Nickel in PDB 3um9: Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase BPRO0530

All present enzymatic activity of Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase BPRO0530:
3.8.1.2;

The structure of Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase BPRO0530, PDB code: 3um9 was solved by P.W.Y.Chan, A.Savchenko, 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)	19.05 / 2.19
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	96.640, 96.640, 92.030, 90.00, 90.00, 120.00
R / Rfree (%)	14.4 / 19.9

The binding sites of Nickel atom in the Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase BPRO0530 (pdb code 3um9). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase BPRO0530, PDB code: 3um9:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase BPRO0530


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 Defluorinating L-2-Haloacid Dehalogenase BPRO0530 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni230 b:31.3 occ:1.00 ND1 A:HIS2 1.9 16.4 1.0 N A:MET1 2.0 27.5 1.0 N A:HIS2 2.1 23.6 1.0 N A:GLY0 2.1 27.3 1.0 C A:GLY0 2.7 28.1 1.0 CA A:GLY0 2.8 27.8 1.0 CG A:HIS2 2.9 22.8 1.0 CE1 A:HIS2 2.9 23.0 1.0 C A:MET1 2.9 25.4 1.0 CA A:MET1 3.0 27.3 1.0 CA A:HIS2 3.1 23.6 1.0 CB A:HIS2 3.2 22.9 1.0 CG A:MET1 3.6 31.0 1.0 N A:ALA3 3.6 21.9 1.0 O A:HOH268 3.6 30.2 1.0 C A:HIS2 3.8 23.3 1.0 CB A:MET1 3.8 28.3 1.0 O A:GLY0 3.9 30.4 1.0 O A:HOH248 3.9 22.4 1.0 NE2 A:HIS2 4.0 19.9 1.0 CD2 A:HIS2 4.0 20.3 1.0 O A:MET1 4.1 25.3 1.0 CB A:ALA3 4.8 20.2 1.0 CA A:ALA3 4.8 21.8 1.0 O A:HIS2 5.0 24.2 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase BPRO0530


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 Defluorinating L-2-Haloacid Dehalogenase BPRO0530 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni230 b:61.0 occ:1.00 ND1 B:HIS2 2.2 54.0 1.0 N B:HIS2 2.2 51.4 1.0 N B:MET1 2.3 52.7 1.0 N B:GLY0 2.5 52.3 1.0 C B:GLY0 2.9 52.9 1.0 CG B:HIS2 2.9 51.3 1.0 CA B:HIS2 3.0 50.2 1.0 CB B:HIS2 3.1 49.8 1.0 C B:MET1 3.1 52.1 1.0 CA B:GLY0 3.1 53.0 1.0 CA B:MET1 3.2 52.7 1.0 CE1 B:HIS2 3.3 53.3 1.0 N B:ALA3 3.4 47.5 1.0 C B:HIS2 3.6 49.4 1.0 CE B:MET1 3.6 52.0 1.0 O B:GLY0 3.9 53.9 1.0 SD B:MET1 4.2 55.0 1.0 CD2 B:HIS2 4.2 51.5 1.0 O B:MET1 4.3 52.0 1.0 NE2 B:HIS2 4.3 52.9 1.0 CB B:MET1 4.5 52.5 1.0 CA B:ALA3 4.6 47.0 1.0 CB B:ALA3 4.6 46.8 1.0 O B:HIS2 4.7 49.7 1.0 CG B:MET1 4.8 54.0 1.0

P.W.Y.Chan, T.K.W.To, P.Petit, C.Tran, M.Waelti, A.Savchenko, A.F.Yakunin, E.A.Edwards, E.F.Pai. Structural Adaptations of L-2-Haloacid Dehalogenases That Enable Hydrolytic Defluorination To Be Published.