Zinc in PDB 1ix1: Crystal Structure of P.Aeruginosa Peptide Deformylase Complexed with Antibiotic Actinonin

All present enzymatic activity of Crystal Structure of P.Aeruginosa Peptide Deformylase Complexed with Antibiotic Actinonin:
3.5.1.88;

The structure of Crystal Structure of P.Aeruginosa Peptide Deformylase Complexed with Antibiotic Actinonin, PDB code: 1ix1 was solved by H.-W.Kim, H.-J.Yoon, J.Y.Lee, B.W.Han, J.K.Yang, B.I.Lee, H.J.Ahn, H.H.Lee, S.W.Suh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.98 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.750, 74.460, 77.180, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 21.4

The binding sites of Zinc atom in the Crystal Structure of P.Aeruginosa Peptide Deformylase Complexed with Antibiotic Actinonin (pdb code 1ix1). 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 P.Aeruginosa Peptide Deformylase Complexed with Antibiotic Actinonin, PDB code: 1ix1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of P.Aeruginosa Peptide Deformylase Complexed with Antibiotic Actinonin


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 P.Aeruginosa Peptide Deformylase Complexed with Antibiotic Actinonin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:18.9 occ:1.00 NE2 A:HIS134 2.1 11.0 1.0 NE2 A:HIS138 2.1 11.6 1.0 SG A:CYS92 2.3 13.2 1.0 O4 A:BB21301 2.4 20.9 1.0 O2 A:BB21301 2.5 18.5 1.0 C3 A:BB21301 2.9 22.9 1.0 N1 A:BB21301 3.0 22.5 1.0 CD2 A:HIS134 3.1 9.6 1.0 CD2 A:HIS138 3.1 11.3 1.0 CE1 A:HIS134 3.1 11.1 1.0 CE1 A:HIS138 3.1 13.0 1.0 NE2 A:GLN51 3.3 12.6 1.0 CB A:CYS92 3.3 13.6 1.0 O A:HOH1311 3.5 9.8 1.0 CA A:CYS92 3.8 13.5 1.0 CD A:GLN51 4.0 12.7 1.0 OE1 A:GLN51 4.1 13.3 1.0 C5 A:BB21301 4.2 23.1 1.0 ND1 A:HIS134 4.2 12.2 1.0 CG A:HIS134 4.2 11.0 1.0 ND1 A:HIS138 4.2 10.4 1.0 N A:LEU93 4.3 13.4 1.0 CG A:HIS138 4.3 10.9 1.0 C A:CYS92 4.5 13.9 1.0 C6 A:BB21301 4.6 21.6 1.0 O A:HOH1304 4.6 9.2 1.0 O A:GLY91 4.7 13.6 1.0 OE2 A:GLU135 4.9 12.9 1.0 N A:SER94 5.0 14.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of P.Aeruginosa Peptide Deformylase Complexed with Antibiotic Actinonin


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 P.Aeruginosa Peptide Deformylase Complexed with Antibiotic Actinonin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:17.2 occ:1.00 NE2 B:HIS138 2.2 9.3 1.0 NE2 B:HIS134 2.2 8.7 1.0 SG B:CYS92 2.3 11.3 1.0 O4 B:BB22301 2.3 18.2 1.0 O2 B:BB22301 2.5 17.2 1.0 C3 B:BB22301 2.9 17.3 1.0 N1 B:BB22301 3.0 20.3 1.0 CD2 B:HIS134 3.1 9.1 1.0 CE1 B:HIS138 3.1 11.4 1.0 CD2 B:HIS138 3.1 8.1 1.0 CE1 B:HIS134 3.2 11.3 1.0 NE2 B:GLN51 3.3 9.2 1.0 CB B:CYS92 3.3 10.4 1.0 O B:HOH2306 3.6 10.8 1.0 CA B:CYS92 3.8 11.0 1.0 CD B:GLN51 4.0 9.6 1.0 OE1 B:GLN51 4.1 10.9 1.0 C5 B:BB22301 4.2 18.5 1.0 ND1 B:HIS138 4.2 9.3 1.0 N B:LEU93 4.2 9.7 1.0 CG B:HIS134 4.2 8.8 1.0 ND1 B:HIS134 4.3 11.1 1.0 CG B:HIS138 4.3 8.2 1.0 C B:CYS92 4.5 10.9 1.0 C6 B:BB22301 4.6 17.4 1.0 O B:HOH2309 4.7 9.6 1.0 O B:GLY91 4.8 12.2 1.0 N B:SER94 4.9 12.9 1.0 OE2 B:GLU135 5.0 11.9 1.0 OE1 B:GLU135 5.0 14.3 1.0

H.-J.Yoon, H.L.Kim, S.K.Lee, H.-W.Kim, H.-W.Kim, J.Y.Lee, B.Mikami, S.W.Suh. Crystal Structure of Peptide Deformylase From Staphylococcus Aureus in Complex with Actinonin, A Naturally Occurring Antibacterial Agent Proteins V. 57 639 2004.
ISSN: ISSN 0887-3585
PubMed: 15382235
DOI: 10.1002/PROT.20231