Nickel in PDB 1bs6: Peptide Deformylase As NI2+ Containing Form in Complex with Tripeptide Met-Ala-Ser

All present enzymatic activity of Peptide Deformylase As NI2+ Containing Form in Complex with Tripeptide Met-Ala-Ser:
3.5.1.31;

The structure of Peptide Deformylase As NI2+ Containing Form in Complex with Tripeptide Met-Ala-Ser, PDB code: 1bs6 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 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	143.800, 64.100, 85.100, 90.00, 123.30, 90.00
R / Rfree (%)	20.6 / 25.8

The binding sites of Nickel atom in the Peptide Deformylase As NI2+ Containing Form in Complex with Tripeptide Met-Ala-Ser (pdb code 1bs6). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Peptide Deformylase As NI2+ Containing Form in Complex with Tripeptide Met-Ala-Ser, PDB code: 1bs6:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Peptide Deformylase As NI2+ Containing Form in Complex with Tripeptide Met-Ala-Ser


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Peptide Deformylase As NI2+ Containing Form in Complex with Tripeptide Met-Ala-Ser within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni2001 b:45.7 occ:1.00 O A:HOH2041 2.2 37.9 1.0 NE2 A:HIS132 2.2 18.3 1.0 O A:HOH2042 2.3 41.4 1.0 NE2 A:HIS136 2.3 24.8 1.0 SG A:CYS90 2.4 35.4 1.0 CE1 A:HIS132 3.1 17.6 1.0 CE1 A:HIS136 3.1 25.3 1.0 CD2 A:HIS132 3.2 15.1 1.0 CB A:CYS90 3.3 39.0 1.0 CD2 A:HIS136 3.5 25.7 1.0 CA A:CYS90 3.7 39.4 1.0 O A:HOH2037 3.7 18.7 1.0 NE2 A:GLN50 3.7 28.4 1.0 CD A:GLN50 4.1 32.0 1.0 OE1 A:GLN50 4.1 30.3 1.0 N D:MET1 4.1 45.0 1.0 ND1 A:HIS132 4.2 17.6 1.0 N A:LEU91 4.3 41.1 1.0 CG A:HIS132 4.3 15.3 1.0 ND1 A:HIS136 4.3 25.8 1.0 CA D:MET1 4.4 45.6 1.0 C A:CYS90 4.4 40.3 1.0 CG A:HIS136 4.5 26.5 1.0 O A:GLY89 4.6 34.3 1.0 OE1 A:GLU133 4.7 24.9 1.0 O A:HOH2005 4.7 24.9 1.0 N A:CYS90 4.9 37.7 1.0 OG A:SER92 5.0 41.3 1.0

Nickel binding site 2 out of 3 in the Peptide Deformylase As NI2+ Containing Form in Complex with Tripeptide Met-Ala-Ser


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Peptide Deformylase As NI2+ Containing Form in Complex with Tripeptide Met-Ala-Ser within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni2001 b:35.9 occ:1.00 O E:HOH3005 1.9 21.0 1.0 NE2 B:HIS632 2.2 21.9 1.0 NE2 B:HIS636 2.2 18.9 1.0 SG B:CYS590 2.3 22.7 1.0 CE1 B:HIS636 3.0 18.9 1.0 CE1 B:HIS632 3.1 20.1 1.0 CD2 B:HIS632 3.1 17.0 1.0 CB B:CYS590 3.3 24.5 1.0 CD2 B:HIS636 3.4 18.3 1.0 O E:HOH137 3.4 36.4 1.0 N E:MET1 3.4 55.4 1.0 NE2 B:GLN550 3.5 17.7 1.0 O B:HOH22 3.8 30.6 1.0 CA B:CYS590 3.9 25.5 1.0 OE1 B:GLN550 3.9 19.9 1.0 CD B:GLN550 3.9 21.0 1.0 CA E:MET1 4.0 55.7 1.0 OE2 B:GLU633 4.2 27.7 1.0 ND1 B:HIS632 4.2 19.4 1.0 ND1 B:HIS636 4.2 17.8 1.0 CG B:HIS632 4.2 20.1 1.0 CG B:HIS636 4.4 18.0 1.0 N B:LEU591 4.6 26.3 1.0 OE1 B:GLU633 4.6 27.6 1.0 O B:GLY589 4.6 24.6 1.0 C B:CYS590 4.7 25.7 1.0 CD B:GLU633 4.8 25.4 1.0 O B:HOH5 4.8 15.8 1.0 CB E:MET1 5.0 54.5 1.0

Nickel binding site 3 out of 3 in the Peptide Deformylase As NI2+ Containing Form in Complex with Tripeptide Met-Ala-Ser


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Peptide Deformylase As NI2+ Containing Form in Complex with Tripeptide Met-Ala-Ser within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni2001 b:41.7 occ:1.00 O C:HOH3006 2.0 33.6 1.0 NE2 C:HIS1132 2.2 20.2 1.0 NE2 C:HIS1136 2.2 19.0 1.0 SG C:CYS1090 2.4 30.8 1.0 O C:HOH3007 2.7 31.4 1.0 CE1 C:HIS1132 3.1 18.6 1.0 CE1 C:HIS1136 3.2 19.2 1.0 CD2 C:HIS1132 3.2 18.9 1.0 CD2 C:HIS1136 3.2 18.2 1.0 CB C:CYS1090 3.5 29.0 1.0 NE2 C:GLN1050 3.7 22.2 1.0 CA C:CYS1090 3.8 29.1 1.0 O C:HOH31 3.8 27.0 1.0 OE1 C:GLN1050 3.9 22.8 1.0 CD C:GLN1050 4.0 24.8 1.0 CA F:MET1 4.1 44.7 1.0 N F:MET1 4.2 43.9 1.0 ND1 C:HIS1132 4.2 18.4 1.0 ND1 C:HIS1136 4.3 19.7 1.0 CG C:HIS1132 4.3 18.1 1.0 CG C:HIS1136 4.4 19.5 1.0 N C:LEU1091 4.5 30.4 1.0 OE2 C:GLU1133 4.5 26.4 1.0 OE1 C:GLU1133 4.5 25.1 1.0 C C:CYS1090 4.5 28.4 1.0 O C:GLY1089 4.7 28.3 1.0 O C:HOH56 4.7 20.6 1.0 CD C:GLU1133 4.9 26.3 1.0 N C:CYS1090 5.0 29.4 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