Magnesium in PDB 6tr3: Ruminococcus Gnavus GH29 Fucosidase E1_10125 in Complex with Fucose

The structure of Ruminococcus Gnavus GH29 Fucosidase E1_10125 in Complex with Fucose, PDB code: 6tr3 was solved by C.D.Owen, H.Wu, E.Crost, A.Colvile, N.Juge, M.A.Walsh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.94 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	144.219, 48.643, 80.287, 90.00, 115.02, 90.00
R / Rfree (%)	18.2 / 21.9

The structure of Ruminococcus Gnavus GH29 Fucosidase E1_10125 in Complex with Fucose also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 in Complex with Fucose (pdb code 6tr3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 in Complex with Fucose, PDB code: 6tr3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 in Complex with Fucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ruminococcus Gnavus GH29 Fucosidase E1_10125 in Complex with Fucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:24.8 occ:1.00 O A:HOH949 2.0 27.6 1.0 O A:HOH813 2.0 22.8 1.0 O A:HOH752 2.0 22.7 1.0 O A:HOH947 2.0 26.8 1.0 O A:HOH960 2.0 26.9 1.0 O A:HOH757 2.0 21.8 1.0 O A:LYS53 4.1 17.6 1.0 O A:HOH758 4.1 33.9 1.0 OD2 A:ASP419 4.2 22.1 1.0 OD1 A:ASP419 4.3 23.1 1.0 OE1 A:GLU450 4.4 18.8 1.0 OE2 A:GLU55 4.5 20.3 1.0 CE A:LYS53 4.5 17.6 1.0 CG A:ASP419 4.7 24.4 1.0

Magnesium binding site 2 out of 4 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 in Complex with Fucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ruminococcus Gnavus GH29 Fucosidase E1_10125 in Complex with Fucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:19.1 occ:1.00 O A:SER123 2.1 21.6 1.0 O A:THR126 2.1 22.0 1.0 O A:HOH765 2.1 18.6 1.0 O A:HOH883 2.1 19.9 1.0 O A:HOH762 2.1 17.7 1.0 OD2 A:ASP129 2.1 19.6 1.0 CG A:ASP129 3.1 19.2 1.0 C A:SER123 3.2 20.6 1.0 C A:THR126 3.3 21.6 1.0 OD1 A:ASP129 3.5 21.7 1.0 CA A:GLU127 4.0 25.8 1.0 N A:SER123 4.0 18.5 1.0 CA A:SER123 4.0 18.9 1.0 N A:GLU127 4.0 23.5 1.0 N A:GLU124 4.2 21.4 1.0 N A:THR126 4.3 21.2 1.0 CA A:GLU124 4.4 22.0 1.0 CA A:THR126 4.4 21.7 1.0 CB A:ASP129 4.4 17.4 1.0 CB A:SER123 4.4 18.9 1.0 OD1 A:ASP122 4.4 24.9 1.0 O A:HOH959 4.6 32.3 1.0 C A:GLU127 4.6 24.2 1.0 C A:GLU124 4.7 21.4 1.0 CG2 A:THR126 4.7 21.1 1.0 C A:ASP122 4.9 18.6 1.0 N A:HIS125 5.0 19.7 1.0 CB A:LYS131 5.0 25.8 1.0

Magnesium binding site 3 out of 4 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 in Complex with Fucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ruminococcus Gnavus GH29 Fucosidase E1_10125 in Complex with Fucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:19.0 occ:1.00 O A:GLY213 2.0 19.1 1.0 O A:HOH827 2.0 16.4 1.0 O A:HOH865 2.1 17.0 1.0 OE2 A:GLU246 2.1 19.4 1.0 O A:LEU204 2.1 19.4 1.0 O A:HOH849 2.1 15.1 1.0 C A:LEU204 3.1 18.3 1.0 CD A:GLU246 3.2 18.8 1.0 C A:GLY213 3.2 18.5 1.0 OE1 A:GLU246 3.6 20.1 1.0 CA A:LEU204 3.7 17.9 1.0 CA A:GLY213 3.9 18.8 1.0 O A:HOH767 4.1 33.6 1.0 N A:HIS214 4.2 19.1 1.0 N A:GLY205 4.3 17.9 1.0 O A:TYR209 4.3 15.7 1.0 O A:ASN206 4.3 20.8 1.0 O A:ASN245 4.3 19.3 1.0 O A:ILE203 4.4 17.7 1.0 O A:HOH774 4.4 27.7 1.0 CG A:GLU246 4.5 17.7 1.0 CB A:LEU204 4.5 17.6 1.0 CA A:HIS214 4.5 17.7 1.0 CA A:GLY205 4.7 20.0 1.0 N A:ASN206 4.7 20.4 1.0 C A:GLY205 4.8 20.7 1.0 C A:ASN206 4.9 21.2 1.0 N A:LEU204 4.9 17.4 1.0 CB A:ASN245 4.9 18.8 1.0 CD1 A:PHE215 5.0 14.9 1.0

Magnesium binding site 4 out of 4 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 in Complex with Fucose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ruminococcus Gnavus GH29 Fucosidase E1_10125 in Complex with Fucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg605 b:26.0 occ:1.00 O A:PHE91 2.1 23.2 1.0 OD1 A:ASP90 2.1 27.1 1.0 O A:HOH860 2.1 25.4 1.0 O A:HOH866 2.1 21.2 1.0 O A:HOH857 2.1 24.3 1.0 OE1 A:GLU147 2.1 24.0 1.0 CG A:ASP90 3.2 29.6 1.0 C A:PHE91 3.2 21.9 1.0 CD A:GLU147 3.3 22.7 1.0 OD2 A:ASP90 3.7 30.7 1.0 N A:PHE91 3.8 20.8 1.0 CA A:PHE91 4.0 21.7 1.0 OE2 A:GLU147 4.1 20.9 1.0 CG A:GLU147 4.1 20.6 1.0 OE1 A:GLU94 4.2 30.4 1.0 C A:ASP90 4.2 22.1 1.0 N A:ASP92 4.3 23.1 1.0 CB A:PHE91 4.3 21.4 1.0 CB A:ASP90 4.3 27.4 1.0 O A:HOH753 4.4 23.2 1.0 CB A:GLU147 4.5 19.8 1.0 CA A:ASP92 4.5 23.2 1.0 N A:ALA93 4.6 21.7 1.0 OH A:TYR135 4.6 19.1 1.0 O A:ASP90 4.6 20.3 1.0 CA A:ASP90 4.7 24.4 1.0 CB A:ASN137 4.7 23.3 1.0 O A:HOH958 4.7 32.3 1.0 ND2 A:ASN137 4.9 22.4 1.0

H.Wu, O.Rebello, E.H.Crost, C.D.Owen, S.Walpole, C.Bennati-Granier, D.Ndeh, S.Monaco, T.Hicks, A.Colvile, P.A.Urbanowicz, M.A.Walsh, J.Angulo, D.I.R.Spencer, N.Juge. Fucosidases From the Human Gut Symbiont Ruminococcus Gnavus. Cell.Mol.Life Sci. 2020.
ISSN: ESSN 1420-9071
PubMed: 32333083
DOI: 10.1007/S00018-020-03514-X