Zinc in PDB 1zy0: X-Ray Structure of Peptide Deformylase From Arabidopsis Thaliana (ATPDF1A); Crystals Grown in Peg-6000

All present enzymatic activity of X-Ray Structure of Peptide Deformylase From Arabidopsis Thaliana (ATPDF1A); Crystals Grown in Peg-6000:
3.5.1.88;

The structure of X-Ray Structure of Peptide Deformylase From Arabidopsis Thaliana (ATPDF1A); Crystals Grown in Peg-6000, PDB code: 1zy0 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 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.500, 76.800, 109.300, 90.00, 90.00, 90.00
R / Rfree (%)	24.3 / 28.3

The binding sites of Zinc atom in the X-Ray Structure of Peptide Deformylase From Arabidopsis Thaliana (ATPDF1A); Crystals Grown in Peg-6000 (pdb code 1zy0). 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-6000, PDB code: 1zy0:
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-6000


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-6000 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn198 b:60.0 occ:1.00 NE2 A:HIS157 1.9 53.7 1.0 O A:HOH199 2.0 33.6 1.0 NE2 A:HIS153 2.0 50.6 1.0 CE1 A:HIS157 2.4 50.7 1.0 SG A:CYS111 2.4 65.6 1.0 CE1 A:HIS153 2.7 49.9 1.0 CB A:CYS111 3.1 62.9 1.0 NE2 A:GLN54 3.1 62.5 1.0 CD2 A:HIS153 3.2 51.0 1.0 CD2 A:HIS157 3.2 53.8 1.0 ND1 A:HIS157 3.6 50.5 1.0 CA A:CYS111 3.6 63.8 1.0 CD A:GLN54 3.8 61.0 1.0 OE2 A:GLU154 3.9 55.8 1.0 OE1 A:GLN54 3.9 62.1 1.0 ND1 A:HIS153 3.9 50.1 1.0 CG A:HIS157 4.0 52.7 1.0 CG A:HIS153 4.2 50.9 1.0 N A:LEU112 4.3 64.6 1.0 C A:CYS111 4.4 64.8 1.0 O A:GLY110 4.5 63.6 1.0 OE1 A:GLU154 4.6 57.2 1.0 CD A:GLU154 4.6 56.0 1.0 CD2 A:LEU162 4.8 53.5 1.0 N A:CYS111 4.8 63.5 1.0 CG A:GLN54 4.9 57.8 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-6000


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-6000 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn198 b:64.9 occ:1.00 NE2 B:HIS153 1.9 53.4 1.0 NE2 B:HIS157 2.0 54.1 1.0 O B:HOH199 2.3 79.5 1.0 SG B:CYS111 2.4 71.8 1.0 CE1 B:HIS153 2.6 51.8 1.0 CE1 B:HIS157 2.8 54.2 1.0 CB B:CYS111 3.1 67.7 1.0 CD2 B:HIS157 3.1 54.6 1.0 CD2 B:HIS153 3.1 53.3 1.0 NE2 B:GLN54 3.1 62.1 1.0 CA B:CYS111 3.6 67.2 1.0 CD B:GLN54 3.8 62.4 1.0 ND1 B:HIS153 3.8 51.6 1.0 OE1 B:GLN54 3.9 63.6 1.0 OE2 B:GLU154 3.9 56.8 1.0 ND1 B:HIS157 4.0 54.6 1.0 CG B:HIS153 4.1 52.9 1.0 CG B:HIS157 4.1 54.9 1.0 N B:LEU112 4.3 66.2 1.0 O B:HOH244 4.3 44.4 1.0 C B:CYS111 4.4 67.0 1.0 O B:GLY110 4.4 67.4 1.0 CD B:GLU154 4.7 56.9 1.0 N B:CYS111 4.8 66.5 1.0 OE1 B:GLU154 4.8 58.3 1.0 CD2 B:LEU162 4.9 54.1 1.0 CG B:GLN54 5.0 61.0 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