Nickel in PDB 3r3u: Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/Apo

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

The structure of Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/Apo, PDB code: 3r3u 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)	90.17 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.230, 122.700, 132.660, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 20.2

The structure of Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/Apo also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Nickel atom in the Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Wt/Apo (pdb code 3r3u). 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/Apo, PDB code: 3r3u:
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/Apo


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/Apo within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni305 b:21.3 occ:1.00 ND1 A:HIS0 2.0 22.4 1.0 N A:HIS0 2.1 22.3 1.0 N A:GLY-1 2.2 29.7 1.0 O A:HOH354 2.8 23.0 1.0 CG A:HIS0 2.9 24.4 1.0 C A:GLY-1 3.0 25.1 1.0 CE1 A:HIS0 3.0 24.0 1.0 CA A:HIS0 3.1 21.9 1.0 CA A:GLY-1 3.1 26.8 1.0 CB A:HIS0 3.2 22.8 1.0 N A:MET1 3.8 23.7 1.0 C A:HIS0 3.9 22.3 1.0 NE2 A:HIS0 4.1 26.2 1.0 CD2 A:HIS0 4.1 23.0 1.0 O A:GLY-1 4.1 25.9 1.0 O A:HOH449 4.5 33.9 1.0

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


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/Apo within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni305 b:15.3 occ:1.00 ND1 B:HIS0 2.0 16.8 1.0 N B:GLY-1 2.1 14.9 1.0 N B:HIS0 2.1 15.7 1.0 O B:HOH329 2.2 15.1 1.0 O B:HOH343 2.2 14.2 1.0 CA B:GLY-1 3.0 15.7 1.0 C B:GLY-1 3.0 16.9 1.0 CE1 B:HIS0 3.0 20.9 1.0 CG B:HIS0 3.1 19.1 1.0 CA B:HIS0 3.1 16.9 1.0 CB B:HIS0 3.3 17.7 1.0 N B:MET1 3.8 16.7 1.0 C B:HIS0 3.9 17.1 1.0 NE2 B:HIS0 4.2 17.8 1.0 CD2 B:HIS0 4.2 19.1 1.0 O B:GLY-1 4.2 19.1 1.0

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


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/Apo within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni305 b:28.2 occ:1.00 N C:HIS0 1.9 26.5 1.0 ND1 C:HIS0 2.1 29.4 1.0 N C:GLY-1 2.5 33.3 1.0 O C:HOH308 2.7 30.7 1.0 C C:GLY-1 2.9 28.1 1.0 CG C:HIS0 3.0 27.8 1.0 CA C:HIS0 3.0 28.9 1.0 CA C:GLY-1 3.1 30.4 1.0 CB C:HIS0 3.1 28.0 1.0 CE1 C:HIS0 3.2 28.0 1.0 N C:MET1 3.7 33.4 1.0 C C:HIS0 3.8 30.8 1.0 O C:GLY-1 4.1 30.3 1.0 CD2 C:HIS0 4.2 24.7 1.0 NE2 C:HIS0 4.2 29.1 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