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Nickel in PDB 2w3t: Chloro Complex of the Ni-Form of E.Coli Deformylase

Enzymatic activity of Chloro Complex of the Ni-Form of E.Coli Deformylase

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

Protein crystallography data

The structure of Chloro Complex of the Ni-Form of E.Coli Deformylase, PDB code: 2w3t 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) 62.02 / 1.69
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 82.080, 35.980, 67.590, 90.00, 113.43, 90.00
R / Rfree (%) 21.3 / 24.3

Nickel Binding Sites:

The binding sites of Nickel atom in the Chloro Complex of the Ni-Form of E.Coli Deformylase (pdb code 2w3t). 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 Chloro Complex of the Ni-Form of E.Coli Deformylase, PDB code: 2w3t:

Nickel binding site 1 out of 1 in 2w3t

Go back to Nickel Binding Sites List in 2w3t
Nickel binding site 1 out of 1 in the Chloro 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 Chloro Complex of the Ni-Form of E.Coli Deformylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1001

b:12.8
occ:1.00
O A:HOH2140 1.9 17.0 0.4
NE2 A:HIS136 2.1 14.9 1.0
NE2 A:HIS132 2.1 15.5 1.0
CL A:CL1002 2.2 14.2 0.6
SG A:CYS90 2.3 15.3 1.0
CD2 A:HIS132 3.0 15.3 1.0
CE1 A:HIS136 3.0 14.0 1.0
CD2 A:HIS136 3.1 15.0 1.0
CE1 A:HIS132 3.2 15.6 1.0
O A:HOH2112 3.3 24.2 0.4
CB A:CYS90 3.3 14.6 1.0
NE2 A:GLN50 3.6 16.3 1.0
O A:HOH2145 3.6 16.8 1.0
CA A:CYS90 3.7 14.9 1.0
CD A:GLN50 4.1 15.6 1.0
OE1 A:GLN50 4.2 14.6 1.0
CG A:HIS132 4.2 14.5 1.0
ND1 A:HIS136 4.2 13.6 1.0
ND1 A:HIS132 4.2 15.6 1.0
CG A:HIS136 4.2 13.8 1.0
N A:LEU91 4.3 15.8 1.0
OE2 A:GLU133 4.3 18.5 1.0
C A:CYS90 4.4 15.2 1.0
O A:HOH2139 4.5 15.4 1.0
OE1 A:GLU133 4.6 19.3 1.0
O A:GLY89 4.6 15.5 1.0
CD A:GLU133 4.8 16.7 1.0
N A:SER92 4.9 15.4 1.0
N A:CYS90 5.0 15.0 1.0

Reference:

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
Page generated: Fri Sep 25 08:15:58 2020
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