Nickel in PDB 7lha: Structure of the Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis

The structure of Structure of the Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis, PDB code: 7lha was solved by C.S.Robb, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.60 / 1.95
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	89.41, 89.41, 264.79, 90, 90, 90
R / Rfree (%)	14.8 / 19.4

The structure of Structure of the Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Nickel atom in the Structure of the Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis (pdb code 7lha). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Structure of the Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis, PDB code: 7lha:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Structure of the Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of the Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni602 b:22.2 occ:1.00 OG A:SER180 2.9 11.8 1.0 N A:LYS208 3.1 6.1 1.0 OG A:SER179 3.2 13.6 1.0 N A:ALA209 3.2 5.7 1.0 N A:SER180 3.4 7.2 1.0 CA A:SER180 3.4 12.0 1.0 CB A:SER180 3.7 12.0 1.0 CB A:LYS208 3.8 8.7 1.0 CA A:LYS208 3.8 12.2 1.0 CD1 A:TYR207 3.8 10.0 1.0 C A:SER179 3.8 7.1 1.0 CD1 A:ILE183 3.9 8.8 1.0 CB A:ALA209 3.9 10.5 1.0 CB A:SER179 4.0 8.0 1.0 C A:LYS208 4.0 9.9 1.0 CB A:TYR207 4.0 6.4 1.0 C A:TYR207 4.0 9.5 1.0 CA A:TYR207 4.1 5.8 1.0 O A:SER179 4.2 7.6 1.0 CA A:ALA209 4.2 8.3 1.0 CG A:TYR207 4.4 8.1 1.0 CA A:SER179 4.5 8.8 1.0 CE1 A:TYR153 4.8 22.4 1.0 C A:SER180 4.9 6.1 1.0 CE1 A:TYR207 4.9 9.6 1.0 CG A:LYS208 4.9 18.2 1.0 CG1 A:ILE183 5.0 6.0 1.0

Nickel binding site 2 out of 4 in the Structure of the Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of the Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni603 b:27.1 occ:1.00 N A:HIS130 3.2 10.3 1.0 O A:HOH1145 3.2 14.1 1.0 NH1 A:ARG84 3.3 7.7 1.0 ND1 A:HIS206 3.5 8.1 1.0 CE1 A:HIS206 3.6 8.2 1.0 CD A:ARG84 3.6 8.4 1.0 O A:LYS128 3.7 8.8 1.0 CA A:TRP129 3.8 8.0 1.0 CG A:ARG84 3.9 8.0 1.0 C A:TRP129 3.9 13.0 1.0 CB A:HIS130 4.0 12.0 1.0 CB A:ARG84 4.0 7.6 1.0 CA A:HIS130 4.1 13.4 1.0 CG A:LEU131 4.1 12.2 1.0 CE3 A:TRP129 4.1 11.9 1.0 CZ A:ARG84 4.3 9.9 1.0 N A:LEU131 4.4 10.7 1.0 NE A:ARG84 4.4 12.0 1.0 CD1 A:LEU131 4.4 12.4 1.0 C A:LYS128 4.6 11.4 1.0 N A:TRP129 4.6 8.7 1.0 CD2 A:TRP129 4.6 8.6 1.0 C A:HIS130 4.7 11.4 1.0 CD2 A:HIS130 4.7 13.5 1.0 CZ3 A:TRP129 4.7 14.4 1.0 CB A:TRP129 4.8 6.1 1.0 CG A:HIS130 4.8 11.2 1.0 CG A:HIS206 4.8 3.7 1.0 O A:HOH964 4.8 19.6 1.0 CD2 A:LEU131 4.9 11.0 1.0 NE2 A:HIS206 4.9 9.6 1.0 CG A:TRP129 4.9 8.7 1.0

