Nickel in PDB 6ow2: X-Ray Structure of Polypeptide Deformylase

All present enzymatic activity of X-Ray Structure of Polypeptide Deformylase:
3.5.1.88;

The structure of X-Ray Structure of Polypeptide Deformylase, PDB code: 6ow2 was solved by N.Campobasso, J.Spletstoser, P.Ward, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.85 / 1.70
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	50.334, 50.334, 91.482, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 22.3

The structure of X-Ray Structure of Polypeptide Deformylase also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Nickel atom in the X-Ray Structure of Polypeptide Deformylase (pdb code 6ow2). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the X-Ray Structure of Polypeptide Deformylase, PDB code: 6ow2:

Nickel binding site 1 out of 1 in the X-Ray Structure of Polypeptide Deformylase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of X-Ray Structure of Polypeptide Deformylase within 5.0Å range: probe atom residue distance (Å) B Occ P:Ni301 b:22.6 occ:1.00 O19 P:NB4302 1.9 24.6 1.0 NE2 P:HIS177 2.0 19.8 1.0 NE2 P:HIS173 2.2 17.9 1.0 O21 P:NB4302 2.3 20.7 1.0 SG P:CYS130 2.4 23.3 1.0 N18 P:NB4302 2.7 21.5 1.0 C20 P:NB4302 2.8 17.2 1.0 CD2 P:HIS177 3.0 20.0 1.0 CE1 P:HIS177 3.0 19.4 1.0 CD2 P:HIS173 3.1 20.4 1.0 CE1 P:HIS173 3.1 20.5 1.0 NE2 P:GLN77 3.3 19.8 1.0 CB P:CYS130 3.5 23.4 1.0 O P:HOH461 3.6 22.3 1.0 CA P:CYS130 3.8 24.1 1.0 H42 P:NB4302 4.0 22.8 1.0 CD P:GLN77 4.0 19.3 1.0 C17 P:NB4302 4.1 21.2 1.0 ND1 P:HIS177 4.1 20.1 1.0 CG P:HIS177 4.2 19.1 1.0 N P:LEU131 4.2 20.5 1.0 H10 P:NB4302 4.2 25.1 1.0 ND1 P:HIS173 4.3 18.7 1.0 CG P:HIS173 4.3 21.3 1.0 OE1 P:GLN77 4.3 19.4 1.0 H53 P:NB4302 4.4 25.5 1.0 C P:CYS130 4.5 22.3 1.0 O P:HOH449 4.6 19.9 1.0 C09 P:NB4302 4.6 20.9 1.0 OE1 P:GLU174 4.6 17.1 1.0 H54 P:NB4302 4.7 25.5 1.0 C11 P:NB4302 4.7 19.0 1.0 O P:GLY129 4.7 29.4 1.0 CG P:GLN77 5.0 18.2 1.0 OE2 P:GLU174 5.0 17.4 1.0

J.T.Spletstoser, J.Dreabit, A.N.Knox, A.Benowitz, N.Campobasso, P.Ward, G.Cui, T.Lewandowski, L.Mccloskey, K.M.Aubart. Discovery of Piperazic Acid Peptide Deformylase Inhibitors with in Vivo Activity For Respiratory Tract and Skin Infections. Bioorg.Med.Chem.Lett. V. 29 2410 2019.
ISSN: ESSN 1464-3405
PubMed: 31160176
DOI: 10.1016/J.BMCL.2019.05.028