Zinc in PDB 2okl: Crystal Structure of Peptide Deformylase 2 with Actinonin From Bacillus Cereus

All present enzymatic activity of Crystal Structure of Peptide Deformylase 2 with Actinonin From Bacillus Cereus:
3.5.1.88;

The structure of Crystal Structure of Peptide Deformylase 2 with Actinonin From Bacillus Cereus, PDB code: 2okl was solved by E.E.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.87 / 1.70
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	69.447, 69.447, 294.412, 90.00, 90.00, 120.00
R / Rfree (%)	22.8 / 25.7

The binding sites of Zinc atom in the Crystal Structure of Peptide Deformylase 2 with Actinonin From Bacillus Cereus (pdb code 2okl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Peptide Deformylase 2 with Actinonin From Bacillus Cereus, PDB code: 2okl:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Peptide Deformylase 2 with Actinonin From Bacillus Cereus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Peptide Deformylase 2 with Actinonin From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:25.7 occ:1.00 NE2 A:HIS153 2.1 21.3 1.0 NE2 A:HIS157 2.2 29.8 1.0 O2 A:BB2401 2.3 21.3 1.0 SG A:CYS110 2.4 23.1 1.0 O4 A:BB2401 2.4 29.2 1.0 N1 A:BB2401 2.8 24.0 1.0 C3 A:BB2401 2.9 25.6 1.0 CD2 A:HIS153 3.0 20.6 1.0 CE1 A:HIS153 3.1 21.6 1.0 CD2 A:HIS157 3.1 24.4 1.0 NE2 A:GLN65 3.2 22.5 1.0 CE1 A:HIS157 3.2 25.4 1.0 CB A:CYS110 3.4 22.9 1.0 O A:HOH620 3.5 23.6 1.0 CD A:GLN65 3.9 26.1 1.0 CA A:CYS110 3.9 25.2 1.0 OE1 A:GLN65 4.1 25.4 1.0 CG A:HIS153 4.1 19.4 1.0 ND1 A:HIS153 4.2 21.6 1.0 CG A:HIS157 4.3 25.6 1.0 N A:LEU111 4.3 23.7 1.0 C5 A:BB2401 4.3 25.3 1.0 ND1 A:HIS157 4.3 25.4 1.0 OE1 A:GLU154 4.6 24.3 1.0 C A:CYS110 4.6 27.4 1.0 O A:HOH604 4.6 21.8 1.0 C6 A:BB2401 4.6 25.5 1.0 OE2 A:GLU154 4.8 24.4 1.0 C7 A:BB2401 4.8 27.2 1.0 O A:GLY109 4.9 27.4 1.0 CG A:GLN65 5.0 24.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Peptide Deformylase 2 with Actinonin From Bacillus Cereus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Peptide Deformylase 2 with Actinonin From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:23.0 occ:1.00 NE2 B:HIS153 2.1 17.4 1.0 NE2 B:HIS157 2.1 18.6 1.0 O2 B:BB2403 2.2 28.4 1.0 O4 B:BB2403 2.4 26.6 1.0 SG B:CYS110 2.4 22.4 1.0 N1 B:BB2403 2.8 26.9 1.0 C3 B:BB2403 2.9 26.6 1.0 CD2 B:HIS153 3.0 18.8 1.0 CE1 B:HIS157 3.1 16.5 1.0 NE2 B:GLN65 3.1 27.0 1.0 CE1 B:HIS153 3.2 21.2 1.0 CD2 B:HIS157 3.2 18.6 1.0 CB B:CYS110 3.4 21.4 1.0 O B:HOH614 3.6 19.8 1.0 CD B:GLN65 3.8 24.1 1.0 CA B:CYS110 3.9 22.6 1.0 OE1 B:GLN65 4.1 22.9 1.0 ND1 B:HIS157 4.2 18.4 1.0 CG B:HIS153 4.2 19.5 1.0 ND1 B:HIS153 4.2 21.2 1.0 N B:LEU111 4.3 26.6 1.0 CG B:HIS157 4.3 17.7 1.0 C5 B:BB2403 4.3 23.7 1.0 C B:CYS110 4.5 24.6 1.0 C6 B:BB2403 4.6 21.9 1.0 O B:HOH609 4.7 19.2 1.0 OE1 B:GLU154 4.7 24.7 1.0 OE2 B:GLU154 4.8 24.8 1.0 C7 B:BB2403 4.9 24.6 1.0 O B:GLY109 4.9 22.2 1.0 CG B:GLN65 5.0 25.5 1.0

J.K.Park, K.H.Kim, J.H.Moon, E.E.Kim. Characterization of Peptide DEFORMYLASE2 From B. Cereus J.Biochem.Mol.Biol. V. 40 1050 2007.
ISSN: ISSN 1225-8687
PubMed: 18047803