Nickel in PDB 4f9d: Structure of Escherichia Coli Pgab 42-655 in Complex with Nickel

The structure of Structure of Escherichia Coli Pgab 42-655 in Complex with Nickel, PDB code: 4f9d was solved by D.J.Little, J.Poloczek, J.C.Whitney, H.Robinson, M.Nitz, P.L.Howell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.33 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	90.669, 102.831, 150.881, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 19.3

The structure of Structure of Escherichia Coli Pgab 42-655 in Complex with Nickel also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Nickel atom in the Structure of Escherichia Coli Pgab 42-655 in Complex with Nickel (pdb code 4f9d). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Structure of Escherichia Coli Pgab 42-655 in Complex with Nickel, PDB code: 4f9d:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Structure of Escherichia Coli Pgab 42-655 in Complex with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of Escherichia Coli Pgab 42-655 in Complex with Nickel within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni701 b:20.9 occ:1.00 OD1 A:ASP115 2.2 17.6 1.0 NE2 A:HIS189 2.3 19.1 1.0 NE2 A:HIS184 2.3 19.0 1.0 O A:HOH1139 2.4 18.7 1.0 O A:ACY702 2.4 19.5 1.0 OXT A:ACY702 2.5 26.1 1.0 C A:ACY702 2.8 24.2 1.0 CD2 A:HIS184 3.1 20.2 1.0 CD2 A:HIS189 3.1 18.5 1.0 CG A:ASP115 3.2 23.0 1.0 CE1 A:HIS189 3.3 24.9 1.0 CE1 A:HIS184 3.4 23.3 1.0 OD2 A:ASP115 3.5 26.2 1.0 CH3 A:ACY702 4.3 18.8 1.0 CG A:HIS184 4.3 14.0 1.0 CG A:HIS189 4.3 18.1 1.0 ND1 A:HIS189 4.4 18.8 1.0 ND1 A:HIS184 4.4 15.2 1.0 O A:HOH1238 4.4 43.4 1.0 NE2 A:HIS55 4.4 20.4 1.0 CB A:ASP114 4.5 19.8 1.0 CB A:ASP115 4.5 16.5 1.0 CA A:PRO251 4.5 16.0 1.0 CD2 A:HIS55 4.7 19.4 1.0 N A:TYR252 4.7 15.2 1.0 CA A:ASP115 4.7 19.2 1.0 N A:ASP115 4.8 16.9 1.0 O A:HOH1262 5.0 56.5 1.0

Nickel binding site 2 out of 2 in the Structure of Escherichia Coli Pgab 42-655 in Complex with Nickel


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of Escherichia Coli Pgab 42-655 in Complex with Nickel within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni701 b:21.1 occ:1.00 OD1 B:ASP115 2.3 20.2 1.0 NE2 B:HIS189 2.3 20.9 1.0 NE2 B:HIS184 2.4 20.8 1.0 O B:ACY702 2.4 21.6 1.0 O B:HOH1081 2.4 19.0 1.0 OXT B:ACY702 2.4 20.3 1.0 C B:ACY702 2.8 24.4 1.0 CD2 B:HIS189 3.1 17.2 1.0 CD2 B:HIS184 3.1 20.7 1.0 CG B:ASP115 3.2 22.5 1.0 CE1 B:HIS189 3.4 25.6 1.0 OD2 B:ASP115 3.5 25.1 1.0 CE1 B:HIS184 3.5 21.2 1.0 CH3 B:ACY702 4.2 24.0 1.0 CG B:HIS189 4.3 19.7 1.0 O B:HOH1095 4.3 44.5 1.0 CG B:HIS184 4.3 15.6 1.0 CB B:ASP114 4.4 17.2 1.0 ND1 B:HIS189 4.4 19.1 1.0 ND1 B:HIS184 4.5 15.0 1.0 NE2 B:HIS55 4.5 20.4 1.0 CB B:ASP115 4.5 15.3 1.0 CA B:PRO251 4.6 16.2 1.0 N B:ASP115 4.7 22.1 1.0 N B:TYR252 4.7 14.8 1.0 CA B:ASP115 4.7 23.0 1.0 CD2 B:HIS55 4.7 22.0 1.0

D.J.Little, J.Poloczek, J.C.Whitney, H.Robinson, M.Nitz, P.L.Howell. The Structure and Metal Dependent Activity of Escherichia Coli Pgab Provides Insight Into the Partial De-N-Acetylation of Poly-B-1,6-N-Acetyl-D-Glucosamine J.Biol.Chem. V. 287 31126 2012.
ISSN: ISSN 0021-9258
PubMed: 22810235
DOI: 10.1074/JBC.M112.390005