Iron in PDB 1bsz: Peptide Deformylase As FE2+ Containing Form (Native) in Complex with Inhibitor Polyethylene Glycol

All present enzymatic activity of Peptide Deformylase As FE2+ Containing Form (Native) in Complex with Inhibitor Polyethylene Glycol:
3.5.1.31;

The structure of Peptide Deformylase As FE2+ Containing Form (Native) in Complex with Inhibitor Polyethylene Glycol, PDB code: 1bsz was solved by A.Becker, I.Schlichting, W.Kabsch, D.Groche, S.Schultz, A.F.V.Wagner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	141.000, 63.400, 86.800, 90.00, 120.60, 90.00
R / Rfree (%)	19.7 / 24.7

The binding sites of Iron atom in the Peptide Deformylase As FE2+ Containing Form (Native) in Complex with Inhibitor Polyethylene Glycol (pdb code 1bsz). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Peptide Deformylase As FE2+ Containing Form (Native) in Complex with Inhibitor Polyethylene Glycol, PDB code: 1bsz:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Peptide Deformylase As FE2+ Containing Form (Native) in Complex with Inhibitor Polyethylene Glycol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Peptide Deformylase As FE2+ Containing Form (Native) in Complex with Inhibitor Polyethylene Glycol within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2001 b:34.4 occ:1.00 NE2 A:HIS132 2.1 15.2 1.0 NE2 A:HIS136 2.1 19.6 1.0 O A:HOH8068 2.2 19.2 1.0 SG A:CYS90 2.3 20.3 1.0 CE1 A:HIS136 3.0 20.2 1.0 CD2 A:HIS132 3.1 16.7 1.0 CE1 A:HIS132 3.1 15.5 1.0 CD2 A:HIS136 3.2 18.6 1.0 CB A:CYS90 3.4 20.8 1.0 O A:HOH8006 3.6 17.4 1.0 O A:HOH8004 3.7 30.1 1.0 NE2 A:GLN50 3.8 19.9 1.0 CA A:CYS90 3.9 21.5 1.0 OE1 A:GLN50 4.0 21.8 1.0 CD A:GLN50 4.0 20.9 1.0 OE2 A:GLU133 4.0 23.0 1.0 ND1 A:HIS136 4.2 18.8 1.0 ND1 A:HIS132 4.2 16.1 1.0 CG A:HIS132 4.2 16.6 1.0 CG A:HIS136 4.3 19.1 1.0 O A:GLY89 4.4 19.2 1.0 O A:HOH8007 4.5 16.0 1.0 C17 A:2PE3000 4.6 52.7 1.0 OE1 A:GLU133 4.7 20.4 1.0 CD A:GLU133 4.7 21.9 1.0 N A:LEU91 4.8 22.4 1.0 C A:CYS90 4.8 21.9 1.0 C15 A:2PE3000 4.9 50.2 1.0

Iron binding site 2 out of 3 in the Peptide Deformylase As FE2+ Containing Form (Native) in Complex with Inhibitor Polyethylene Glycol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Peptide Deformylase As FE2+ Containing Form (Native) in Complex with Inhibitor Polyethylene Glycol within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe2002 b:26.5 occ:1.00 O B:HOH9254 2.0 16.8 1.0 NE2 B:HIS636 2.1 13.8 1.0 NE2 B:HIS632 2.3 14.6 1.0 SG B:CYS590 2.3 15.3 1.0 CE1 B:HIS636 2.9 12.7 1.0 CD2 B:HIS632 3.1 12.8 1.0 CD2 B:HIS636 3.2 12.5 1.0 CE1 B:HIS632 3.4 13.3 1.0 CB B:CYS590 3.5 15.3 1.0 O B:HOH9006 3.6 17.9 1.0 NE2 B:GLN550 3.7 12.4 1.0 O B:HOH9004 3.7 19.5 1.0 OE1 B:GLN550 3.8 17.1 1.0 CD B:GLN550 3.9 14.9 1.0 CA B:CYS590 4.0 16.8 1.0 OE2 B:GLU633 4.0 11.6 1.0 ND1 B:HIS636 4.1 13.3 1.0 CG B:HIS636 4.3 12.9 1.0 CG B:HIS632 4.3 15.1 1.0 ND1 B:HIS632 4.4 13.2 1.0 OE1 B:GLU633 4.5 13.8 1.0 O B:HOH9007 4.5 12.7 1.0 CD B:GLU633 4.6 14.0 1.0 N B:LEU591 4.6 17.1 1.0 O B:GLY589 4.6 16.2 1.0 C B:CYS590 4.8 17.0 1.0 C17 B:2PE3002 4.8 52.1 1.0 C15 B:2PE3002 4.8 55.4 1.0

Iron binding site 3 out of 3 in the Peptide Deformylase As FE2+ Containing Form (Native) in Complex with Inhibitor Polyethylene Glycol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Peptide Deformylase As FE2+ Containing Form (Native) in Complex with Inhibitor Polyethylene Glycol within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe2003 b:40.5 occ:1.00 NE2 C:HIS1132 2.2 16.7 1.0 NE2 C:HIS1136 2.2 17.9 1.0 SG C:CYS1090 2.2 20.1 1.0 O C:HOH9255 2.3 15.3 1.0 CE1 C:HIS1136 3.0 17.4 1.0 CD2 C:HIS1132 3.0 16.1 1.0 CE1 C:HIS1132 3.2 17.8 1.0 CD2 C:HIS1136 3.3 16.4 1.0 CB C:CYS1090 3.4 21.7 1.0 O C:HOH7 3.5 27.3 1.0 O C:HOH7004 3.6 25.3 1.0 NE2 C:GLN1050 3.8 16.1 1.0 CA C:CYS1090 3.9 22.1 1.0 OE1 C:GLN1050 4.0 16.1 1.0 CD C:GLN1050 4.1 16.0 1.0 OE2 C:GLU1133 4.2 18.6 1.0 ND1 C:HIS1136 4.2 16.8 1.0 CG C:HIS1132 4.2 17.0 1.0 ND1 C:HIS1132 4.3 16.9 1.0 CG C:HIS1136 4.4 15.9 1.0 O C:HOH7007 4.4 19.4 1.0 C12 C:2PE3003 4.5 54.8 1.0 O C:GLY1089 4.5 22.7 1.0 C11 C:2PE3003 4.6 55.1 1.0 OE1 C:GLU1133 4.7 17.3 1.0 N C:LEU1091 4.8 22.5 1.0 CD C:GLU1133 4.8 16.1 1.0 C C:CYS1090 4.8 22.3 1.0

A.Becker, I.Schlichting, W.Kabsch, D.Groche, S.Schultz, A.F.Wagner. Iron Center, Substrate Recognition and Mechanism of Peptide Deformylase. Nat.Struct.Biol. V. 5 1053 1998.
ISSN: ISSN 1072-8368
PubMed: 9846875
DOI: 10.1038/4162