Iron in PDB 6dyh: Vanadyl-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y

The structure of Vanadyl-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y, PDB code: 6dyh 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)	38.37 / 1.83
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	31.973, 83.482, 39.033, 90.00, 100.57, 90.00
R / Rfree (%)	18.3 / 23.4

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

Vanadium

(V)

1 atom

The binding sites of Iron atom in the Vanadyl-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y (pdb code 6dyh). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Vanadyl-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y, PDB code: 6dyh:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Vanadyl-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 Vanadyl-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:23.1 occ:1.00 FE A:HEC202 0.0 23.1 1.0 NA A:HEC202 2.0 27.1 1.0 NC A:HEC202 2.0 20.6 1.0 NE2 A:HIS102 2.0 25.7 1.0 NB A:HEC202 2.0 25.9 1.0 ND A:HEC202 2.1 25.9 1.0 SD A:MET7 2.4 20.8 1.0 CD2 A:HIS102 3.0 24.5 1.0 C4A A:HEC202 3.0 27.0 1.0 C1C A:HEC202 3.0 22.7 1.0 C1B A:HEC202 3.1 21.1 1.0 C1A A:HEC202 3.1 25.9 1.0 C4C A:HEC202 3.1 20.2 1.0 CE1 A:HIS102 3.1 27.5 1.0 C4B A:HEC202 3.1 21.2 1.0 C1D A:HEC202 3.1 21.9 1.0 C4D A:HEC202 3.1 25.1 1.0 CE A:MET7 3.3 23.5 1.0 CHB A:HEC202 3.4 25.8 1.0 CG A:MET7 3.4 22.5 1.0 CHC A:HEC202 3.4 22.6 1.0 CHD A:HEC202 3.4 21.2 1.0 CHA A:HEC202 3.5 26.1 1.0 CG A:HIS102 4.1 22.3 1.0 ND1 A:HIS102 4.1 22.0 1.0 CB A:MET7 4.3 23.3 1.0 C3A A:HEC202 4.3 27.5 1.0 C2A A:HEC202 4.3 27.5 1.0 C2C A:HEC202 4.3 21.0 1.0 C2B A:HEC202 4.3 26.0 1.0 C3C A:HEC202 4.3 17.8 1.0 C3B A:HEC202 4.3 21.1 1.0 C2D A:HEC202 4.3 23.2 1.0 C3D A:HEC202 4.3 24.8 1.0 NH1 A:ARG106 4.9 35.2 1.0

Iron binding site 2 out of 2 in the Vanadyl-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 Vanadyl-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:22.6 occ:1.00 FE D:HEC201 0.0 22.6 1.0 NE2 D:HIS102 1.9 22.0 1.0 NB D:HEC201 2.0 24.2 1.0 NC D:HEC201 2.0 21.9 1.0 ND D:HEC201 2.1 21.9 1.0 NA D:HEC201 2.1 19.1 1.0 SD D:MET7 2.3 23.6 1.0 CE1 D:HIS102 2.9 20.2 1.0 CD2 D:HIS102 3.0 20.8 1.0 C4B D:HEC201 3.0 24.6 1.0 C1B D:HEC201 3.1 22.2 1.0 C1C D:HEC201 3.1 21.7 1.0 C4C D:HEC201 3.1 21.6 1.0 C1D D:HEC201 3.1 19.8 1.0 C1A D:HEC201 3.1 23.2 1.0 C4D D:HEC201 3.1 21.9 1.0 C4A D:HEC201 3.1 23.4 1.0 CE D:MET7 3.4 26.8 1.0 CHC D:HEC201 3.4 20.3 1.0 CHD D:HEC201 3.4 21.7 1.0 CHB D:HEC201 3.5 25.0 1.0 CG D:MET7 3.5 21.5 1.0 CHA D:HEC201 3.5 24.6 1.0 ND1 D:HIS102 4.0 25.1 1.0 CG D:HIS102 4.1 23.0 1.0 CB D:MET7 4.2 23.0 1.0 C3B D:HEC201 4.2 22.4 1.0 C2B D:HEC201 4.2 24.1 1.0 C3C D:HEC201 4.3 17.4 1.0 C2C D:HEC201 4.3 20.1 1.0 C2D D:HEC201 4.3 20.8 1.0 C2A D:HEC201 4.3 22.2 1.0 C3D D:HEC201 4.3 20.9 1.0 C3A D:HEC201 4.3 23.0 1.0 CA D:MET7 5.0 22.5 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