Nickel in PDB 2w3u: Formate Complex of the Ni-Form of E.Coli Deformylase

All present enzymatic activity of Formate Complex of the Ni-Form of E.Coli Deformylase:
3.5.1.31;

The structure of Formate Complex of the Ni-Form of E.Coli Deformylase, PDB code: 2w3u was solved by Y.H.T.Ngo, G.J.Palm, W.Hinrichs, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.30 / 1.96
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	54.590, 54.590, 228.610, 90.00, 90.00, 120.00
R / Rfree (%)	24.7 / 28.5

The binding sites of Nickel atom in the Formate Complex of the Ni-Form of E.Coli Deformylase (pdb code 2w3u). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Formate Complex of the Ni-Form of E.Coli Deformylase, PDB code: 2w3u:

Nickel binding site 1 out of 1 in the Formate Complex of the Ni-Form of E.Coli Deformylase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Formate Complex of the Ni-Form of E.Coli Deformylase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1001 b:17.7 occ:1.00 O1 A:FMT1002 2.0 32.1 1.0 NE2 A:HIS136 2.0 17.9 1.0 NE2 A:HIS132 2.1 9.4 1.0 SG A:CYS90 2.2 20.5 1.0 C A:FMT1002 2.9 33.1 1.0 CE1 A:HIS136 3.0 17.9 1.0 CD2 A:HIS132 3.0 11.6 1.0 CE1 A:HIS132 3.0 9.6 1.0 CD2 A:HIS136 3.1 17.0 1.0 CB A:CYS90 3.2 18.9 1.0 O2 A:FMT1002 3.2 33.9 1.0 NE2 A:GLN50 3.5 17.7 1.0 O A:HOH2087 3.5 16.0 1.0 CA A:CYS90 3.7 19.1 1.0 CD A:GLN50 4.1 18.2 1.0 ND1 A:HIS136 4.1 17.9 1.0 ND1 A:HIS132 4.1 9.5 1.0 CG A:HIS132 4.1 9.3 1.0 OE2 A:GLU133 4.2 19.1 1.0 CG A:HIS136 4.2 17.7 1.0 OE1 A:GLN50 4.2 19.7 1.0 N A:LEU91 4.4 20.3 1.0 O A:HOH2086 4.4 15.3 1.0 C A:CYS90 4.5 19.6 1.0 O A:GLY89 4.6 16.9 1.0 OE1 A:GLU133 4.7 16.9 1.0 CD A:GLU133 4.8 16.4 1.0 N A:CYS90 5.0 18.1 1.0 N A:SER92 5.0 20.8 1.0

N.T.H.Yen, X.Bogdanovic, G.J.Palm, O.Kuhl, W.Hinrichs. Structure of the Ni(II) Complex of Escherichia Coli Peptide Deformylase and Suggestions on Deformylase Activities Depending on Different Metal(II) Centres. J.Biol.Inorg.Chem. V. 15 195 2010.
ISSN: ISSN 0949-8257
PubMed: 20112455
DOI: 10.1007/S00775-009-0583-8