Nickel binding site 3 out of 4 in the Structure of the Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of the Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni602 b:24.3 occ:1.00 OG B:SER180 3.0 10.8 1.0 N B:LYS208 3.1 8.1 1.0 OG B:SER179 3.2 16.4 1.0 N B:ALA209 3.3 7.1 1.0 N B:SER180 3.4 5.6 1.0 CA B:SER180 3.4 8.8 1.0 C B:SER179 3.7 6.4 1.0 CB B:LYS208 3.7 12.7 1.0 CD1 B:TYR207 3.8 12.0 1.0 CB B:SER180 3.8 6.9 1.0 CA B:LYS208 3.8 11.1 1.0 CD1 B:ILE183 3.9 8.8 1.0 CB B:SER179 3.9 11.9 1.0 CB B:ALA209 4.0 8.6 1.0 CB B:TYR207 4.0 6.7 1.0 C B:TYR207 4.0 9.6 1.0 C B:LYS208 4.0 11.6 1.0 CA B:TYR207 4.0 9.6 1.0 O B:SER179 4.1 7.8 1.0 CA B:ALA209 4.2 11.2 1.0 CG B:TYR207 4.4 7.9 1.0 CA B:SER179 4.4 8.4 1.0 CE1 B:TYR153 4.8 22.9 1.0 CG B:LYS208 4.8 17.1 1.0 CE1 B:TYR207 4.8 8.5 1.0 C B:SER180 4.8 8.0 1.0 CG1 B:ILE183 5.0 9.2 1.0

Nickel binding site 4 out of 4 in the Structure of the Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Structure of the Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni603 b:31.3 occ:1.00 N B:HIS130 3.0 15.0 1.0 O B:HOH1112 3.2 24.8 1.0 NH1 B:ARG84 3.3 7.3 1.0 ND1 B:HIS206 3.5 14.8 1.0 CA B:TRP129 3.5 13.6 1.0 CE1 B:HIS206 3.6 10.2 1.0 O B:LYS128 3.6 13.1 1.0 CD B:ARG84 3.7 10.1 1.0 C B:TRP129 3.8 17.5 1.0 CG B:ARG84 3.9 12.2 1.0 CE3 B:TRP129 3.9 16.7 1.0 CG B:LEU131 4.0 20.1 1.0 CA B:HIS130 4.1 16.1 1.0 CB B:ARG84 4.1 10.3 1.0 CB B:HIS130 4.1 10.3 1.0 N B:LEU131 4.2 16.3 1.0 CZ B:ARG84 4.3 12.7 1.0 CD1 B:LEU131 4.4 22.7 1.0 N B:TRP129 4.4 15.0 1.0 C B:LYS128 4.4 12.8 1.0 CD2 B:TRP129 4.4 11.8 1.0 NE B:ARG84 4.4 9.1 1.0 CB B:TRP129 4.5 10.3 1.0 C B:HIS130 4.6 17.7 1.0 CZ3 B:TRP129 4.6 14.2 1.0 CG B:TRP129 4.6 14.1 1.0 CG B:HIS206 4.8 7.5 1.0 CD2 B:LEU131 4.8 17.4 1.0 O B:HOH978 4.8 18.3 1.0 NE2 B:HIS206 4.9 13.6 1.0 CB B:LEU131 4.9 14.0 1.0 CG B:HIS130 4.9 11.5 1.0 CD2 B:HIS130 5.0 11.9 1.0 CE B:MET125 5.0 15.0 1.0

C.S.Robb, J.K.Hobbs, B.Pluvinage, G.Reintjes, L.Klassen, S.Monteith, G.Giljan, C.Amundsen, C.Vickers, A.G.Hettle, R.Hills, X.Xing, T.Montina, W.F.Zandberg, D.W.Abbott, A.B.Boraston. Metabolism of A Hybrid Algal Galactan By Members of the Human Gut Microbiome. Nat.Chem.Biol. V. 18 501 2022.
ISSN: ESSN 1552-4469
PubMed: 35289327
DOI: 10.1038/S41589-022-00983-Y