Zinc in PDB 8rhr: E.Coli Peptide Deformylase with Bound Inhibitor BB4

The structure of E.Coli Peptide Deformylase with Bound Inhibitor BB4, PDB code: 8rhr 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)	46.51 / 1.42
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	54.85, 54.85, 228.58, 90, 90, 120
R / Rfree (%)	16.3 / 18.7

The structure of E.Coli Peptide Deformylase with Bound Inhibitor BB4 also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Zinc atom in the E.Coli Peptide Deformylase with Bound Inhibitor BB4 (pdb code 8rhr). 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 BB4, PDB code: 8rhr:

Zinc binding site 1 out of 1 in the E.Coli Peptide Deformylase with Bound Inhibitor BB4


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 BB4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:26.1 occ:1.00 O14 A:BB4202 1.9 35.2 0.8 NE2 A:HIS136 2.1 24.7 1.0 NE2 A:HIS132 2.1 23.4 1.0 SG A:CYS90 2.2 27.1 1.0 N1 A:BB4202 2.2 26.1 0.8 HN1 A:BB4202 2.7 31.3 0.8 HO14 A:BB4202 2.8 42.2 0.8 CD2 A:HIS132 3.0 23.7 1.0 CE1 A:HIS136 3.1 25.3 1.0 C13 A:BB4202 3.1 26.8 0.8 CD2 A:HIS136 3.1 25.2 1.0 HD2 A:HIS132 3.1 28.5 1.0 CE1 A:HIS132 3.1 24.7 1.0 HE1 A:HIS136 3.2 30.4 1.0 HE22 A:GLN50 3.3 33.7 1.0 HD2 A:HIS136 3.3 30.2 1.0 HA A:CYS90 3.3 32.5 1.0 HB2 A:CYS90 3.3 33.7 1.0 CB A:CYS90 3.3 28.1 1.0 O2 A:BB4202 3.4 25.5 0.8 HE1 A:HIS132 3.4 29.6 1.0 O A:HOH358 3.6 24.7 1.0 NE2 A:GLN50 3.6 28.1 1.0 CA A:CYS90 3.8 27.1 1.0 CD A:GLN50 4.0 27.9 1.0 HE21 A:GLN50 4.0 33.7 1.0 H A:LEU91 4.0 32.2 1.0 OE1 A:GLN50 4.1 26.0 1.0 ND1 A:HIS136 4.2 26.1 1.0 HB3 A:CYS90 4.2 33.7 1.0 CG A:HIS132 4.2 22.6 1.0 CG A:HIS136 4.2 25.5 1.0 ND1 A:HIS132 4.2 23.7 1.0 C12 A:BB4202 4.3 29.7 0.8 OE2 A:GLU133 4.3 28.9 1.0 H A:SER92 4.3 34.0 1.0 H12A A:BB4202 4.3 35.7 0.8 OE1 A:GLU133 4.5 27.6 1.0 O A:HOH351 4.5 23.5 1.0 N A:LEU91 4.5 26.9 1.0 O A:GLY89 4.6 26.1 1.0 C A:CYS90 4.6 28.1 1.0 CD A:GLU133 4.7 25.6 1.0 HB2 A:SER92 4.8 36.9 1.0 C5 A:BB4202 4.8 27.4 0.8 H7 A:BB4202 4.8 30.9 0.8 HD2 A:PHE142 4.8 34.0 1.0 HG2 A:GLN50 4.9 33.0 1.0 HD1 A:HIS136 4.9 31.4 1.0 H12 A:BB4202 5.0 35.7 0.8

H.Kirschner, N.Heister, M.Zouatom, T.Zhou, E.Hofmann, J.Scherkenbeck, R.Stoll. Toward More Selective Antibiotic Inhibitors: A Structural View of the Complexed Binding Pocket of E. Coli Peptide Deformylase. J.Med.Chem. 2024.
ISSN: ISSN 0022-2623
PubMed: 38574272
DOI: 10.1021/ACS.JMEDCHEM.3C02382