Nickel in PDB 4al2: Peptide Deformylase (Ni-Form) with Hydrosulfide

All present enzymatic activity of Peptide Deformylase (Ni-Form) with Hydrosulfide:
3.5.1.88;

The structure of Peptide Deformylase (Ni-Form) with Hydrosulfide, PDB code: 4al2 was solved by G.J.Palm, W.Hinrichs, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.00 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	142.206, 63.222, 118.175, 90.00, 144.28, 90.00
R / Rfree (%)	20.6 / 29.8

The binding sites of Nickel atom in the Peptide Deformylase (Ni-Form) with Hydrosulfide (pdb code 4al2). 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 (Ni-Form) with Hydrosulfide, PDB code: 4al2:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Peptide Deformylase (Ni-Form) with Hydrosulfide


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Peptide Deformylase (Ni-Form) with Hydrosulfide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1001 b:57.7 occ:1.00 NE2 A:HIS136 2.0 56.4 1.0 SG A:CYS90 2.3 51.5 1.0 NE2 A:HIS132 2.4 47.5 1.0 S A:H2S1002 2.6 70.2 1.0 CE1 A:HIS136 2.9 54.8 1.0 CD2 A:HIS136 3.1 51.3 1.0 CE1 A:HIS132 3.3 46.2 1.0 CB A:CYS90 3.4 54.2 1.0 CD2 A:HIS132 3.4 44.6 1.0 O A:HOH2015 3.6 49.9 1.0 NE2 A:GLN50 3.7 54.9 1.0 CA A:CYS90 3.8 56.3 1.0 ND1 A:HIS136 4.1 54.8 1.0 OE1 A:GLN50 4.1 56.0 1.0 CD A:GLN50 4.1 54.7 1.0 CG A:HIS136 4.2 50.7 1.0 ND1 A:HIS132 4.4 43.1 1.0 N A:LEU91 4.4 57.1 1.0 O A:GLY89 4.5 65.5 1.0 CG A:HIS132 4.5 44.6 1.0 OE2 A:GLU133 4.5 42.5 1.0 C A:CYS90 4.5 57.9 1.0 O A:HOH2019 4.6 53.2 1.0 N A:CYS90 4.9 56.2 1.0 OE1 A:GLU133 5.0 46.5 1.0

Nickel binding site 2 out of 3 in the Peptide Deformylase (Ni-Form) with Hydrosulfide


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Peptide Deformylase (Ni-Form) with Hydrosulfide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1001 b:58.1 occ:1.00 NE2 B:HIS136 2.2 55.2 1.0 SG B:CYS90 2.2 48.2 1.0 NE2 B:HIS132 2.3 45.0 1.0 S B:H2S1002 2.6 78.8 1.0 CE1 B:HIS136 3.0 55.8 1.0 CD2 B:HIS132 3.1 42.8 1.0 CB B:CYS90 3.3 50.4 1.0 CD2 B:HIS136 3.3 55.3 1.0 O B:HOH2013 3.3 49.6 1.0 CE1 B:HIS132 3.4 40.8 1.0 NE2 B:GLN50 3.6 65.1 1.0 CA B:CYS90 3.7 49.7 1.0 OE1 B:GLN50 3.8 55.6 1.0 CD B:GLN50 3.9 60.2 1.0 ND1 B:HIS136 4.2 55.3 1.0 N B:LEU91 4.2 56.1 1.0 OE2 B:GLU133 4.2 59.4 1.0 CG B:HIS132 4.4 44.1 1.0 CG B:HIS136 4.4 56.6 1.0 C B:CYS90 4.5 54.5 1.0 OE1 B:GLU133 4.5 57.8 1.0 ND1 B:HIS132 4.5 42.4 1.0 O B:GLY89 4.6 58.2 1.0 O B:HOH2017 4.7 59.5 1.0 CD B:GLU133 4.7 58.0 1.0 N B:CYS90 4.9 49.4 1.0

Nickel binding site 3 out of 3 in the Peptide Deformylase (Ni-Form) with Hydrosulfide


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Peptide Deformylase (Ni-Form) with Hydrosulfide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni1001 b:61.0 occ:1.00 NE2 C:HIS136 2.3 54.1 1.0 SG C:CYS90 2.3 63.1 1.0 NE2 C:HIS132 2.3 61.4 1.0 S C:H2S1002 2.6 80.2 1.0 CE1 C:HIS136 3.2 57.1 1.0 CD2 C:HIS132 3.3 60.1 1.0 CD2 C:HIS136 3.3 53.9 1.0 CE1 C:HIS132 3.3 65.1 1.0 CB C:CYS90 3.4 67.9 1.0 NE2 C:GLN50 3.5 62.5 1.0 O C:HOH2007 3.5 49.7 1.0 CA C:CYS90 3.8 69.5 1.0 CD C:GLN50 4.2 66.2 1.0 ND1 C:HIS136 4.4 55.6 1.0 N C:LEU91 4.4 70.1 1.0 CG C:HIS136 4.4 55.9 1.0 O C:HOH2011 4.5 53.3 1.0 ND1 C:HIS132 4.5 62.9 1.0 CG C:HIS132 4.5 60.0 1.0 O C:GLY89 4.5 70.8 1.0 OE1 C:GLN50 4.5 67.6 1.0 OE2 C:GLU133 4.5 63.7 1.0 C C:CYS90 4.6 70.3 1.0 OE1 C:GLU133 4.8 68.8 1.0 N C:CYS90 4.9 67.8 1.0

M.Strianese, G.J.Palm, S.Milione, O.Kuehl, W.Hinrichs, C.Pellecchia. A Fret Enzyme-Based Probe For Monitoring Hydrogen Sulfide. Inorg.Chem. V. 51 11220 2012.
ISSN: ISSN 0020-1669
PubMed: 23072298
DOI: 10.1021/IC301363D