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

Enzymatic activity of 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;

Protein crystallography data

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

Nickel Binding Sites:

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 6ow7

Go back to Nickel Binding Sites List in 6ow7
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 6ow7

Go back to Nickel Binding Sites List in 6ow7
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

Reference:

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
Page generated: Wed Dec 16 01:53:01 2020

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