Copper in PDB 9d5t: Crystal Structure of Cu(II)-Bound Polysaccharide Deacetylase From Bacteroides Ovatus

The structure of Crystal Structure of Cu(II)-Bound Polysaccharide Deacetylase From Bacteroides Ovatus, PDB code: 9d5t was solved by O.G.Yost, K.J.Mclaughlin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.71 / 1.56
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.764, 73.183, 95.41, 90, 90, 90
R / Rfree (%)	17.5 / 20.1

The binding sites of Copper atom in the Crystal Structure of Cu(II)-Bound Polysaccharide Deacetylase From Bacteroides Ovatus (pdb code 9d5t). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total only one binding site of Copper was determined in the Crystal Structure of Cu(II)-Bound Polysaccharide Deacetylase From Bacteroides Ovatus, PDB code: 9d5t:

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


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Cu(II)-Bound Polysaccharide Deacetylase From Bacteroides Ovatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu507 b:17.5 occ:0.75 NE2 A:HIS213 2.0 13.7 1.0 O2 A:GOL506 2.1 38.4 0.5 O1 A:GOL506 2.3 33.9 0.5 O1 A:GOL506 2.3 33.8 0.5 OD1 A:ASP102 2.3 28.7 1.0 O A:HOH681 2.4 23.5 1.0 C1 A:GOL506 2.6 35.6 0.5 C1 A:GOL506 2.8 35.5 0.5 C2 A:GOL506 2.9 38.0 0.5 CD2 A:HIS213 3.0 17.8 1.0 CE1 A:HIS213 3.1 16.2 1.0 O2 A:GOL506 3.2 39.1 0.5 CG A:ASP102 3.3 26.2 1.0 C2 A:GOL506 3.3 38.0 0.5 OD2 A:ASP102 3.6 25.7 1.0 O A:HOH945 3.7 39.3 1.0 C3 A:GOL506 3.7 40.3 0.5 OD2 A:ASP214 4.0 23.4 1.0 CB A:ASP101 4.1 13.2 1.0 C3 A:GOL506 4.1 40.2 0.5 NE2 A:HIS337 4.1 25.0 1.0 ND1 A:HIS213 4.1 17.2 1.0 OD2 A:ASP101 4.2 17.3 1.0 CG A:HIS213 4.2 17.7 1.0 CD2 A:HIS337 4.5 23.4 1.0 CG A:ASP101 4.5 16.6 1.0 N A:ASP102 4.6 15.0 1.0 CB A:PRO253 4.6 19.6 1.0 CB A:ASP102 4.6 19.0 1.0 CA A:PRO253 4.7 18.1 1.0 CA A:ASP102 4.9 15.0 1.0 N A:ASN254 4.9 25.0 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