE2 B:MET7 4.2 25.7 1.0 HD2 B:ARG106 4.2 15.8 1.0 C3B B:HEC201 4.2 12.9 1.0 C3D B:HEC201 4.2 12.0 1.0 C2D B:HEC201 4.2 13.6 1.0 C3A B:HEC201 4.3 11.9 1.0 C2A B:HEC201 4.3 11.9 1.0 C2B B:HEC201 4.3 12.1 1.0 C2C B:HEC201 4.3 11.6 1.0 C3C B:HEC201 4.3 12.9 1.0 HHB B:HEC201 4.4 13.7 1.0 HHC B:HEC201 4.4 13.1 1.0 HHA B:HEC201 4.4 12.2 1.0 HHD B:HEC201 4.4 12.7 1.0 HA B:MET7 4.6 14.1 1.0 HB3 B:CYS98 4.6 16.0 1.0 HD13 B:LEU10 4.7 17.9 1.0 HD1 B:HIS102 4.9 14.7 1.0 HH21 B:ARG106 4.9 18.2 1.0 HB2 B:ARG106 4.9 13.1 1.0 HB2 B:MET7 4.9 16.0 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