Magnesium in PDB 5ta9: Crystal Structure of BUGH117BWT in Complex with Neoagarobiose

The structure of Crystal Structure of BUGH117BWT in Complex with Neoagarobiose, PDB code: 5ta9 was solved by B.Pluvinage, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	99.25 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	83.511, 104.380, 198.500, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 25.3

The binding sites of Magnesium atom in the Crystal Structure of BUGH117BWT in Complex with Neoagarobiose (pdb code 5ta9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of BUGH117BWT in Complex with Neoagarobiose, PDB code: 5ta9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of BUGH117BWT in Complex with Neoagarobiose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of BUGH117BWT in Complex with Neoagarobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:28.6 occ:1.00 O A:HOH664 1.9 34.9 1.0 O A:HOH622 1.9 25.3 1.0 O A:HOH724 2.0 28.6 1.0 O A:HOH680 2.1 37.2 1.0 O A:HOH696 2.2 30.6 1.0 O A:HOH634 2.3 23.1 1.0 O A:PRO91 3.7 31.1 1.0 O A:HOH627 3.7 30.9 1.0 O A:ILE349 4.0 22.9 1.0 O A:ALA348 4.1 25.1 1.0 OE2 A:GLU167 4.2 30.6 1.0 OD1 A:ASP245 4.4 30.5 1.0 C A:ALA348 4.4 27.8 1.0 O A:ASP90 4.4 28.2 1.0 O A:PRO166 4.5 28.8 1.0 C A:ASP90 4.5 28.2 1.0 C A:PRO91 4.5 29.8 1.0 CA A:ALA348 4.5 30.1 1.0 O A:HOH662 4.6 19.9 1.0 OD1 A:ASP90 4.6 28.9 1.0 CB A:ALA348 4.6 30.7 1.0 CG2 A:THR165 4.7 31.3 1.0 O A:ILE304 4.7 28.9 1.0 CB A:ASP90 4.8 29.6 1.0 CA A:ASP90 4.8 28.7 1.0 CD A:GLU167 4.9 30.0 1.0 CG A:GLU167 4.9 30.0 1.0 C A:ILE349 4.9 25.1 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of BUGH117BWT in Complex with Neoagarobiose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of BUGH117BWT in Complex with Neoagarobiose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:19.7 occ:1.00 O B:HOH619 1.9 16.5 1.0 O B:HOH733 2.0 18.3 1.0 O B:HOH646 2.0 17.0 1.0 O B:HOH615 2.2 17.5 1.0 O B:HOH659 2.3 44.6 1.0 O B:HOH654 2.3 24.4 1.0 O B:PRO91 3.8 26.9 1.0 O B:HOH673 4.1 23.5 1.0 O B:HOH674 4.1 15.6 1.0 O B:ALA348 4.1 25.5 1.0 O B:ASP90 4.2 27.1 1.0 OD1 B:ASP245 4.2 31.2 1.0 OD1 B:ASP90 4.3 34.8 1.0 C B:ASP90 4.3 27.1 1.0 C B:ALA348 4.3 27.2 1.0 CA B:ALA348 4.4 28.0 1.0 O B:ILE349 4.4 26.6 1.0 CB B:ASP90 4.4 29.9 1.0 O B:PRO166 4.4 25.6 1.0 CG2 B:THR165 4.4 24.7 1.0 CB B:ALA348 4.5 28.5 1.0 CA B:ASP90 4.5 28.3 1.0 C B:PRO91 4.6 26.4 1.0 OE2 B:GLU167 4.8 32.3 1.0 CG B:ASP90 4.8 31.1 1.0 O B:ILE304 4.8 25.5 1.0 N B:PRO91 4.9 27.0 1.0 CG B:GLU167 4.9 30.2 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of BUGH117BWT in Complex with Neoagarobiose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of BUGH117BWT in Complex with Neoagarobiose within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:24.3 occ:1.00 O C:HOH616 1.9 39.3 1.0 O C:HOH659 1.9 32.3 1.0 O C:HOH634 2.1 19.8 1.0 O C:HOH669 2.1 34.3 1.0 O C:HOH617 2.2 19.8 1.0 O C:HOH652 2.2 19.2 1.0 O C:PRO91 3.6 33.2 1.0 O C:HOH627 3.7 52.0 1.0 O C:ILE349 3.9 32.0 1.0 O C:ALA348 4.2 32.3 1.0 OD1 C:ASP245 4.2 38.9 1.0 O C:PRO166 4.3 37.1 1.0 OE2 C:GLU167 4.3 44.5 1.0 C C:ALA348 4.4 33.3 1.0 O C:HOH615 4.4 32.7 1.0 O C:ASP90 4.5 34.5 1.0 CG C:GLU167 4.6 43.5 1.0 C C:PRO91 4.6 36.0 1.0 O C:ILE304 4.6 33.9 1.0 C C:ASP90 4.6 34.8 1.0 OD1 C:ASP90 4.6 28.3 1.0 CA C:ALA348 4.6 31.9 1.0 C C:ILE349 4.7 31.9 1.0 CD C:GLU167 4.8 43.8 1.0 CB C:ALA348 4.8 31.4 1.0 CG2 C:THR165 4.8 34.1 1.0 CA C:ASP90 4.9 32.9 1.0 N C:ILE349 4.9 32.7 1.0 N C:PRO91 5.0 35.9 1.0 CB C:ASP90 5.0 32.0 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of BUGH117BWT in Complex with Neoagarobiose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of BUGH117BWT in Complex with Neoagarobiose within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:31.4 occ:1.00 O D:HOH632 1.9 28.4 1.0 O D:HOH685 1.9 34.4 1.0 O D:HOH606 2.1 33.6 1.0 O D:HOH604 2.2 23.4 1.0 O D:HOH641 2.2 30.3 1.0 O D:HOH656 2.4 26.1 1.0 O D:PRO91 3.6 31.9 1.0 O D:HOH651 3.8 31.5 1.0 O D:HOH667 3.9 32.6 1.0 OD1 D:ASP245 4.1 34.4 1.0 O D:PRO166 4.1 41.2 1.0 OE2 D:GLU167 4.2 52.7 1.0 CG2 D:THR165 4.3 31.5 1.0 O D:ILE349 4.4 35.4 1.0 O D:ASP90 4.4 32.8 1.0 O D:ALA348 4.5 38.0 1.0 C D:ASP90 4.6 35.3 1.0 C D:PRO91 4.6 34.9 1.0 O D:ILE304 4.6 40.2 1.0 OD1 D:ASP90 4.7 33.4 1.0 CB D:ASP90 4.7 35.4 1.0 CG D:GLU167 4.7 52.6 1.0 C D:ALA348 4.8 38.8 1.0 CD D:GLU167 4.9 53.3 1.0 CA D:ASP90 4.9 36.5 1.0 CA D:ALA348 4.9 41.2 1.0 CB D:ASP245 5.0 36.4 1.0 CG D:ASP245 5.0 34.9 1.0 CB D:ALA348 5.0 40.7 1.0

B.Pluvinage, J.M.Grondin, C.Amundsen, L.Klassen, P.E.Moote, Y.Xiao, D.Thomas, N.A.Pudlo, A.Anele, E.C.Martens, G.D.Inglis, R.E.R.Uwiera, A.B.Boraston, D.W.Abbott. Molecular Basis of An Agarose Metabolic Pathway Acquired By A Human Intestinal Symbiont. Nat Commun V. 9 1043 2018.
ISSN: ESSN 2041-1723
PubMed: 29535379
DOI: 10.1038/S41467-018-03366-X