Zinc in PDB 3cpm: Plant Peptide Deformylase PDF1B Crystal Structure

All present enzymatic activity of Plant Peptide Deformylase PDF1B Crystal Structure:
3.5.1.88;

The structure of Plant Peptide Deformylase PDF1B Crystal Structure, PDB code: 3cpm was solved by D.W.Rodgers, R.L.Houtz, L.M.A.Dirk, J.J.Schmidt, Y.Cai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.64 / 2.40
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	50.902, 50.902, 144.783, 90.00, 90.00, 90.00
R / Rfree (%)	23.5 / 29.7

The binding sites of Zinc atom in the Plant Peptide Deformylase PDF1B Crystal Structure (pdb code 3cpm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Plant Peptide Deformylase PDF1B Crystal Structure, PDB code: 3cpm:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Plant Peptide Deformylase PDF1B Crystal Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Plant Peptide Deformylase PDF1B Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:15.8 occ:1.00 NE2 A:HIS217 1.9 16.1 1.0 NE2 A:HIS213 2.1 17.5 1.0 O A:HOH293 2.2 13.0 1.0 SG A:CYS171 2.4 14.8 1.0 CD2 A:HIS217 2.9 15.4 1.0 CE1 A:HIS217 2.9 13.1 1.0 CD2 A:HIS213 3.0 17.5 1.0 CE1 A:HIS213 3.1 17.3 1.0 NE2 A:GLN128 3.3 17.0 1.0 CB A:CYS171 3.4 16.6 1.0 O A:HOH265 3.5 2.4 1.0 CD A:GLN128 3.8 19.7 1.0 OE1 A:GLN128 3.8 21.3 1.0 O A:HOH258 3.9 13.1 1.0 CA A:CYS171 4.0 17.1 1.0 ND1 A:HIS217 4.0 14.2 1.0 CG A:HIS217 4.1 13.6 1.0 CG A:HIS213 4.1 16.2 1.0 ND1 A:HIS213 4.2 18.8 1.0 OE2 A:GLU214 4.2 21.9 1.0 O A:HOH278 4.3 11.1 1.0 OE1 A:GLU214 4.4 14.4 1.0 N A:LEU172 4.6 18.7 1.0 CD A:GLU214 4.6 16.8 1.0 C A:CYS171 4.7 17.4 1.0 O A:GLY170 4.8 18.0 1.0

Zinc binding site 2 out of 4 in the Plant Peptide Deformylase PDF1B Crystal Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Plant Peptide Deformylase PDF1B Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:24.3 occ:1.00 OD1 A:ASP110 2.0 21.1 1.0 OD2 A:ASP114 2.1 17.2 1.0 CG A:ASP114 2.9 18.4 1.0 CG A:ASP110 3.0 21.8 1.0 OD1 A:ASP114 3.1 18.1 1.0 OD2 A:ASP110 3.3 25.1 1.0 O A:ASP110 3.9 15.8 1.0 C A:ASP110 4.2 17.0 1.0 CB A:ASP110 4.3 20.0 1.0 CB A:ASP114 4.4 19.1 1.0 N A:ALA111 4.6 16.8 1.0 CA A:ALA111 4.6 17.6 1.0 CA A:ASP110 4.9 18.2 1.0

Zinc binding site 3 out of 4 in the Plant Peptide Deformylase PDF1B Crystal Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Plant Peptide Deformylase PDF1B Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn4 b:21.4 occ:1.00 OD2 A:ASP99 1.9 22.4 1.0 OD1 A:ASP74 2.4 39.9 1.0 CG A:ASP99 2.8 23.2 1.0 OD1 A:ASP99 2.9 23.6 1.0 CG A:ASP74 3.3 39.3 1.0 OD2 A:ASP74 3.6 37.3 1.0 CB A:ASP99 4.2 23.1 1.0 CG1 A:ILE100 4.2 19.1 1.0 N A:ASP99 4.3 22.7 1.0 CD1 A:ILE100 4.4 15.2 1.0 CB A:ASP74 4.5 39.2 1.0 CA A:ASP99 4.6 22.6 1.0 O A:ARG97 4.6 26.7 1.0 C A:ASP99 4.7 22.4 1.0 N A:ILE100 4.9 21.9 1.0 O A:ASP99 5.0 21.1 1.0 CB A:ILE100 5.0 20.3 1.0

Zinc binding site 4 out of 4 in the Plant Peptide Deformylase PDF1B Crystal Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Plant Peptide Deformylase PDF1B Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn5 b:41.0 occ:0.50 OE1 A:GLU237 2.2 29.0 1.0 OE1 A:GLU240 2.5 36.5 1.0 O A:HOH272 2.5 16.5 1.0 OE2 A:GLU237 2.8 32.4 1.0 CD A:GLU237 2.8 28.8 1.0 OE2 A:GLU240 2.9 38.6 1.0 CD A:GLU240 3.0 36.3 1.0 O A:HOH268 4.0 27.5 1.0 CG A:GLU237 4.3 25.2 1.0 CG A:GLU240 4.5 31.0 1.0 CA A:GLU237 4.9 21.6 1.0 CB A:GLU240 5.0 25.5 1.0

L.M.Dirk, J.J.Schmidt, Y.Cai, J.C.Barnes, K.M.Hanger, N.R.Nayak, M.A.Williams, R.B.Grossman, R.L.Houtz, D.W.Rodgers. Insights Into the Substrate Specificity of Plant Peptide Deformylase, An Essential Enzyme with Potential For the Development of Novel Biotechnology Applications in Agriculture Biochem.J. V. 413 417 2008.
ISSN: ISSN 0264-6021
PubMed: 18412546
DOI: 10.1042/BJ20071641