Nickel in PDB 3r3z: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/Glycolate

All present enzymatic activity of Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/Glycolate:
3.8.1.3;

The structure of Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/Glycolate, PDB code: 3r3z was solved by P.W.Y.Chan, A.F.Yakunin, E.A.Edwards, E.F.Pai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.23 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.080, 122.120, 132.460, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 21.8

The binding sites of Nickel atom in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/Glycolate (pdb code 3r3z). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/Glycolate, PDB code: 3r3z:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/Glycolate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/Glycolate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni306 b:20.7 occ:1.00 N A:HIS0 2.0 21.3 1.0 ND1 A:HIS0 2.1 20.9 1.0 N A:GLY-1 2.2 25.7 1.0 O A:HOH1262 2.7 31.4 1.0 C A:GLY-1 2.9 23.9 1.0 CG A:HIS0 3.0 21.9 1.0 CA A:HIS0 3.0 22.1 1.0 CA A:GLY-1 3.1 24.8 1.0 CE1 A:HIS0 3.1 23.1 1.0 CB A:HIS0 3.2 21.6 1.0 N A:MET1 3.7 23.8 1.0 C A:HIS0 3.8 23.0 1.0 O A:GLY-1 4.0 24.2 1.0 CD2 A:HIS0 4.1 22.5 1.0 NE2 A:HIS0 4.2 23.6 1.0

Nickel binding site 2 out of 3 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/Glycolate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/Glycolate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni306 b:13.0 occ:1.00 ND1 B:HIS0 2.1 14.2 1.0 N B:HIS0 2.1 12.9 1.0 N B:GLY-1 2.1 12.1 1.0 O B:HOH1264 2.2 12.3 1.0 O B:HOH1263 2.3 12.3 1.0 C B:GLY-1 2.9 15.4 1.0 CA B:GLY-1 2.9 13.4 1.0 CG B:HIS0 3.0 14.9 1.0 CE1 B:HIS0 3.1 19.0 1.0 CA B:HIS0 3.1 13.5 1.0 CB B:HIS0 3.3 12.5 1.0 N B:MET1 3.9 14.2 1.0 C B:HIS0 4.0 15.3 1.0 O B:GLY-1 4.1 12.3 1.0 CD2 B:HIS0 4.2 15.4 1.0 NE2 B:HIS0 4.2 16.1 1.0

Nickel binding site 3 out of 3 in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/Glycolate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/Glycolate within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni306 b:25.8 occ:1.00 N C:HIS0 2.0 23.2 1.0 ND1 C:HIS0 2.2 26.4 1.0 O C:HOH1261 2.4 36.1 1.0 N C:GLY-1 2.8 29.1 1.0 C C:GLY-1 2.9 26.0 1.0 CG C:HIS0 3.0 21.2 1.0 CA C:HIS0 3.0 23.9 1.0 CB C:HIS0 3.1 24.8 1.0 CA C:GLY-1 3.1 27.7 1.0 CE1 C:HIS0 3.2 24.3 1.0 N C:MET1 3.7 26.9 1.0 C C:HIS0 3.9 26.1 1.0 O C:GLY-1 4.1 26.1 1.0 CD2 C:HIS0 4.1 23.7 1.0 NE2 C:HIS0 4.2 26.6 1.0

P.W.Chan, A.F.Yakunin, E.A.Edwards, E.F.Pai. Mapping the Reaction Coordinates of Enzymatic Defluorination. J.Am.Chem.Soc. V. 133 7461 2011.
ISSN: ISSN 0002-7863
PubMed: 21510690
DOI: 10.1021/JA200277D