Iron in PDB 6ldf: Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96K AB5

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96K AB5, PDB code: 6ldf 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)	28.62 / 2.35
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	53.748, 53.748, 253.813, 90, 90, 120
R / Rfree (%)	17.3 / 24.5

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96K AB5 also contains other interesting chemical elements:

Zinc	(Zn)	8 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Iron atom in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96K AB5 (pdb code 6ldf). 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, C96K AB5, PDB code: 6ldf:
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, C96K 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, C96K AB5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:35.0 occ:1.00 FE A:HEC201 0.0 35.0 1.0 ND A:HEC201 1.9 34.8 1.0 NE2 A:HIS102 2.0 36.0 1.0 NA A:HEC201 2.0 38.6 1.0 NB A:HEC201 2.1 29.2 1.0 NC A:HEC201 2.1 35.0 1.0 SD A:MET7 2.3 34.9 1.0 C4D A:HEC201 2.9 38.7 1.0 CE1 A:HIS102 2.9 31.9 1.0 C1D A:HEC201 2.9 37.8 1.0 C1A A:HEC201 3.0 36.1 1.0 C4B A:HEC201 3.0 34.1 1.0 CD2 A:HIS102 3.0 31.2 1.0 C1B A:HEC201 3.1 34.8 1.0 C4A A:HEC201 3.1 38.9 1.0 C4C A:HEC201 3.1 35.6 1.0 C1C A:HEC201 3.1 34.3 1.0 CE A:MET7 3.2 36.0 1.0 CHA A:HEC201 3.3 35.8 1.0 CG A:MET7 3.4 34.3 1.0 CHD A:HEC201 3.4 36.0 1.0 CHC A:HEC201 3.5 31.1 1.0 CHB A:HEC201 3.5 35.6 1.0 ND1 A:HIS102 4.0 31.1 1.0 CB A:MET7 4.1 34.3 1.0 CG A:HIS102 4.1 33.1 1.0 C2D A:HEC201 4.2 35.0 1.0 C3D A:HEC201 4.2 39.2 1.0 C2A A:HEC201 4.2 40.1 1.0 C3A A:HEC201 4.2 36.4 1.0 C2B A:HEC201 4.3 30.7 1.0 C2C A:HEC201 4.3 34.4 1.0 C3B A:HEC201 4.3 30.5 1.0 C3C A:HEC201 4.3 31.4 1.0 NH2 A:ARG106 4.8 40.5 1.0 CA A:MET7 4.9 32.7 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, C96K 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, C96K AB5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:37.8 occ:1.00 FE C:HEC201 0.0 37.8 1.0 ND C:HEC201 1.9 38.0 1.0 NE2 C:HIS102 1.9 35.5 1.0 NA C:HEC201 2.0 41.3 1.0 NB C:HEC201 2.1 37.9 1.0 NC C:HEC201 2.1 35.1 1.0 SD C:MET7 2.3 37.6 1.0 CE1 C:HIS102 2.9 34.8 1.0 C4D C:HEC201 2.9 38.2 1.0 C1D C:HEC201 2.9 39.7 1.0 C1A C:HEC201 3.0 39.0 1.0 CD2 C:HIS102 3.0 34.4 1.0 C4B C:HEC201 3.0 38.7 1.0 C1B C:HEC201 3.1 40.6 1.0 C4A C:HEC201 3.1 42.4 1.0 C4C C:HEC201 3.1 35.1 1.0 C1C C:HEC201 3.1 33.1 1.0 CE C:MET7 3.3 36.2 1.0 CG C:MET7 3.3 40.7 1.0 CHA C:HEC201 3.3 38.3 1.0 CHD C:HEC201 3.4 33.6 1.0 CHB C:HEC201 3.5 37.5 1.0 CHC C:HEC201 3.5 36.9 1.0 ND1 C:HIS102 4.0 35.4 1.0 CG C:HIS102 4.1 32.5 1.0 CB C:MET7 4.1 37.8 1.0 C3D C:HEC201 4.2 34.7 1.0 C2D C:HEC201 4.2 33.8 1.0 C2A C:HEC201 4.2 48.7 1.0 C3A C:HEC201 4.3 46.5 1.0 C2B C:HEC201 4.3 38.1 1.0 C3B C:HEC201 4.3 37.5 1.0 C2C C:HEC201 4.3 35.7 1.0 C3C C:HEC201 4.4 31.3 1.0 CA C:MET7 4.8 37.4 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