Zinc in PDB 1bs8: Peptide Deformylase As ZN2+ Containing Form in Complex with Tripeptide Met-Ala-Ser

All present enzymatic activity of Peptide Deformylase As ZN2+ Containing Form in Complex with Tripeptide Met-Ala-Ser:
3.5.1.31;

The structure of Peptide Deformylase As ZN2+ Containing Form in Complex with Tripeptide Met-Ala-Ser, PDB code: 1bs8 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 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	143.100, 64.200, 84.700, 90.00, 123.30, 90.00
R / Rfree (%)	20.4 / 26.1

The binding sites of Zinc atom in the Peptide Deformylase As ZN2+ Containing Form in Complex with Tripeptide Met-Ala-Ser (pdb code 1bs8). 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 in Complex with Tripeptide Met-Ala-Ser, PDB code: 1bs8:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Peptide Deformylase As ZN2+ Containing Form in Complex with Tripeptide Met-Ala-Ser


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 in Complex with Tripeptide Met-Ala-Ser within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:28.3 occ:1.00 O A:HOH2040 1.9 63.0 1.0 SG A:CYS90 2.1 25.1 1.0 NE2 A:HIS136 2.1 20.2 1.0 O A:HOH2041 2.3 33.2 1.0 NE2 A:HIS132 2.3 14.6 1.0 CE1 A:HIS136 3.0 21.5 1.0 CD2 A:HIS132 3.2 12.7 1.0 CB A:CYS90 3.2 28.9 1.0 CD2 A:HIS136 3.2 22.5 1.0 CE1 A:HIS132 3.4 15.6 1.0 NE2 A:GLN50 3.6 27.1 1.0 CA A:CYS90 3.7 30.2 1.0 O A:HOH2036 3.8 17.6 1.0 N D:MET1 4.0 38.8 1.0 CD A:GLN50 4.0 28.7 1.0 OE1 A:GLN50 4.1 28.6 1.0 ND1 A:HIS136 4.2 21.5 1.0 N A:LEU91 4.2 31.8 1.0 CA D:MET1 4.3 40.1 1.0 CG A:HIS136 4.3 23.4 1.0 CG A:HIS132 4.4 13.8 1.0 ND1 A:HIS132 4.4 15.9 1.0 C A:CYS90 4.5 31.2 1.0 O A:HOH2005 4.5 16.2 1.0 OE1 A:GLU133 4.5 19.0 1.0 O A:GLY89 4.6 25.5 1.0 N A:CYS90 4.9 28.5 1.0 N A:SER92 5.0 31.0 1.0

Zinc binding site 2 out of 3 in the Peptide Deformylase As ZN2+ Containing Form in Complex with Tripeptide Met-Ala-Ser


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 in Complex with Tripeptide Met-Ala-Ser within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2001 b:23.2 occ:1.00 O B:HOH3005 1.9 24.1 1.0 NE2 B:HIS636 2.0 8.4 1.0 NE2 B:HIS632 2.1 19.4 1.0 SG B:CYS590 2.2 19.9 1.0 CD2 B:HIS632 3.0 14.7 1.0 CE1 B:HIS636 3.0 10.4 1.0 CD2 B:HIS636 3.0 11.0 1.0 CE1 B:HIS632 3.2 16.5 1.0 CB B:CYS590 3.3 21.8 1.0 O B:HOH22 3.5 24.8 1.0 NE2 B:GLN550 3.7 15.0 1.0 O B:HOH137 3.7 28.1 1.0 OE1 B:GLN550 3.8 18.4 1.0 CA B:CYS590 3.8 23.3 1.0 CD B:GLN550 3.9 18.0 1.0 ND1 B:HIS636 4.1 11.3 1.0 CG B:HIS632 4.1 17.8 1.0 CG B:HIS636 4.2 12.1 1.0 ND1 B:HIS632 4.2 17.0 1.0 OE2 B:GLU633 4.2 22.4 1.0 CA E:MET1 4.3 58.0 1.0 OE1 B:GLU633 4.3 18.9 1.0 N E:MET1 4.4 59.4 1.0 N B:LEU591 4.5 22.2 1.0 O B:HOH5 4.6 15.5 1.0 C B:CYS590 4.6 22.2 1.0 O B:GLY589 4.7 22.1 1.0 CD B:GLU633 4.7 19.1 1.0 N B:CYS590 5.0 21.8 1.0

Zinc binding site 3 out of 3 in the Peptide Deformylase As ZN2+ Containing Form in Complex with Tripeptide Met-Ala-Ser


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 in Complex with Tripeptide Met-Ala-Ser within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn2001 b:24.0 occ:1.00 NE2 C:HIS1136 2.0 12.7 1.0 NE2 C:HIS1132 2.0 16.5 1.0 SG C:CYS1090 2.2 21.4 1.0 O C:HOH3007 2.2 31.1 1.0 O C:HOH3006 2.3 44.8 1.0 CE1 C:HIS1136 2.9 14.2 1.0 CE1 C:HIS1132 3.0 15.8 1.0 CD2 C:HIS1132 3.0 16.1 1.0 CD2 C:HIS1136 3.2 13.5 1.0 CB C:CYS1090 3.3 19.9 1.0 NE2 C:GLN1050 3.6 18.0 1.0 CA C:CYS1090 3.7 21.6 1.0 O C:HOH31 3.8 22.3 1.0 CD C:GLN1050 4.0 21.3 1.0 OE1 C:GLN1050 4.0 18.3 1.0 ND1 C:HIS1136 4.0 16.9 1.0 ND1 C:HIS1132 4.1 18.6 1.0 CG C:HIS1132 4.2 17.7 1.0 CA F:MET1 4.2 42.3 1.0 N C:LEU1091 4.2 19.5 1.0 CG C:HIS1136 4.2 16.0 1.0 N F:MET1 4.4 41.1 1.0 C C:CYS1090 4.4 20.0 1.0 O C:HOH56 4.4 15.6 1.0 OE1 C:GLU1133 4.5 17.6 1.0 CB F:MET1 4.7 40.6 1.0 OE2 C:GLU1133 4.7 18.4 1.0 O C:GLY1089 4.8 20.8 1.0 N C:CYS1090 4.9 22.6 1.0 N C:SER1092 4.9 18.6 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