Zinc in PDB 1dff: Peptide Deformylase

All present enzymatic activity of Peptide Deformylase:
3.5.1.31;

The structure of Peptide Deformylase, PDB code: 1dff was solved by M.K.Chan, W.Gong, P.T.R.Rajagopalan, B.Hao, C.M.Tsai, D.Pei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.88
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	55.350, 55.350, 230.920, 90.00, 90.00, 120.00
R / Rfree (%)	18.4 / 28.9

The binding sites of Zinc atom in the Peptide Deformylase (pdb code 1dff). 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 Peptide Deformylase, PDB code: 1dff:

Zinc binding site 1 out of 1 in the Peptide Deformylase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Peptide Deformylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn165 b:16.6 occ:1.00 NE2 A:HIS136 2.1 7.9 1.0 NE2 A:HIS132 2.2 7.8 1.0 SG A:CYS90 2.3 12.8 1.0 O A:HOH166 2.3 12.7 1.0 CE1 A:HIS136 3.1 12.1 1.0 CD2 A:HIS136 3.1 8.4 1.0 CB A:CYS90 3.1 11.6 1.0 CE1 A:HIS132 3.2 6.0 1.0 CD2 A:HIS132 3.2 2.5 1.0 CA A:CYS90 3.7 11.9 1.0 NE2 A:GLN50 3.8 13.9 1.0 OE1 A:GLN50 4.0 16.0 1.0 CD A:GLN50 4.1 7.2 1.0 ND1 A:HIS136 4.2 4.7 1.0 CG A:HIS136 4.2 4.6 1.0 ND1 A:HIS132 4.3 6.5 1.0 CG A:HIS132 4.4 4.6 1.0 O A:HOH212 4.4 49.2 1.0 N A:LEU91 4.5 21.2 1.0 C A:CYS90 4.6 16.6 1.0 OE1 A:GLU133 4.6 21.4 1.0 O A:GLY89 4.7 14.1 1.0 OE2 A:GLU133 4.7 14.8 1.0 N A:CYS90 4.9 8.7 1.0 CD A:GLU133 5.0 17.4 1.0

M.K.Chan, W.Gong, P.T.Rajagopalan, B.Hao, C.M.Tsai, D.Pei. Crystal Structure of the Escherichia Coli Peptide Deformylase. Biochemistry V. 36 13904 1997.
ISSN: ISSN 0006-2960
PubMed: 9374869
DOI: 10.1021/BI9711543