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Nickel 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:

Calcium (Ca) 2 atoms

Nickel Binding Sites:

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 4f9d

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

Go back to Nickel Binding Sites List in 4f9d
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

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: Wed Dec 16 01:30:08 2020

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