Calcium in PDB 4f9j: Structure of Escherichia Coli Pgab 42-655 in Complex with Iron

The structure of Structure of Escherichia Coli Pgab 42-655 in Complex with Iron, PDB code: 4f9j 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)	45.53 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	91.055, 102.428, 150.901, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 19.8

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

Iron

(Fe)

2 atoms

The binding sites of Calcium atom in the Structure of Escherichia Coli Pgab 42-655 in Complex with Iron (pdb code 4f9j). 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 Iron, PDB code: 4f9j:
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 Iron


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 Iron within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:28.7 occ:1.00 O A:HOH954 2.6 26.5 1.0 O A:HOH955 2.6 24.6 1.0 O A:LEU364 2.6 22.8 1.0 OD1 A:ASP362 2.7 24.0 1.0 OD1 A:ASP358 2.7 31.7 1.0 OD1 A:ASP360 2.9 44.3 1.0 OD2 A:ASP360 3.0 45.2 1.0 CG A:ASP360 3.3 41.9 1.0 CG A:ASP362 3.4 22.5 1.0 C A:LEU364 3.7 25.0 1.0 OD2 A:ASP362 3.7 22.8 1.0 CG A:ASP358 3.8 29.6 1.0 N A:LEU364 4.0 19.1 1.0 CA A:LEU364 4.2 18.6 1.0 N A:ASP362 4.2 24.2 1.0 CB A:LEU364 4.3 17.6 1.0 CA A:ASP358 4.4 24.5 1.0 CB A:ASP362 4.6 17.1 1.0 OD2 A:ASP358 4.6 35.2 1.0 CB A:ASP358 4.6 18.8 1.0 N A:GLY363 4.6 27.8 1.0 O A:HOH856 4.7 20.3 1.0 N A:GLY361 4.7 34.6 1.0 CA A:ASP362 4.7 21.2 1.0 CB A:ASP360 4.7 34.5 1.0 C A:ASP358 4.8 33.5 1.0 N A:VAL365 4.8 20.3 1.0 C A:ASP362 4.9 20.4 1.0 O A:HOH1001 4.9 42.7 1.0 C A:GLY363 5.0 26.6 1.0 N A:ASP360 5.0 36.4 1.0

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


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 Iron within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca703 b:32.0 occ:1.00 O B:HOH923 2.5 27.8 1.0 O B:LEU364 2.6 22.1 1.0 OD1 B:ASP362 2.7 21.8 1.0 OD1 B:ASP358 2.7 29.8 1.0 O B:HOH954 2.8 29.2 1.0 OD1 B:ASP360 2.9 49.2 1.0 OD2 B:ASP360 2.9 41.0 1.0 CG B:ASP360 3.3 40.8 1.0 CG B:ASP362 3.4 22.8 1.0 C B:LEU364 3.7 26.1 1.0 CG B:ASP358 3.7 26.2 1.0 OD2 B:ASP362 3.7 24.7 1.0 N B:LEU364 3.9 19.4 1.0 CA B:LEU364 4.1 23.2 1.0 CB B:LEU364 4.1 22.7 1.0 N B:ASP362 4.3 32.4 1.0 OD2 B:ASP358 4.4 31.4 1.0 CA B:ASP358 4.5 21.5 1.0 CB B:ASP358 4.5 18.7 1.0 CB B:ASP362 4.6 18.2 1.0 O B:HOH1040 4.6 39.9 1.0 N B:GLY363 4.6 29.7 1.0 N B:GLY361 4.7 31.2 1.0 O B:HOH848 4.7 23.1 1.0 CB B:ASP360 4.8 32.0 1.0 N B:VAL365 4.8 18.1 1.0 CA B:ASP362 4.8 23.6 1.0 C B:ASP358 4.9 26.6 1.0 C B:ASP362 4.9 27.5 1.0 CG B:LEU364 4.9 23.3 1.0 CG B:LYS366 5.0 29.2 1.0 C B:GLY363 5.0 28.1 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