Calcium in PDB 4awd: Crystal Structure of the Beta-Porphyranase BPGH16B (BACPLE_01689) From the Human Gut Bacterium Bacteroides Plebeius

All present enzymatic activity of Crystal Structure of the Beta-Porphyranase BPGH16B (BACPLE_01689) From the Human Gut Bacterium Bacteroides Plebeius:
3.2.1.178;

The structure of Crystal Structure of the Beta-Porphyranase BPGH16B (BACPLE_01689) From the Human Gut Bacterium Bacteroides Plebeius, PDB code: 4awd was solved by J.H.Hehemann, A.G.Kelly, N.A.Pudlo, E.C.Martens, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.40
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.120, 107.230, 137.260, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 25

The binding sites of Calcium atom in the Crystal Structure of the Beta-Porphyranase BPGH16B (BACPLE_01689) From the Human Gut Bacterium Bacteroides Plebeius (pdb code 4awd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the Beta-Porphyranase BPGH16B (BACPLE_01689) From the Human Gut Bacterium Bacteroides Plebeius, PDB code: 4awd:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of the Beta-Porphyranase BPGH16B (BACPLE_01689) From the Human Gut Bacterium Bacteroides Plebeius


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Beta-Porphyranase BPGH16B (BACPLE_01689) From the Human Gut Bacterium Bacteroides Plebeius within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1321 b:17.7 occ:1.00 O A:GLY91 2.2 17.2 1.0 O A:HOH2038 2.4 9.9 1.0 OD1 A:ASP309 2.4 9.7 1.0 OD1 A:ASN56 2.4 18.5 1.0 O A:GLU54 2.4 13.4 1.0 O A:ASP309 2.5 12.6 1.0 C A:GLY91 3.2 18.1 1.0 CG A:ASN56 3.4 17.7 1.0 C A:ASP309 3.5 12.4 1.0 CG A:ASP309 3.6 11.4 1.0 C A:GLU54 3.6 13.1 1.0 CA A:GLY91 3.7 18.9 1.0 ND2 A:ASN56 3.8 15.3 1.0 CA A:ASP309 4.0 12.3 1.0 CA A:GLU54 4.3 12.7 1.0 N A:CYS92 4.4 17.3 1.0 CB A:ASP309 4.4 12.1 1.0 O A:PHE55 4.4 14.9 1.0 C A:PHE55 4.5 14.7 1.0 OD2 A:ASP309 4.5 12.1 1.0 CB A:GLU54 4.5 12.4 1.0 N A:TRP310 4.6 12.5 1.0 OE1 A:GLU54 4.6 11.5 1.0 N A:PHE55 4.7 13.5 1.0 N A:ASN56 4.7 16.0 1.0 CB A:ASN56 4.7 16.9 1.0 O A:HOH2210 4.7 16.0 1.0 CB A:TRP310 4.9 12.8 1.0 CA A:CYS92 4.9 16.6 1.0 CA A:PHE55 4.9 14.0 1.0 CA A:ASN56 4.9 17.4 1.0 CD1 A:TRP310 4.9 14.7 1.0 CB A:PHE55 4.9 12.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of the Beta-Porphyranase BPGH16B (BACPLE_01689) From the Human Gut Bacterium Bacteroides Plebeius


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Beta-Porphyranase BPGH16B (BACPLE_01689) From the Human Gut Bacterium Bacteroides Plebeius within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1321 b:23.1 occ:1.00 O B:GLY91 2.3 21.8 1.0 O B:GLU54 2.4 17.5 1.0 O B:HOH2027 2.5 10.6 1.0 O B:HOH2024 2.5 27.1 1.0 OD1 B:ASN56 2.5 20.3 1.0 OD1 B:ASP309 2.6 15.0 1.0 O B:ASP309 2.6 16.6 1.0 C B:GLY91 3.3 21.8 1.0 CG B:ASN56 3.4 22.2 1.0 C B:GLU54 3.6 17.5 1.0 C B:ASP309 3.6 16.6 1.0 ND2 B:ASN56 3.6 21.5 1.0 CA B:GLY91 3.7 22.2 1.0 CG B:ASP309 3.7 16.4 1.0 CA B:ASP309 4.1 16.6 1.0 O B:PHE55 4.2 21.0 1.0 CA B:GLU54 4.3 16.6 1.0 CB B:GLU54 4.4 16.2 1.0 C B:PHE55 4.4 20.8 1.0 CB B:ASP309 4.5 16.7 1.0 N B:CYS92 4.5 20.9 1.0 OD2 B:ASP309 4.6 17.1 1.0 N B:PHE55 4.6 18.8 1.0 O B:HOH2050 4.7 27.4 1.0 OE1 B:GLU54 4.7 16.3 1.0 N B:TRP310 4.7 16.6 1.0 CB B:ASN56 4.7 22.3 1.0 CD1 B:TRP310 4.8 16.8 1.0 N B:ASN56 4.8 21.8 1.0 CB B:TRP310 4.8 16.4 1.0 CA B:PHE55 4.9 20.1 1.0

J.H.Hehemann, A.G.Kelly, N.A.Pudlo, E.C.Martens, A.B.Boraston. Bacteria of the Human Gut Microbiome Catabolize Red Seaweed Glycans with Carbohydrate-Active Enzyme Updates From Extrinsic Microbes. Proc. Natl. Acad. Sci. V. 109 19786 2012U.S.A..
ISSN: ESSN 1091-6490
PubMed: 23150581
DOI: 10.1073/PNAS.1211002109