Calcium in PDB 7lj2: Structure of Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis in Complex with Neoporphyrabiose

The structure of Structure of Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis in Complex with Neoporphyrabiose, PDB code: 7lj2 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)	29.79 / 2.40
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	89.67, 89.67, 267.06, 90, 90, 90
R / Rfree (%)	18.2 / 23.1

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

Sodium

(Na)

2 atoms

The binding sites of Calcium atom in the Structure of Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis in Complex with Neoporphyrabiose (pdb code 7lj2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis in Complex with Neoporphyrabiose, PDB code: 7lj2:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis in Complex with Neoporphyrabiose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis in Complex with Neoporphyrabiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:29.7 occ:0.46 OD2 A:ASP330 2.3 25.4 1.0 OD1 A:ASP37 2.3 30.5 1.0 OD1 A:ASP38 2.4 25.7 1.0 OE1 A:GLN331 2.4 29.3 1.0 O3S C:L6S2 2.4 32.9 1.0 CG A:ASP330 2.9 30.3 1.0 OD1 A:ASP330 3.0 29.3 1.0 CD A:GLN331 3.3 31.8 1.0 CG A:ASP38 3.3 27.5 1.0 CG A:ASP37 3.5 31.2 1.0 N A:ASP38 3.6 27.8 1.0 NE2 A:GLN331 3.6 26.2 1.0 CB A:SER80 3.8 29.2 1.0 S1 C:L6S2 3.8 32.0 1.0 NZ A:LYS343 3.9 33.1 1.0 OD2 A:ASP38 4.0 32.2 1.0 O1S C:L6S2 4.1 34.1 1.0 CE A:LYS343 4.1 36.3 1.0 C A:ASP37 4.1 27.9 1.0 CA A:ASP38 4.2 25.9 1.0 CA A:ASP37 4.2 27.0 1.0 CA A:SER80 4.2 30.5 1.0 OD2 A:ASP37 4.3 34.0 1.0 CB A:ASP38 4.3 26.6 1.0 O2S C:L6S2 4.3 31.6 1.0 CB A:ASP330 4.4 29.9 1.0 OG A:SER80 4.4 37.1 1.0 NZ A:LYS128 4.4 32.5 1.0 CD2 A:HIS211 4.4 30.7 1.0 CB A:ASP37 4.5 29.4 1.0 N A:SER80 4.5 31.6 1.0 CG A:GLN331 4.6 28.9 1.0 NH2 A:ARG84 4.6 27.7 1.0 CD A:LYS343 4.9 30.8 1.0 O6 C:L6S2 5.0 37.1 1.0 N A:GLN331 5.0 27.8 1.0

Calcium binding site 2 out of 2 in the Structure of Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis in Complex with Neoporphyrabiose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis in Complex with Neoporphyrabiose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:28.0 occ:0.56 OD2 B:ASP330 2.3 26.1 1.0 OD1 B:ASP38 2.3 27.0 1.0 O2S D:L6S2 2.4 35.8 1.0 OD1 B:ASP37 2.4 29.0 1.0 OE1 B:GLN331 2.4 26.4 1.0 CG B:ASP330 2.9 27.2 1.0 OD1 B:ASP330 3.0 27.5 1.0 CD B:GLN331 3.3 25.1 1.0 CG B:ASP38 3.4 29.6 1.0 CG B:ASP37 3.5 28.8 1.0 N B:ASP38 3.6 26.4 1.0 CB B:SER80 3.6 24.4 1.0 NE2 B:GLN331 3.7 23.4 1.0 S1 D:L6S2 3.8 30.5 1.0 OD2 B:ASP38 4.1 30.3 1.0 NZ B:LYS128 4.1 23.7 1.0 O1S D:L6S2 4.2 27.6 1.0 C B:ASP37 4.2 28.4 1.0 CA B:SER80 4.2 26.3 1.0 CA B:ASP37 4.2 28.7 1.0 OD2 B:ASP37 4.2 29.6 1.0 CA B:ASP38 4.2 23.0 1.0 OG B:SER80 4.3 28.1 1.0 O3S D:L6S2 4.3 28.9 1.0 CB B:ASP330 4.3 26.9 1.0 CB B:ASP38 4.4 26.3 1.0 CB B:ASP37 4.4 25.8 1.0 N B:SER80 4.4 27.0 1.0 NZ B:LYS343 4.5 28.3 1.0 NH2 B:ARG84 4.5 21.6 1.0 CD2 B:HIS211 4.6 29.3 1.0 CG B:GLN331 4.6 26.4 1.0 CE B:LYS343 4.7 36.1 1.0 O6 D:L6S2 5.0 38.2 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