Nickel in PDB 9d4i: Crystal Structure of Ni(II)-Bound Polysaccharide Deacetylase From Bacteroides Ovatus

The structure of Crystal Structure of Ni(II)-Bound Polysaccharide Deacetylase From Bacteroides Ovatus, PDB code: 9d4i was solved by E.Dzuong, K.J.Mclaughlin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.58 / 1.48
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.945, 73.041, 95.163, 90, 90, 90
R / Rfree (%)	16.6 / 19.3

The binding sites of Nickel atom in the Crystal Structure of Ni(II)-Bound Polysaccharide Deacetylase From Bacteroides Ovatus (pdb code 9d4i). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Crystal Structure of Ni(II)-Bound Polysaccharide Deacetylase From Bacteroides Ovatus, PDB code: 9d4i:

Nickel binding site 1 out of 1 in the Crystal Structure of Ni(II)-Bound Polysaccharide Deacetylase From Bacteroides Ovatus


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Ni(II)-Bound Polysaccharide Deacetylase From Bacteroides Ovatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni505 b:13.0 occ:0.90 O3 A:GOL504 2.0 23.1 1.0 O2 A:GOL504 2.0 22.2 1.0 OD1 A:ASP102 2.1 14.1 1.0 O1 A:GOL504 2.1 20.1 1.0 O A:HOH663 2.1 14.7 1.0 NE2 A:HIS213 2.1 11.8 1.0 C2 A:GOL504 2.5 23.0 1.0 C3 A:GOL504 2.7 23.6 1.0 C1 A:GOL504 2.9 22.0 1.0 CD2 A:HIS213 3.0 11.4 1.0 CG A:ASP102 3.1 12.0 1.0 CE1 A:HIS213 3.2 12.4 1.0 OD2 A:ASP102 3.4 17.7 1.0 O A:HOH626 3.7 35.6 1.0 NE2 A:HIS337 4.1 16.7 1.0 OD2 A:ASP214 4.1 20.5 1.0 OD2 A:ASP101 4.1 14.2 1.0 O A:HOH1071 4.2 27.7 1.0 CB A:ASP101 4.2 10.4 1.0 CG A:HIS213 4.2 12.9 1.0 ND1 A:HIS213 4.2 12.6 1.0 CB A:ASP102 4.4 13.3 1.0 CD2 A:HIS337 4.5 16.1 1.0 O A:HOH1064 4.6 39.5 1.0 CG A:ASP101 4.6 12.5 1.0 N A:ASP102 4.6 10.7 1.0 CA A:ASP102 4.8 10.6 1.0 CA A:PRO253 4.9 12.2 1.0 CB A:PRO253 4.9 20.9 1.0

L.A.Schwartz, J.O.Norman, S.Hasan, O.E.Adamek, E.Dzuong, J.C.Lowenstein, O.G.Yost, B.Sankaran, K.J.Mclaughlin. Carbohydrate Deacetylase Unique to Gut Microbe Bacteroides Reveals Atypical Structure. Biochemistry 2024.
ISSN: ISSN 0006-2960
PubMed: 39663570
DOI: 10.1021/ACS.BIOCHEM.4C00519