Calcium in PDB 6q63: BT0459

All present enzymatic activity of BT0459:
3.2.1.52;

The structure of BT0459, PDB code: 6q63 was solved by A.Basle, L.Crouch, D.Bolam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.80 / 2.44
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	175.842, 186.880, 242.279, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 23.5

The structure of BT0459 also contains other interesting chemical elements:

Copper

(Cu)

3 atoms

The binding sites of Calcium atom in the BT0459 (pdb code 6q63). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the BT0459, PDB code: 6q63:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the BT0459


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of BT0459 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:46.5 occ:1.00 O A:LEU646 2.2 48.9 1.0 OE1 A:GLU770 2.3 44.8 1.0 O A:THR641 2.3 45.7 1.0 O A:ASP769 2.4 43.4 1.0 OD1 A:ASP644 2.4 48.8 1.0 O A:HOH1023 2.4 42.6 1.0 CG A:ASP644 3.3 49.2 1.0 C A:LEU646 3.4 48.9 1.0 CD A:GLU770 3.5 44.9 1.0 C A:ASP769 3.5 43.5 1.0 C A:THR641 3.6 47.1 1.0 OD2 A:ASP644 3.7 49.4 1.0 N A:LEU646 3.8 49.8 1.0 CB A:GLU770 3.9 44.1 1.0 CA A:LEU646 4.0 49.5 1.0 CB A:LEU646 4.1 49.8 1.0 CA A:GLU770 4.1 44.2 1.0 CG A:GLU770 4.2 44.7 1.0 N A:GLU770 4.3 43.7 1.0 N A:ASP644 4.3 49.1 1.0 CA A:LEU642 4.3 46.8 1.0 CG2 A:THR641 4.4 46.2 1.0 N A:LEU642 4.4 47.2 1.0 O A:ARG656 4.4 47.0 1.0 OE2 A:GLU770 4.4 45.9 1.0 C A:LEU642 4.5 47.3 1.0 N A:LYS647 4.5 48.8 1.0 CA A:ASP769 4.6 43.1 1.0 N A:GLY645 4.6 49.8 1.0 CB A:ASP644 4.6 49.9 1.0 CA A:THR641 4.6 47.7 1.0 N A:VAL643 4.7 47.9 1.0 C A:GLY645 4.8 49.8 1.0 CA A:ASP644 4.8 49.9 1.0 CB A:ASP769 4.8 43.0 1.0 O A:LEU642 4.9 46.5 1.0 C A:ASP644 4.9 50.0 1.0 CA A:LYS647 4.9 49.1 1.0

Calcium binding site 2 out of 3 in the BT0459


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of BT0459 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca902 b:50.9 occ:1.00 O B:LEU646 2.3 49.8 1.0 O B:THR641 2.3 50.0 1.0 O B:ASP769 2.3 47.4 1.0 OE2 B:GLU770 2.4 49.4 1.0 O B:HOH1003 2.4 48.0 1.0 OD1 B:ASP644 2.5 50.5 1.0 C B:LEU646 3.4 49.9 1.0 C B:ASP769 3.4 47.1 1.0 CG B:ASP644 3.5 51.0 1.0 C B:THR641 3.5 50.4 1.0 CD B:GLU770 3.6 49.4 1.0 CB B:GLU770 3.8 47.9 1.0 N B:LEU646 3.9 50.5 1.0 OD2 B:ASP644 3.9 51.0 1.0 CA B:GLU770 4.0 47.5 1.0 CA B:LEU646 4.0 50.3 1.0 N B:GLU770 4.1 47.2 1.0 CB B:LEU646 4.2 50.2 1.0 CG B:GLU770 4.3 48.5 1.0 CA B:LEU642 4.3 49.9 1.0 N B:LEU642 4.3 50.1 1.0 CG2 B:THR641 4.4 49.1 1.0 N B:ASP644 4.4 51.7 1.0 C B:LEU642 4.4 50.6 1.0 O B:ARG656 4.4 50.4 1.0 CA B:ASP769 4.5 46.7 1.0 N B:LYS647 4.5 49.8 1.0 OE1 B:GLU770 4.5 51.0 1.0 CA B:THR641 4.5 50.6 1.0 N B:GLY645 4.6 51.1 1.0 CB B:ASP644 4.7 51.8 1.0 N B:VAL643 4.7 51.5 1.0 O B:LEU642 4.8 50.3 1.0 CB B:ASP769 4.8 46.8 1.0 C B:GLY645 4.9 50.8 1.0 CA B:ASP644 4.9 52.0 1.0 CA B:LYS647 4.9 50.3 1.0 C B:ASP644 4.9 51.6 1.0

Calcium binding site 3 out of 3 in the BT0459


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of BT0459 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca902 b:40.2 occ:1.00 OE1 C:GLU770 2.3 40.5 1.0 O C:ASP769 2.3 39.3 1.0 O C:THR641 2.3 40.6 1.0 O C:LEU646 2.3 41.3 1.0 O C:HOH1025 2.4 35.3 1.0 OD1 C:ASP644 2.4 41.3 1.0 CG C:ASP644 3.4 41.8 1.0 C C:LEU646 3.5 41.9 1.0 CD C:GLU770 3.5 40.1 1.0 C C:ASP769 3.5 39.4 1.0 C C:THR641 3.5 41.2 1.0 OD2 C:ASP644 3.8 41.4 1.0 N C:LEU646 3.9 42.0 1.0 CB C:GLU770 3.9 39.4 1.0 CA C:LEU646 4.0 42.0 1.0 CA C:GLU770 4.1 39.2 1.0 CB C:LEU646 4.2 42.3 1.0 N C:GLU770 4.2 39.2 1.0 CG C:GLU770 4.3 39.8 1.0 O C:HOH1004 4.3 41.5 1.0 CA C:LEU642 4.3 40.2 1.0 N C:LEU642 4.3 41.1 1.0 N C:ASP644 4.4 41.5 1.0 CG2 C:THR641 4.4 41.0 1.0 O C:ARG656 4.4 41.9 1.0 OE2 C:GLU770 4.4 40.4 1.0 C C:LEU642 4.5 40.1 1.0 CA C:ASP769 4.5 39.4 1.0 N C:LYS647 4.6 42.5 1.0 CA C:THR641 4.6 41.8 1.0 CB C:ASP644 4.6 42.5 1.0 N C:GLY645 4.6 42.5 1.0 N C:VAL643 4.7 40.7 1.0 CA C:ASP644 4.9 42.7 1.0 CB C:ASP769 4.9 39.6 1.0 C C:GLY645 4.9 42.4 1.0 O C:LEU642 4.9 39.3 1.0 C C:ASP644 5.0 43.1 1.0 CA C:LYS647 5.0 43.1 1.0

J.Briliute, P.A.Urbanowicz, A.S.Luis, A.Basle, N.Paterson, O.Rebello, J.Hendel, D.A.Ndeh, E.C.Lowe, E.C.Martens, D.I.R.Spencer, D.N.Bolam, L.I.Crouch. Complex N-Glycan Breakdown By Gut Bacteroides Involves An Extensive Enzymatic Apparatus Encoded By Multiple Co-Regulated Genetic Loci. Nat Microbiol V. 4 1571 2019.
ISSN: ESSN 2058-5276
PubMed: 31160824
DOI: 10.1038/S41564-019-0466-X