Nickel in PDB 8bdd: Crystal Structure of Bacteroides Ovatus CP926 PL17 Alginate Lyase

The structure of Crystal Structure of Bacteroides Ovatus CP926 PL17 Alginate Lyase, PDB code: 8bdd was solved by M.E.Roenne, T.Tandrup, C.Wilkens, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.21 / 1.61
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.59, 120.95, 90.24, 90, 117.76, 90
R / Rfree (%)	19 / 21.2

The binding sites of Nickel atom in the Crystal Structure of Bacteroides Ovatus CP926 PL17 Alginate Lyase (pdb code 8bdd). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Bacteroides Ovatus CP926 PL17 Alginate Lyase, PDB code: 8bdd:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Bacteroides Ovatus CP926 PL17 Alginate Lyase


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 Bacteroides Ovatus CP926 PL17 Alginate Lyase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni801 b:19.0 occ:0.55 NE2 A:HIS467 2.1 22.9 1.0 O A:HOH920 2.1 27.4 1.0 O A:HOH923 2.2 30.5 1.0 ND1 A:HIS418 2.2 22.7 1.0 OD1 A:ASP436 2.3 28.8 1.0 O A:HOH1220 2.4 26.6 1.0 CE1 A:HIS418 2.9 23.5 1.0 CD2 A:HIS467 2.9 22.0 1.0 CE1 A:HIS467 3.2 20.6 1.0 CG A:ASP436 3.2 31.3 1.0 CG A:HIS418 3.4 24.1 1.0 OD2 A:ASP436 3.4 28.9 1.0 O A:HOH970 3.8 32.1 1.0 CB A:HIS418 3.9 22.9 1.0 N A:ASN312 4.1 31.0 1.0 CG A:HIS467 4.1 18.8 1.0 NE2 A:HIS418 4.1 24.0 1.0 ND1 A:HIS467 4.2 20.0 1.0 O A:ALA461 4.2 21.8 1.0 O A:ASN312 4.2 31.9 1.0 O A:HIS310 4.3 32.0 1.0 CD2 A:HIS418 4.3 23.6 1.0 N A:GLY438 4.3 30.7 1.0 OD2 A:ASP420 4.4 25.9 1.0 CA A:ASN312 4.5 31.4 1.0 CB A:ASP436 4.6 26.8 1.0 N A:TYR437 4.7 27.6 1.0 O A:GLY438 4.7 28.1 1.0 C A:ASN312 4.7 33.9 1.0 CA A:GLY438 4.9 28.9 1.0 C A:ILE311 4.9 30.2 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Bacteroides Ovatus CP926 PL17 Alginate Lyase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Bacteroides Ovatus CP926 PL17 Alginate Lyase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni801 b:25.7 occ:0.44 NE2 B:HIS467 2.1 23.3 1.0 ND1 B:HIS418 2.2 24.7 1.0 O B:HOH909 2.3 36.5 1.0 O B:HOH904 2.4 37.6 1.0 O B:HOH1046 2.5 32.4 1.0 OD1 B:ASP436 2.5 49.6 1.0 CD2 B:HIS467 2.8 24.7 1.0 CE1 B:HIS418 2.8 26.1 1.0 OD2 B:ASP436 3.2 41.2 1.0 CG B:ASP436 3.2 45.2 1.0 CE1 B:HIS467 3.3 21.2 1.0 CG B:HIS418 3.4 24.9 1.0 CG B:HIS467 4.0 19.3 1.0 NE2 B:HIS418 4.0 24.7 1.0 CB B:HIS418 4.1 23.4 1.0 N B:ASN312 4.1 42.1 1.0 O B:ALA461 4.1 22.8 1.0 O B:ASN312 4.2 42.0 1.0 ND1 B:HIS467 4.2 21.1 1.0 N B:GLY438 4.2 42.1 1.0 CD2 B:HIS418 4.3 27.9 1.0 O B:HIS310 4.4 64.2 1.0 CA B:ASN312 4.4 40.3 1.0 OD2 B:ASP420 4.5 30.0 1.0 N B:TYR437 4.6 43.1 1.0 C B:ASN312 4.6 44.2 1.0 CB B:ASP436 4.6 42.4 1.0 O B:GLY438 4.6 39.1 1.0 CA B:GLY438 4.7 41.7 1.0

M.E.Roenne, T.Tandrup, C.Wilkens. Three Alginate Lyases Providing A New Gut Bacteroides Ovatus Isolate with the Ability to Grow on Alginate Appl.Environ.Microbiol. 2023.
ISSN: ESSN 1098-5336