Nickel in PDB 1bs7: Peptide Deformylase As NI2+ Containing Form

All present enzymatic activity of Peptide Deformylase As NI2+ Containing Form:
3.5.1.31;

The structure of Peptide Deformylase As NI2+ Containing Form, PDB code: 1bs7 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, 64.000, 84.500, 90.00, 123.00, 90.00
R / Rfree (%)	20.3 / 27.2

The binding sites of Nickel atom in the Peptide Deformylase As NI2+ Containing Form (pdb code 1bs7). 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, PDB code: 1bs7:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Peptide Deformylase As NI2+ Containing Form


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni2001 b:47.2 occ:1.00 NE2 A:HIS132 2.1 18.7 1.0 SG A:CYS90 2.1 30.3 1.0 NE2 A:HIS136 2.4 16.6 1.0 O A:HOH2034 2.5 37.8 1.0 CE1 A:HIS132 3.0 19.5 1.0 CB A:CYS90 3.1 34.1 1.0 CD2 A:HIS132 3.1 19.0 1.0 CE1 A:HIS136 3.1 16.8 1.0 O A:HOH2023 3.2 31.1 1.0 CA A:CYS90 3.5 36.6 1.0 CD2 A:HIS136 3.5 18.6 1.0 NE2 A:GLN50 3.9 28.1 1.0 O A:HOH2026 3.9 68.8 1.0 ND1 A:HIS132 4.1 21.2 1.0 OE1 A:GLN50 4.1 32.1 1.0 O A:GLY89 4.2 37.9 1.0 CD A:GLN50 4.2 31.0 1.0 CG A:HIS132 4.2 18.4 1.0 O A:HOH2009 4.3 29.5 1.0 ND1 A:HIS136 4.3 17.9 1.0 C A:CYS90 4.4 37.1 1.0 N A:LEU91 4.4 37.4 1.0 CG A:HIS136 4.6 20.4 1.0 OE2 A:GLU133 4.6 25.5 1.0 N A:CYS90 4.6 37.8 1.0 OE1 A:GLU133 4.8 23.7 1.0 C A:GLY89 4.8 37.9 1.0

Nickel binding site 2 out of 3 in the Peptide Deformylase As NI2+ Containing Form


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni2001 b:32.1 occ:1.00 O B:HOH3004 1.9 9.3 1.0 NE2 B:HIS636 2.0 13.9 1.0 NE2 B:HIS632 2.2 21.9 1.0 SG B:CYS590 2.2 24.6 1.0 CE1 B:HIS636 2.8 16.0 1.0 CD2 B:HIS632 3.1 20.2 1.0 CD2 B:HIS636 3.1 14.9 1.0 CE1 B:HIS632 3.2 20.6 1.0 CB B:CYS590 3.4 30.3 1.0 O B:HOH114 3.5 23.7 1.0 NE2 B:GLN550 3.7 24.6 1.0 O B:HOH60 3.7 13.2 1.0 CA B:CYS590 3.8 33.5 1.0 OE1 B:GLN550 3.9 27.4 1.0 CD B:GLN550 4.0 27.8 1.0 ND1 B:HIS636 4.0 14.6 1.0 CG B:HIS636 4.2 17.1 1.0 CG B:HIS632 4.2 19.9 1.0 ND1 B:HIS632 4.3 20.6 1.0 OE2 B:GLU633 4.4 20.1 1.0 O B:HOH4 4.5 10.4 1.0 OE1 B:GLU633 4.5 21.2 1.0 O B:GLY589 4.5 35.5 1.0 N B:LEU591 4.6 34.6 1.0 C B:CYS590 4.7 34.3 1.0 CD B:GLU633 4.9 21.8 1.0 O B:HOH97 4.9 46.2 1.0

Nickel binding site 3 out of 3 in the Peptide Deformylase As NI2+ Containing Form


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni2001 b:37.5 occ:1.00 NE2 C:HIS1136 2.1 12.3 1.0 SG C:CYS1090 2.2 25.1 1.0 O C:HOH3005 2.2 25.9 1.0 NE2 C:HIS1132 2.2 22.4 1.0 CE1 C:HIS1136 2.9 13.3 1.0 CD2 C:HIS1132 3.1 20.8 1.0 CE1 C:HIS1132 3.2 22.0 1.0 CD2 C:HIS1136 3.3 12.9 1.0 CB C:CYS1090 3.3 31.0 1.0 NE2 C:GLN1050 3.7 25.8 1.0 CA C:CYS1090 3.7 32.2 1.0 O C:HOH43 3.7 19.8 1.0 OE1 C:GLN1050 3.9 28.7 1.0 CD C:GLN1050 4.0 28.6 1.0 ND1 C:HIS1136 4.1 13.7 1.0 CG C:HIS1132 4.3 18.6 1.0 ND1 C:HIS1132 4.3 20.6 1.0 CG C:HIS1136 4.3 14.4 1.0 OE2 C:GLU1133 4.4 21.7 1.0 N C:LEU1091 4.4 34.9 1.0 O C:GLY1089 4.4 35.2 1.0 C C:CYS1090 4.5 33.2 1.0 OE1 C:GLU1133 4.6 18.7 1.0 O C:HOH102 4.6 20.3 1.0 O C:HOH51 4.8 41.2 1.0 N C:CYS1090 4.9 34.3 1.0 CD C:GLU1133 4.9 21.5 1.0

A.Becker, I.Schlichting, W.Kabsch, S.Schultz, A.F.Wagner. Structure of Peptide Deformylase and Identification of the Substrate Binding Site. J.Biol.Chem. V. 273 11413 1998.
ISSN: ISSN 0021-9258
PubMed: 9565550
DOI: 10.1074/JBC.273.19.11413