Nickel in PDB 6ow7: X-Ray Structure of Polypeptide Deformylase with A Piperazic Acid

All present enzymatic activity of X-Ray Structure of Polypeptide Deformylase with A Piperazic Acid:
3.5.1.88;

The structure of X-Ray Structure of Polypeptide Deformylase with A Piperazic Acid, PDB code: 6ow7 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)	38.28 / 1.45
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	69.229, 69.229, 91.879, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 21.8

The binding sites of Nickel atom in the X-Ray Structure of Polypeptide Deformylase with A Piperazic Acid (pdb code 6ow7). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the X-Ray Structure of Polypeptide Deformylase with A Piperazic Acid, PDB code: 6ow7:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the X-Ray Structure of Polypeptide Deformylase with A Piperazic Acid


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 with A Piperazic Acid within 5.0Å range: probe atom residue distance (Å) B Occ P:Ni301 b:21.7 occ:1.00 O01 P:N9Y303 2.0 23.9 1.0 NE2 P:HIS173 2.1 17.6 1.0 NE2 P:HIS177 2.1 21.7 1.0 H32 P:N9Y303 2.1 28.7 1.0 O31 P:N9Y303 2.3 19.7 1.0 SG P:CYS130 2.3 21.5 1.0 N02 P:N9Y303 2.8 21.6 1.0 C30 P:N9Y303 2.9 20.8 1.0 CD2 P:HIS177 3.1 20.3 1.0 CD2 P:HIS173 3.1 19.6 1.0 CE1 P:HIS173 3.1 20.5 1.0 CE1 P:HIS177 3.1 21.4 1.0 NE2 P:GLN77 3.3 19.7 1.0 CB P:CYS130 3.4 21.8 1.0 O P:HOH482 3.7 22.4 1.0 H58 P:N9Y303 3.8 25.0 1.0 CA P:CYS130 3.8 21.5 1.0 CD P:GLN77 4.0 20.1 1.0 C03 P:N9Y303 4.1 22.2 1.0 N P:LEU131 4.2 21.7 1.0 H35 P:N9Y303 4.2 25.3 1.0 ND1 P:HIS173 4.2 21.4 1.0 OE1 P:GLN77 4.2 18.9 1.0 ND1 P:HIS177 4.2 21.8 1.0 CG P:HIS173 4.2 19.1 1.0 CG P:HIS177 4.2 18.1 1.0 H05 P:N9Y303 4.4 26.6 1.0 H34 P:N9Y303 4.4 26.7 1.0 C P:CYS130 4.5 22.3 1.0 O P:HOH453 4.6 20.3 1.0 C04 P:N9Y303 4.7 22.1 1.0 OE1 P:GLU174 4.7 20.3 1.0 O P:GLY129 4.7 24.0 1.0 H33 P:N9Y303 4.8 26.7 1.0 C06 P:N9Y303 4.9 21.1 1.0 CG P:GLN77 5.0 17.6 1.0

Nickel binding site 2 out of 2 in the X-Ray Structure of Polypeptide Deformylase with A Piperazic Acid


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of X-Ray Structure of Polypeptide Deformylase with A Piperazic Acid within 5.0Å range: probe atom residue distance (Å) B Occ Q:Ni301 b:23.8 occ:1.00 H32 Q:N9Y303 2.0 33.1 1.0 NE2 Q:HIS177 2.1 21.4 1.0 NE2 Q:HIS173 2.1 19.8 1.0 O01 Q:N9Y303 2.2 27.6 1.0 O31 Q:N9Y303 2.3 20.1 1.0 SG Q:CYS130 2.4 23.9 1.0 C30 Q:N9Y303 2.9 18.8 1.0 N02 Q:N9Y303 2.9 23.4 1.0 CD2 Q:HIS177 3.0 17.1 1.0 CD2 Q:HIS173 3.0 22.6 1.0 CE1 Q:HIS177 3.1 20.3 1.0 CE1 Q:HIS173 3.1 24.2 1.0 NE2 Q:GLN77 3.2 22.1 1.0 CB Q:CYS130 3.4 27.1 1.0 O Q:HOH455 3.8 23.3 1.0 H58 Q:N9Y303 3.8 22.6 1.0 CA Q:CYS130 3.8 24.8 1.0 CD Q:GLN77 3.9 19.5 1.0 N Q:LEU131 4.2 24.1 1.0 CG Q:HIS177 4.2 18.9 1.0 ND1 Q:HIS177 4.2 21.3 1.0 CG Q:HIS173 4.2 20.9 1.0 OE1 Q:GLN77 4.2 21.7 1.0 ND1 Q:HIS173 4.2 25.8 1.0 C03 Q:N9Y303 4.2 25.4 1.0 H05 Q:N9Y303 4.4 31.2 1.0 H35 Q:N9Y303 4.5 31.2 1.0 C Q:CYS130 4.5 27.1 1.0 H34 Q:N9Y303 4.5 30.4 1.0 O Q:HOH441 4.6 22.6 1.0 OE1 Q:GLU174 4.6 20.5 1.0 C04 Q:N9Y303 4.7 26.0 1.0 O Q:GLY129 4.8 24.2 1.0 H33 Q:N9Y303 4.8 30.4 1.0 CG Q:GLN77 4.9 19.1 1.0 H37 Q:N9Y303 5.0 36.8 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