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

Protein crystallography data

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

Other elements in 4f9d:

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

Nickel (Ni) 2 atoms

Calcium Binding Sites:

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 4f9d

Go back to Calcium Binding Sites List in 4f9d
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 4f9d

Go back to Calcium Binding Sites List in 4f9d
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

Reference:

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
Page generated: Sat Dec 12 04:45:58 2020

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