Zinc in PDB 1bs5: Peptide Deformylase As ZN2+ Containing Form

All present enzymatic activity of Peptide Deformylase As ZN2+ Containing Form:
3.5.1.31;

The structure of Peptide Deformylase As ZN2+ Containing Form, PDB code: 1bs5 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 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	143.400, 64.100, 84.600, 90.00, 123.20, 90.00
R / Rfree (%)	20.8 / 25.8

The binding sites of Zinc atom in the Peptide Deformylase As ZN2+ Containing Form (pdb code 1bs5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Peptide Deformylase As ZN2+ Containing Form, PDB code: 1bs5:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Peptide Deformylase As ZN2+ Containing Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Peptide Deformylase As ZN2+ Containing Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:26.1 occ:1.00 NE2 A:HIS132 2.0 23.3 1.0 SG A:CYS90 2.1 26.3 1.0 NE2 A:HIS136 2.2 17.5 1.0 O A:HOH2034 2.2 20.2 1.0 CD2 A:HIS132 3.0 21.0 1.0 CE1 A:HIS132 3.0 23.0 1.0 CD2 A:HIS136 3.1 17.9 1.0 CE1 A:HIS136 3.1 18.4 1.0 O A:HOH2021 3.1 44.5 1.0 CB A:CYS90 3.3 26.4 1.0 NE2 A:GLN50 3.7 24.0 1.0 CA A:CYS90 3.8 28.8 1.0 OE1 A:GLN50 4.0 26.3 1.0 CD A:GLN50 4.0 26.9 1.0 O A:HOH2024 4.1 35.3 1.0 ND1 A:HIS132 4.1 22.7 1.0 CG A:HIS132 4.1 19.8 1.0 OE2 A:GLU133 4.2 23.1 1.0 ND1 A:HIS136 4.3 15.9 1.0 CG A:HIS136 4.3 18.1 1.0 O A:GLY89 4.5 30.7 1.0 N A:LEU91 4.6 29.6 1.0 C A:CYS90 4.6 29.3 1.0 OE1 A:GLU133 4.6 25.4 1.0 O A:HOH2007 4.7 26.1 1.0 CD A:GLU133 4.8 23.5 1.0 N A:CYS90 5.0 30.5 1.0

Zinc binding site 2 out of 3 in the Peptide Deformylase As ZN2+ Containing Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Peptide Deformylase As ZN2+ Containing Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2001 b:21.8 occ:1.00 O B:HOH3004 1.8 8.3 1.0 NE2 B:HIS636 2.1 14.9 1.0 NE2 B:HIS632 2.1 22.3 1.0 SG B:CYS590 2.1 22.8 1.0 CD2 B:HIS632 3.0 21.1 1.0 CE1 B:HIS636 3.0 16.6 1.0 CE1 B:HIS632 3.1 21.0 1.0 CD2 B:HIS636 3.1 15.5 1.0 CB B:CYS590 3.3 24.1 1.0 NE2 B:GLN550 3.6 20.1 1.0 O B:HOH60 3.7 15.8 1.0 O B:HOH114 3.7 24.7 1.0 CA B:CYS590 3.8 26.3 1.0 OE1 B:GLN550 4.0 22.8 1.0 CD B:GLN550 4.0 23.3 1.0 ND1 B:HIS636 4.1 12.6 1.0 CG B:HIS632 4.2 20.0 1.0 ND1 B:HIS632 4.2 21.5 1.0 OE2 B:GLU633 4.2 19.6 1.0 CG B:HIS636 4.2 15.1 1.0 O B:HOH4 4.4 6.2 1.0 O B:GLY589 4.6 27.3 1.0 OE1 B:GLU633 4.6 23.4 1.0 N B:LEU591 4.6 26.1 1.0 C B:CYS590 4.7 25.9 1.0 CD B:GLU633 4.8 22.2 1.0

Zinc binding site 3 out of 3 in the Peptide Deformylase As ZN2+ Containing Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Peptide Deformylase As ZN2+ Containing Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn2001 b:22.9 occ:1.00 O C:HOH3005 1.8 22.2 1.0 NE2 C:HIS1136 2.1 13.9 1.0 SG C:CYS1090 2.1 22.4 1.0 NE2 C:HIS1132 2.1 22.5 1.0 CE1 C:HIS1136 3.0 13.7 1.0 CD2 C:HIS1132 3.1 21.4 1.0 CD2 C:HIS1136 3.1 13.0 1.0 CE1 C:HIS1132 3.2 21.9 1.0 CB C:CYS1090 3.3 24.5 1.0 NE2 C:GLN1050 3.6 23.1 1.0 O C:HOH43 3.8 19.0 1.0 CA C:CYS1090 3.8 25.6 1.0 OE1 C:GLN1050 3.8 23.3 1.0 CD C:GLN1050 3.9 24.4 1.0 ND1 C:HIS1136 4.1 12.6 1.0 OE2 C:GLU1133 4.2 20.6 1.0 CG C:HIS1136 4.2 14.8 1.0 CG C:HIS1132 4.2 20.7 1.0 ND1 C:HIS1132 4.3 22.5 1.0 N C:LEU1091 4.6 25.3 1.0 O C:HOH102 4.6 15.6 1.0 O C:GLY1089 4.6 28.5 1.0 C C:CYS1090 4.6 25.5 1.0 OE1 C:GLU1133 4.7 21.4 1.0 CD C:GLU1133 4.8 21.2 1.0 O C:HOH51 4.9 29.2 1.0 CG C:GLN1050 5.0 26.5 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