Iron in PDB 7dcl: Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5, PDB code: 7dcl was solved by W.J.Song, J.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.53 / 2.45
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	53.408, 53.408, 251.61, 90, 90, 120
R / Rfree (%)	19.7 / 25.6

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5 also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Zinc	(Zn)	8 atoms

The binding sites of Iron atom in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5 (pdb code 7dcl). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5, PDB code: 7dcl:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:26.2 occ:1.00 FE A:HEC201 0.0 26.2 1.0 ND A:HEC201 1.9 27.1 1.0 NA A:HEC201 2.0 27.6 1.0 NE2 A:HIS102 2.1 26.6 1.0 NC A:HEC201 2.1 26.3 1.0 NB A:HEC201 2.1 26.4 1.0 SD A:MET7 2.3 28.6 1.0 C4D A:HEC201 2.9 27.5 1.0 C1D A:HEC201 2.9 27.0 1.0 C1A A:HEC201 3.0 28.2 1.0 CD2 A:HIS102 3.0 27.5 1.0 C4C A:HEC201 3.1 26.2 1.0 CE1 A:HIS102 3.1 27.4 1.0 C4B A:HEC201 3.1 25.9 1.0 C4A A:HEC201 3.1 28.5 1.0 C1C A:HEC201 3.1 25.7 1.0 C1B A:HEC201 3.1 26.2 1.0 CE A:MET7 3.3 28.2 1.0 CG A:MET7 3.3 31.1 1.0 CHA A:HEC201 3.4 27.9 1.0 CHD A:HEC201 3.4 25.7 1.0 CHC A:HEC201 3.5 26.2 1.0 CHB A:HEC201 3.5 26.5 1.0 CB A:MET7 4.1 30.0 1.0 ND1 A:HIS102 4.2 28.3 1.0 C2D A:HEC201 4.2 27.0 1.0 C3D A:HEC201 4.2 27.6 1.0 CG A:HIS102 4.2 27.8 1.0 C2A A:HEC201 4.2 31.0 1.0 C3A A:HEC201 4.3 29.2 1.0 C3C A:HEC201 4.3 26.6 1.0 C2C A:HEC201 4.3 26.8 1.0 C2B A:HEC201 4.3 24.4 1.0 C3B A:HEC201 4.4 25.0 1.0 CA A:MET7 4.9 30.4 1.0

Iron binding site 2 out of 2 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:25.1 occ:1.00 FE B:HEC201 0.0 25.1 1.0 ND B:HEC201 1.9 27.0 1.0 NA B:HEC201 2.0 26.4 1.0 NE2 B:HIS102 2.1 25.3 1.0 NC B:HEC201 2.1 25.1 1.0 NB B:HEC201 2.1 24.8 1.0 SD B:MET7 2.3 25.4 1.0 C4D B:HEC201 2.9 28.5 1.0 C1D B:HEC201 3.0 27.3 1.0 C1A B:HEC201 3.0 26.4 1.0 CD2 B:HIS102 3.0 25.1 1.0 C4A B:HEC201 3.1 25.6 1.0 C4C B:HEC201 3.1 25.4 1.0 C1B B:HEC201 3.1 24.6 1.0 C4B B:HEC201 3.1 24.4 1.0 CE1 B:HIS102 3.1 25.9 1.0 C1C B:HEC201 3.1 24.7 1.0 CHA B:HEC201 3.4 26.9 1.0 CE B:MET7 3.4 25.7 1.0 CG B:MET7 3.4 24.6 1.0 CHD B:HEC201 3.4 26.8 1.0 CHB B:HEC201 3.5 24.5 1.0 CHC B:HEC201 3.5 24.2 1.0 CB B:MET7 4.2 25.1 1.0 ND1 B:HIS102 4.2 25.7 1.0 CG B:HIS102 4.2 26.1 1.0 C2A B:HEC201 4.2 27.6 1.0 C3D B:HEC201 4.2 29.8 1.0 C2D B:HEC201 4.2 28.4 1.0 C3A B:HEC201 4.2 25.6 1.0 C3C B:HEC201 4.3 24.9 1.0 C2B B:HEC201 4.3 24.0 1.0 C2C B:HEC201 4.3 24.4 1.0 C3B B:HEC201 4.3 23.7 1.0 NH2 B:ARG106 5.0 38.3 1.0 CA B:MET7 5.0 26.2 1.0

J.Yu, J.Yang, C.Seok, W.J.Song. Symmetry-Related Residues As Promising Hotspots For the Evolution of De Novo Oligomeric Enzymes Chem Sci 2021.
ISSN: ESSN 2041-6539
DOI: 10.1039/D0SC06823C