Zinc in PDB 1zxz: X-Ray Structure of Peptide Deformylase From Arabidopsis Thaliana (ATPDF1A); Crystals Grown in Peg-5000 Mme As Precipitant

All present enzymatic activity of X-Ray Structure of Peptide Deformylase From Arabidopsis Thaliana (ATPDF1A); Crystals Grown in Peg-5000 Mme As Precipitant:
3.5.1.88;

The structure of X-Ray Structure of Peptide Deformylase From Arabidopsis Thaliana (ATPDF1A); Crystals Grown in Peg-5000 Mme As Precipitant, PDB code: 1zxz was solved by S.Fieulaine, C.Juillan-Binard, A.Serero, F.Dardel, C.Giglione, T.Meinnel, J.-L.Ferrer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.200, 73.800, 109.400, 90.00, 90.00, 90.00
R / Rfree (%)	23.6 / 29.1

The binding sites of Zinc atom in the X-Ray Structure of Peptide Deformylase From Arabidopsis Thaliana (ATPDF1A); Crystals Grown in Peg-5000 Mme As Precipitant (pdb code 1zxz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the X-Ray Structure of Peptide Deformylase From Arabidopsis Thaliana (ATPDF1A); Crystals Grown in Peg-5000 Mme As Precipitant, PDB code: 1zxz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the X-Ray Structure of Peptide Deformylase From Arabidopsis Thaliana (ATPDF1A); Crystals Grown in Peg-5000 Mme As Precipitant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of Peptide Deformylase From Arabidopsis Thaliana (ATPDF1A); Crystals Grown in Peg-5000 Mme As Precipitant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn198 b:26.5 occ:1.00 NE2 A:HIS153 2.0 19.9 1.0 NE2 A:HIS157 2.1 19.6 1.0 O A:HOH199 2.1 31.2 1.0 SG A:CYS111 2.4 28.7 1.0 CE1 A:HIS153 3.0 21.0 1.0 CE1 A:HIS157 3.0 18.9 1.0 CD2 A:HIS157 3.0 21.0 1.0 CD2 A:HIS153 3.0 19.8 1.0 CB A:CYS111 3.3 24.0 1.0 OE1 A:GLN54 3.4 25.5 1.0 NE2 A:GLN54 3.7 23.6 1.0 CD A:GLN54 3.7 24.6 1.0 O A:HOH277 3.8 15.8 1.0 CA A:CYS111 3.9 25.0 1.0 ND1 A:HIS153 4.1 21.0 1.0 ND1 A:HIS157 4.1 19.6 1.0 CG A:HIS157 4.2 21.3 1.0 CG A:HIS153 4.2 20.1 1.0 OE2 A:GLU154 4.3 34.7 1.0 N A:LEU112 4.5 24.8 1.0 C A:CYS111 4.7 24.8 1.0 O A:GLY110 4.7 23.9 1.0 OE1 A:GLU154 4.8 36.4 1.0 CD A:GLU154 4.8 32.5 1.0 O A:HOH205 4.8 10.7 1.0 CG A:GLN54 4.9 25.0 1.0

Zinc binding site 2 out of 2 in the X-Ray Structure of Peptide Deformylase From Arabidopsis Thaliana (ATPDF1A); Crystals Grown in Peg-5000 Mme As Precipitant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of Peptide Deformylase From Arabidopsis Thaliana (ATPDF1A); Crystals Grown in Peg-5000 Mme As Precipitant within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn198 b:24.5 occ:1.00 NE2 B:HIS153 2.0 23.2 1.0 NE2 B:HIS157 2.3 25.6 1.0 O B:HOH199 2.3 29.0 1.0 SG B:CYS111 2.4 29.6 1.0 CE1 B:HIS153 2.9 24.0 1.0 CB B:CYS111 3.0 25.6 1.0 CD2 B:HIS153 3.1 23.1 1.0 CD2 B:HIS157 3.3 26.6 1.0 CE1 B:HIS157 3.3 26.3 1.0 O B:HOH239 3.5 12.9 1.0 NE2 B:GLN54 3.5 22.6 1.0 CA B:CYS111 3.5 25.2 1.0 OE1 B:GLN54 3.9 25.9 1.0 CD B:GLN54 4.0 24.5 1.0 ND1 B:HIS153 4.1 23.4 1.0 CG B:HIS153 4.2 24.0 1.0 OE2 B:GLU154 4.2 27.9 1.0 N B:LEU112 4.3 24.7 1.0 C B:CYS111 4.3 25.5 1.0 ND1 B:HIS157 4.4 26.3 1.0 CG B:HIS157 4.4 27.8 1.0 O B:GLY110 4.5 25.1 1.0 N B:CYS111 4.7 25.1 1.0 CD B:GLU154 4.9 26.6 1.0

S.Fieulaine, C.Juillan-Binard, A.Serero, F.Dardel, C.Giglione, T.Meinnel, J.-L.Ferrer. The Crystal Structure of Mitochondrial (Type 1A) Peptide Deformylase Provides Clear Guidelines For the Design of Inhibitors Specific For the Bacterial Forms J.Biol.Chem. V. 280 42315 2005.
ISSN: ISSN 0021-9258
PubMed: 16192279
DOI: 10.1074/JBC.M507155200