Iron in PDB 6lde: Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96V AB5

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96V AB5, PDB code: 6lde 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)	46.55 / 2.00
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	53.757, 53.757, 250.721, 90, 90, 120
R / Rfree (%)	17.9 / 24

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96V AB5 also contains other interesting chemical elements:

Zinc	(Zn)	6 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Iron atom in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96V AB5 (pdb code 6lde). 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, C96V AB5, PDB code: 6lde:
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, C96V 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, C96V AB5 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 ND A:HEC201 1.9 13.8 1.0 NE2 A:HIS102 1.9 12.8 1.0 NA A:HEC201 2.0 16.9 1.0 NB A:HEC201 2.1 14.5 1.0 NC A:HEC201 2.1 14.2 1.0 SD A:MET7 2.3 14.4 1.0 CE1 A:HIS102 2.9 12.8 1.0 C4D A:HEC201 2.9 15.7 1.0 C1D A:HEC201 2.9 14.5 1.0 C1A A:HEC201 3.0 17.1 1.0 CD2 A:HIS102 3.0 13.4 1.0 C4A A:HEC201 3.0 16.0 1.0 C4B A:HEC201 3.0 15.2 1.0 C1B A:HEC201 3.1 15.5 1.0 C4C A:HEC201 3.1 14.1 1.0 C1C A:HEC201 3.1 15.2 1.0 CE A:MET7 3.4 15.0 1.0 CHA A:HEC201 3.4 15.5 1.0 CG A:MET7 3.4 14.5 1.0 CHD A:HEC201 3.4 13.8 1.0 CHB A:HEC201 3.4 15.4 1.0 CHC A:HEC201 3.5 14.8 1.0 ND1 A:HIS102 4.0 12.2 1.0 CG A:HIS102 4.1 13.5 1.0 CB A:MET7 4.1 15.2 1.0 C2D A:HEC201 4.2 13.7 1.0 C3D A:HEC201 4.2 15.7 1.0 C2A A:HEC201 4.2 18.9 1.0 C3A A:HEC201 4.2 17.4 1.0 C2C A:HEC201 4.3 15.7 1.0 C2B A:HEC201 4.3 15.6 1.0 C3C A:HEC201 4.3 14.8 1.0 C3B A:HEC201 4.3 15.3 1.0 CA A:MET7 4.9 16.5 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, C96V 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, C96V AB5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:12.0 occ:1.00 FE C:HEC201 0.0 12.0 1.0 ND C:HEC201 1.9 12.0 1.0 NE2 C:HIS102 1.9 11.2 1.0 NA C:HEC201 2.0 11.8 1.0 NB C:HEC201 2.0 12.1 1.0 NC C:HEC201 2.1 11.3 1.0 SD C:MET7 2.3 12.2 1.0 CE1 C:HIS102 3.0 11.9 1.0 C4D C:HEC201 3.0 12.5 1.0 CD2 C:HIS102 3.0 11.6 1.0 C1D C:HEC201 3.0 12.0 1.0 C1B C:HEC201 3.0 13.1 1.0 C1A C:HEC201 3.0 11.7 1.0 C4B C:HEC201 3.0 12.1 1.0 C4A C:HEC201 3.0 12.8 1.0 C1C C:HEC201 3.1 11.3 1.0 C4C C:HEC201 3.1 11.6 1.0 CHA C:HEC201 3.4 12.5 1.0 CE C:MET7 3.4 14.3 1.0 CHB C:HEC201 3.4 12.9 1.0 CHC C:HEC201 3.4 10.7 1.0 CG C:MET7 3.5 12.8 1.0 CHD C:HEC201 3.5 11.1 1.0 ND1 C:HIS102 4.1 11.7 1.0 CG C:HIS102 4.1 11.7 1.0 C2B C:HEC201 4.2 13.1 1.0 C3D C:HEC201 4.2 13.7 1.0 C2D C:HEC201 4.2 12.4 1.0 C2A C:HEC201 4.2 13.2 1.0 C3A C:HEC201 4.2 12.9 1.0 CB C:MET7 4.3 12.8 1.0 C2C C:HEC201 4.3 10.7 1.0 C3B C:HEC201 4.3 13.0 1.0 C3C C:HEC201 4.3 10.7 1.0 NH2 C:ARG106 4.7 19.5 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