Nickel in PDB 5bu6: Structure of Bpsb Deaceylase Domain From Bordetella Bronchiseptica

All present enzymatic activity of Structure of Bpsb Deaceylase Domain From Bordetella Bronchiseptica:
3.5.1.33;

The structure of Structure of Bpsb Deaceylase Domain From Bordetella Bronchiseptica, PDB code: 5bu6 was solved by D.J.Little, N.C.Bamford, P.L.Howell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.60 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.947, 77.785, 76.861, 90.00, 108.00, 90.00
R / Rfree (%)	16.9 / 20.8

The binding sites of Nickel atom in the Structure of Bpsb Deaceylase Domain From Bordetella Bronchiseptica (pdb code 5bu6). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 5 binding sites of Nickel where determined in the Structure of Bpsb Deaceylase Domain From Bordetella Bronchiseptica, PDB code: 5bu6:
Jump to Nickel binding site number: 1; 2; 3; 4; 5;

Nickel binding site 1 out of 5 in the Structure of Bpsb Deaceylase Domain From Bordetella Bronchiseptica


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of Bpsb Deaceylase Domain From Bordetella Bronchiseptica within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni401 b:34.4 occ:1.00 NE2 A:HIS189 2.1 33.5 1.0 OD1 A:ASP114 2.1 33.9 1.0 O A:HOH522 2.1 43.4 1.0 S A:SCN404 2.1 73.0 1.0 O A:HOH502 2.2 33.6 1.0 NE2 A:HIS184 2.2 24.8 1.0 CD2 A:HIS184 3.0 28.9 1.0 CG A:ASP114 3.0 38.9 1.0 CE1 A:HIS189 3.1 38.6 1.0 CD2 A:HIS189 3.1 34.0 1.0 OD2 A:ASP114 3.3 44.9 1.0 CE1 A:HIS184 3.3 31.4 1.0 C A:SCN404 3.8 55.7 1.0 ND1 A:HIS189 4.2 34.5 1.0 CG A:HIS189 4.2 30.7 1.0 CB A:ASP113 4.2 62.1 1.0 CG A:HIS184 4.2 27.0 1.0 ND1 A:HIS184 4.3 28.3 1.0 CB A:ASP114 4.4 33.2 1.0 OD2 A:ASP113 4.5 92.8 1.0 N A:ASP114 4.8 33.1 1.0 CA A:ASP114 4.8 38.1 1.0 N A:SCN404 4.9 46.2 1.0 CG A:ASP113 4.9 85.0 1.0 C A:ASP113 4.9 42.1 1.0

Nickel binding site 2 out of 5 in the Structure of Bpsb Deaceylase Domain From Bordetella Bronchiseptica


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of Bpsb Deaceylase Domain From Bordetella Bronchiseptica within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni402 b:82.0 occ:1.00 CD2 A:HIS239 2.6 42.2 1.0 CE1 A:HIS235 2.7 48.9 1.0 CG A:HIS239 3.3 43.5 1.0 NE2 A:HIS235 3.4 48.5 1.0 CB A:HIS239 3.6 36.4 1.0 ND1 A:HIS235 3.6 50.5 1.0 N A:SCN406 3.7 66.6 1.0 NE2 A:HIS239 3.7 49.4 1.0 C A:SCN406 4.3 69.6 1.0 ND1 A:HIS239 4.5 50.6 1.0 CA A:HIS239 4.5 32.9 1.0 CD2 A:HIS235 4.6 44.4 1.0 CE1 A:HIS239 4.7 52.2 1.0 CG A:HIS235 4.7 50.3 1.0

Nickel binding site 3 out of 5 in the Structure of Bpsb Deaceylase Domain From Bordetella Bronchiseptica


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of Bpsb Deaceylase Domain From Bordetella Bronchiseptica within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni403 b:33.4 occ:1.00 S A:SCN405 2.1 74.5 1.0 S A:SCN407 2.1 67.7 1.0 NE2 A:HIS240 2.2 27.9 1.0 CD2 A:HIS240 3.1 27.5 1.0 CE1 A:HIS240 3.2 37.5 1.0 C A:SCN405 3.9 55.6 1.0 C A:SCN407 3.9 58.6 1.0 OD1 A:ASP144 3.9 41.2 1.0 S A:SCN406 4.0 89.0 1.0 CG A:HIS240 4.3 26.4 1.0 ND1 A:HIS240 4.3 28.4 1.0 CE1 A:HIS239 4.6 52.2 1.0 ND1 A:HIS239 4.7 50.6 1.0 CD1 A:TRP167 4.9 38.4 1.0 NE1 A:TRP167 4.9 35.9 1.0 CG A:ASP144 5.0 39.1 1.0

Nickel binding site 4 out of 5 in the Structure of Bpsb Deaceylase Domain From Bordetella Bronchiseptica


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Structure of Bpsb Deaceylase Domain From Bordetella Bronchiseptica within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni401 b:39.7 occ:1.00 O B:HOH532 2.0 46.0 1.0 NE2 B:HIS189 2.1 35.2 1.0 NE2 B:HIS184 2.2 32.5 1.0 OD1 B:ASP114 2.2 41.1 1.0 S B:SCN403 2.2 76.3 1.0 O B:HOH502 2.3 42.7 1.0 CD2 B:HIS184 3.0 26.1 1.0 CD2 B:HIS189 3.0 35.3 1.0 CE1 B:HIS189 3.1 38.7 1.0 CG B:ASP114 3.1 44.6 1.0 CE1 B:HIS184 3.2 35.0 1.0 OD2 B:ASP114 3.3 47.7 1.0 C B:SCN403 3.8 62.9 1.0 ND1 B:HIS189 4.2 36.1 1.0 CG B:HIS189 4.2 32.7 1.0 CG B:HIS184 4.2 29.3 1.0 ND1 B:HIS184 4.3 31.3 1.0 CB B:ASP113 4.3 66.8 1.0 CB B:ASP114 4.5 40.8 1.0 N B:ASP114 4.8 37.9 1.0 N B:SCN403 4.9 58.7 1.0 CA B:ASP114 4.9 40.5 1.0 OD2 B:ASP113 5.0 96.0 1.0

Nickel binding site 5 out of 5 in the Structure of Bpsb Deaceylase Domain From Bordetella Bronchiseptica


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Structure of Bpsb Deaceylase Domain From Bordetella Bronchiseptica within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni402 b:96.7 occ:1.00 ND1 B:HIS239 2.7 41.7 1.0 NE2 B:HIS235 3.0 70.6 1.0 CG B:HIS239 3.5 40.5 1.0 CE1 B:HIS239 3.6 42.8 1.0 CD2 B:HIS235 3.6 62.9 1.0 CB B:HIS239 3.6 35.8 1.0 CE1 B:HIS235 4.0 72.0 1.0 CA B:HIS239 4.4 33.7 1.0 CD2 B:HIS239 4.7 42.6 1.0 NE2 B:HIS239 4.7 46.2 1.0 CG B:HIS235 4.8 52.2 1.0 ND1 B:HIS235 5.0 66.4 1.0

D.J.Little, S.Milek, N.C.Bamford, T.Ganguly, B.R.Difrancesco, M.Nitz, R.Deora, P.L.Howell. The Protein Bpsb Is A Poly-Beta-1,6-N-Acetyl-D-Glucosamine Deacetylase Required For Biofilm Formation in Bordetella Bronchiseptica. J.Biol.Chem. V. 290 22827 2015.
ISSN: ESSN 1083-351X
PubMed: 26203190
DOI: 10.1074/JBC.M115.672469