Zinc in PDB 8ofe: E.Coli Peptide Deformylase with Bound Inhibitor

The structure of E.Coli Peptide Deformylase with Bound Inhibitor, PDB code: 8ofe was solved by H.Kirschner, R.Stoll, E.Hofmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.79 / 1.40
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	54.62, 54.62, 231.73, 90, 90, 120
R / Rfree (%)	17.1 / 20.4

The binding sites of Zinc atom in the E.Coli Peptide Deformylase with Bound Inhibitor (pdb code 8ofe). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the E.Coli Peptide Deformylase with Bound Inhibitor, PDB code: 8ofe:

Zinc binding site 1 out of 1 in the E.Coli Peptide Deformylase with Bound Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of E.Coli Peptide Deformylase with Bound Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:24.9 occ:1.00 H15 A:VLK201 1.7 37.6 0.8 O1 A:VLK201 2.1 31.4 0.8 NE2 A:HIS132 2.1 23.6 1.0 O2 A:VLK201 2.1 30.1 0.8 NE2 A:HIS136 2.2 25.9 1.0 SG A:CYS90 2.3 27.2 0.9 C8 A:VLK201 2.9 29.4 0.8 N1 A:VLK201 2.9 29.9 0.8 CD2 A:HIS132 3.0 25.4 1.0 HE22 A:GLN50 3.1 32.4 1.0 HD2 A:HIS132 3.1 30.5 1.0 CE1 A:HIS136 3.1 26.0 1.0 CD2 A:HIS136 3.1 25.4 1.0 CE1 A:HIS132 3.2 23.8 1.0 HA A:CYS90 3.2 34.0 1.0 HD2 A:HIS136 3.3 30.5 1.0 HE1 A:HIS136 3.3 31.2 1.0 HB2 A:CYS90 3.3 33.5 1.0 CB A:CYS90 3.3 27.9 1.0 HE1 A:HIS132 3.4 28.5 1.0 NE2 A:GLN50 3.5 27.0 1.0 O A:HOH363 3.6 26.3 1.0 H A:LEU91 3.7 35.8 1.0 CA A:CYS90 3.8 28.3 1.0 H16 A:VLK201 3.8 35.3 0.8 HE21 A:GLN50 3.8 32.4 1.0 H12 A:VLK201 3.9 38.6 0.8 CD A:GLN50 4.0 27.0 1.0 H11 A:VLK201 4.0 38.1 0.8 OE1 A:GLN50 4.2 25.9 1.0 H A:SER92 4.2 35.5 1.0 HB3 A:CYS90 4.2 33.5 1.0 C7 A:VLK201 4.2 28.9 0.8 CG A:HIS132 4.2 23.1 1.0 ND1 A:HIS132 4.3 23.6 1.0 ND1 A:HIS136 4.3 27.3 1.0 N A:LEU91 4.3 29.9 1.0 CG A:HIS136 4.3 25.0 1.0 C6 A:VLK201 4.4 32.2 0.8 C A:CYS90 4.5 27.9 1.0 O A:HOH353 4.6 24.3 1.0 H13 A:VLK201 4.6 34.7 0.8 OE1 A:GLU133 4.6 27.7 1.0 O A:GLY89 4.7 30.4 1.0 C5 A:VLK201 4.7 31.8 0.8 HB2 A:SER92 4.7 37.3 1.0 OE2 A:GLU133 4.8 30.2 1.0 H14 A:VLK201 4.9 34.7 0.8 HD2 A:PHE142 4.9 35.0 1.0 HG2 A:GLN50 4.9 32.3 1.0 N A:CYS90 5.0 29.7 1.0

H.Kirschner, M.John, T.Zhou, N.Bachmann, A.Schultz, E.Hofmann, J.E.Bandow, J.Scherkenbeck, N.Metzler-Nolte, R.Stoll. Structural Insights Into Antibacterial Payload Release From Gold Nanoparticles Bound to E. Coli Peptide Deformylase. Chemmedchem 00538 2023.
ISSN: ESSN 1860-7187
PubMed: 38057137
DOI: 10.1002/CMDC.202300538