Calcium 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:

Magnesium

(Mg)

4 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 in Complex with Fucose, PDB code: 6tr3:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Ruminococcus Gnavus GH29 Fucosidase E1_10125 in Complex with Fucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca606 b:22.2 occ:1.00 O A:ASN413 2.2 19.2 1.0 O A:ASN418 2.4 20.5 1.0 OG1 A:THR421 2.4 21.2 1.0 OD1 A:ASP416 2.4 22.4 1.0 O A:SER514 2.4 17.5 1.0 OE2 A:GLU515 2.4 28.0 1.0 O A:THR421 2.5 20.0 1.0 C A:THR421 3.4 21.0 1.0 C A:ASN413 3.4 22.8 1.0 CG A:ASP416 3.4 25.0 1.0 C A:ASN418 3.4 23.7 1.0 CD A:GLU515 3.5 25.1 1.0 C A:SER514 3.6 18.6 1.0 CB A:THR421 3.6 23.1 1.0 OD2 A:ASP416 3.8 25.2 1.0 CA A:THR421 3.9 22.2 1.0 N A:ASN418 4.0 24.9 1.0 N A:THR421 4.0 23.3 1.0 CA A:ASN418 4.1 25.8 1.0 CA A:SER514 4.1 19.8 1.0 CB A:ASN418 4.2 26.2 1.0 CA A:ASN413 4.2 22.9 1.0 CG A:GLU515 4.2 22.3 1.0 N A:MET414 4.4 21.9 1.0 OE1 A:GLU515 4.4 27.2 1.0 CB A:SER514 4.4 19.4 1.0 N A:TYR422 4.4 22.6 1.0 CB A:ASN413 4.5 23.6 1.0 N A:ASP419 4.5 22.2 1.0 CA A:MET414 4.5 22.6 1.0 N A:ASP416 4.7 24.6 1.0 N A:GLU515 4.7 18.5 1.0 CG2 A:THR421 4.8 23.9 1.0 CB A:ASP416 4.8 26.1 1.0 CA A:ASP419 4.8 23.4 1.0 CA A:TYR422 4.8 22.9 1.0 C A:MET414 4.9 21.6 1.0 C A:ASP419 4.9 23.1 1.0 N A:ASP417 4.9 24.3 1.0 CA A:GLU515 5.0 19.2 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca607 b:24.7 occ:1.00 O A:GLY174 2.3 21.5 1.0 O A:SER172 2.3 18.8 1.0 O A:LYS190 2.3 23.5 1.0 O A:HOH768 2.3 15.7 1.0 O A:HOH822 2.5 28.0 1.0 OD1 A:ASP188 2.5 20.9 1.0 OD2 A:ASP188 2.6 22.5 1.0 CG A:ASP188 2.9 22.1 1.0 C A:SER172 3.3 21.0 1.0 C A:GLY174 3.5 21.8 1.0 C A:LYS190 3.5 27.4 1.0 CA A:SER172 3.9 21.1 1.0 O A:HOH702 4.0 25.1 1.0 N A:TYR192 4.0 21.0 1.0 N A:GLY174 4.2 20.4 1.0 OE1 A:GLN231 4.2 18.5 1.0 CA A:ASP191 4.3 26.3 1.0 N A:ASP191 4.3 25.4 1.0 N A:TYR175 4.3 21.5 1.0 C A:TYR173 4.3 20.4 1.0 CB A:SER172 4.3 20.6 1.0 CA A:TYR175 4.3 22.4 1.0 N A:TYR173 4.4 20.6 1.0 CB A:ASP188 4.4 22.5 1.0 CA A:GLY174 4.4 21.2 1.0 N A:LYS176 4.5 24.5 1.0 CA A:LYS190 4.6 29.9 1.0 N A:LYS190 4.6 28.6 1.0 C A:ASP191 4.6 24.2 1.0 CA A:TYR173 4.7 20.2 1.0 O A:TYR173 4.8 21.7 1.0 CG A:LYS190 4.8 48.0 1.0 CB A:TYR192 4.8 21.4 1.0 CD1 A:TYR175 4.9 21.2 1.0 CA A:TYR192 5.0 20.2 1.0 C A:TYR175 5.0 23.5 1.0 O A:HOH789 5.0 24.6 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