Vanadium 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:

Iron

(Fe)

2 atoms

The binding sites of Vanadium 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 Vanadium atom.
In total only one binding site of Vanadium was determined in the Vanadyl-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y, PDB code: 6dyh:

Vanadium binding site 1 out of 1 in the Vanadyl-Bound Structure of the Engineered Cyt CB562 Variant, CH3Y


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V 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:V201 b:16.8 occ:1.00 NE2 A:HIS71 2.0 20.6 1.0 NE2 A:HIS97 2.1 21.0 1.0 NE2 A:HIS67 2.1 20.2 1.0 NE2 D:HIS67 2.1 21.8 1.0 NE2 D:HIS71 2.1 19.8 1.0 O A:HOH343 2.2 23.5 1.0 CD2 D:HIS67 3.0 21.2 1.0 CE1 A:HIS97 3.0 22.1 1.0 CE1 A:HIS67 3.0 23.6 1.0 CE1 A:HIS71 3.0 24.4 1.0 CD2 A:HIS71 3.0 23.3 1.0 CE1 D:HIS71 3.1 23.3 1.0 CD2 D:HIS71 3.1 19.1 1.0 CD2 A:HIS97 3.1 24.6 1.0 CD2 A:HIS67 3.1 21.9 1.0 CE1 D:HIS67 3.2 24.0 1.0 ND1 A:HIS97 4.1 20.7 1.0 ND1 A:HIS71 4.1 25.0 1.0 O A:HOH372 4.2 34.0 1.0 ND1 A:HIS67 4.2 23.3 1.0 CG A:HIS71 4.2 27.2 1.0 CG D:HIS67 4.2 22.3 1.0 CG A:HIS97 4.2 17.6 1.0 ND1 D:HIS71 4.2 22.1 1.0 CG A:HIS67 4.2 23.5 1.0 ND1 D:HIS67 4.3 22.6 1.0 CG D:HIS71 4.3 21.2 1.0 CD2 D:TYR70 4.5 22.8 1.0 CE2 D:TYR70 4.6 24.6 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