Calcium 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:

Nickel

(Ni)

2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Escherichia Coli Pgab 42-655 in Complex with Nickel, PDB code: 4f9d:
Jump to Calcium binding site number: 1; 2;

Calcium 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 Calcium with other atoms in the Ca 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:Ca703 b:26.2 occ:1.00 O A:HOH1141 2.5 26.0 1.0 O A:HOH1140 2.5 29.7 1.0 OD1 A:ASP358 2.6 29.6 1.0 O A:LEU364 2.6 23.0 1.0 OD1 A:ASP362 2.6 24.9 1.0 OD2 A:ASP360 2.8 38.9 1.0 OD1 A:ASP360 2.9 40.7 1.0 CG A:ASP360 3.2 40.0 1.0 CG A:ASP362 3.4 23.6 1.0 C A:LEU364 3.7 23.7 1.0 OD2 A:ASP362 3.7 30.0 1.0 CG A:ASP358 3.7 28.9 1.0 N A:LEU364 4.0 25.7 1.0 CA A:LEU364 4.2 23.1 1.0 N A:ASP362 4.2 31.2 1.0 CB A:LEU364 4.3 22.6 1.0 OD2 A:ASP358 4.5 29.0 1.0 CA A:ASP358 4.5 23.4 1.0 CB A:ASP362 4.5 25.8 1.0 O A:HOH856 4.6 23.8 1.0 O A:HOH1143 4.6 37.6 1.0 CB A:ASP358 4.6 22.4 1.0 N A:GLY363 4.6 20.2 1.0 CB A:ASP360 4.7 30.2 1.0 CA A:ASP362 4.7 24.6 1.0 N A:GLY361 4.8 37.6 1.0 O A:HOH1246 4.8 49.1 1.0 N A:VAL365 4.8 17.2 1.0 C A:ASP358 4.9 30.3 1.0 C A:ASP362 4.9 24.6 1.0 C A:GLY363 5.0 25.2 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca703 b:29.2 occ:1.00 O B:HOH1083 2.4 31.9 1.0 O B:HOH1085 2.5 27.1 1.0 O B:LEU364 2.6 23.3 1.0 OD1 B:ASP358 2.6 30.6 1.0 OD1 B:ASP362 2.6 24.6 1.0 OD2 B:ASP360 2.9 49.5 1.0 OD1 B:ASP360 2.9 50.5 1.0 CG B:ASP360 3.3 47.0 1.0 CG B:ASP362 3.3 28.0 1.0 OD2 B:ASP362 3.6 29.5 1.0 C B:LEU364 3.7 25.9 1.0 CG B:ASP358 3.8 34.1 1.0 N B:LEU364 4.0 27.5 1.0 CA B:LEU364 4.2 27.1 1.0 CB B:LEU364 4.2 28.2 1.0 N B:ASP362 4.2 32.2 1.0 CA B:ASP358 4.4 27.1 1.0 CB B:ASP362 4.5 29.4 1.0 O B:HOH1086 4.5 44.0 1.0 OD2 B:ASP358 4.5 34.3 1.0 O B:HOH848 4.6 22.1 1.0 CB B:ASP358 4.6 28.3 1.0 N B:GLY363 4.6 24.5 1.0 O B:HOH1270 4.6 49.5 1.0 CA B:ASP362 4.7 27.0 1.0 CB B:ASP360 4.7 34.0 1.0 N B:VAL365 4.8 19.6 1.0 N B:GLY361 4.8 37.6 1.0 C B:ASP362 4.9 29.7 1.0 O B:HOH1267 4.9 56.6 1.0 C B:ASP358 4.9 35.3 1.0 CG B:LYS366 5.0 28.8 1.0 C B:GLY363 5.0 27.4 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