Calcium in PDB 5ta0: Crystal Structure of BUGH86E322Q in Complex with Neoagarooctaose

The structure of Crystal Structure of BUGH86E322Q in Complex with Neoagarooctaose, PDB code: 5ta0 was solved by B.Pluvinage, A.B.Boraston, W.D.Abbott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	82.88 / 1.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	60.719, 73.540, 83.190, 85.87, 86.20, 71.87
R / Rfree (%)	14.2 / 16.2

The binding sites of Calcium atom in the Crystal Structure of BUGH86E322Q in Complex with Neoagarooctaose (pdb code 5ta0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of BUGH86E322Q in Complex with Neoagarooctaose, PDB code: 5ta0:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of BUGH86E322Q in Complex with Neoagarooctaose


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 BUGH86E322Q in Complex with Neoagarooctaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca731 b:9.4 occ:1.00 O A:HOH1346 3.1 8.1 1.0 N A:LEU202 3.2 6.8 1.0 N A:ALA245 3.2 6.2 1.0 C A:GLU200 3.4 6.5 1.0 N A:PRO201 3.5 6.2 1.0 N A:TRP203 3.5 7.6 1.0 CA A:GLU200 3.6 6.4 1.0 CB A:LEU202 3.7 7.4 1.0 CA A:THR244 3.7 6.4 1.0 CA A:LEU202 3.7 7.2 1.0 CD A:PRO201 3.8 6.2 1.0 CE1 A:TYR242 3.9 6.1 1.0 O A:GLU200 3.9 6.5 1.0 C A:THR244 4.0 6.3 1.0 CB A:ALA245 4.0 6.6 1.0 C A:LEU202 4.0 7.6 1.0 C A:PRO201 4.1 6.7 1.0 CA A:ALA245 4.2 6.6 1.0 O A:CYS243 4.2 6.5 0.5 O A:CYS243 4.3 6.8 0.5 CB A:GLU200 4.3 6.7 1.0 CD1 A:TYR242 4.3 6.0 1.0 CA A:PRO201 4.3 6.5 1.0 CG2 A:THR244 4.4 6.8 1.0 CG A:PRO201 4.4 6.4 1.0 CG A:LEU202 4.5 7.8 1.0 O A:HOH1002 4.5 7.6 1.0 CB A:THR244 4.6 6.4 1.0 CA A:TRP203 4.6 8.0 1.0 CB A:TRP203 4.6 8.5 1.0 N A:THR244 4.7 6.3 1.0 N A:GLU200 4.7 6.2 1.0 O A:HOH844 4.8 11.9 1.0 C A:CYS243 4.8 6.8 0.5 C A:CYS243 4.8 6.4 0.5 CG A:GLU200 5.0 7.1 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of BUGH86E322Q in Complex with Neoagarooctaose


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 BUGH86E322Q in Complex with Neoagarooctaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca732 b:10.5 occ:1.00 O A:HOH1288 3.1 9.1 1.0 O A:HOH1002 3.1 7.6 1.0 NE A:ARG256 3.2 9.7 1.0 N A:ASP248 3.3 8.0 1.0 CA A:PRO247 3.6 7.1 1.0 O A:PHE246 3.6 7.2 1.0 CG A:ARG256 3.8 9.3 1.0 C A:PRO247 3.9 7.5 1.0 OH A:TYR242 4.0 7.0 1.0 CD1 A:PHE249 4.0 7.7 1.0 CD A:ARG256 4.0 9.6 1.0 CD A:ARG260 4.0 7.7 1.0 NH1 A:ARG256 4.1 10.5 1.0 CZ A:ARG256 4.1 10.2 1.0 CE1 A:PHE249 4.1 7.4 1.0 C A:ASP248 4.3 8.2 1.0 CA A:ASP248 4.3 8.5 1.0 CB A:ARG260 4.4 7.9 1.0 CG2 A:THR244 4.5 6.8 1.0 C A:PHE246 4.5 7.2 1.0 O A:ASP248 4.5 8.9 1.0 N A:PRO247 4.5 6.9 1.0 CD1 A:TRP261 4.5 7.5 1.0 CB A:PRO247 4.6 7.2 1.0 N A:PHE249 4.8 8.1 1.0 O A:ARG256 4.8 9.2 1.0 CG A:ARG260 4.8 7.9 1.0 CB A:ASP248 4.8 9.3 1.0 NH1 A:ARG260 5.0 7.8 1.0 NE A:ARG260 5.0 8.1 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of BUGH86E322Q in Complex with Neoagarooctaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of BUGH86E322Q in Complex with Neoagarooctaose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca723 b:10.2 occ:1.00 O B:HOH1273 3.1 8.5 1.0 N B:LEU202 3.2 7.2 1.0 N B:ALA245 3.2 6.6 1.0 C B:GLU200 3.5 7.1 1.0 N B:PRO201 3.6 6.6 1.0 CA B:GLU200 3.6 6.9 1.0 N B:TRP203 3.6 8.9 1.0 CB B:LEU202 3.6 8.2 1.0 CD B:PRO201 3.7 6.8 1.0 CA B:LEU202 3.7 8.0 1.0 CA B:THR244 3.7 6.9 1.0 O B:GLU200 3.9 7.4 1.0 C B:THR244 4.0 6.8 1.0 CE1 B:TYR242 4.0 6.6 1.0 CB B:ALA245 4.0 7.1 1.0 C B:LEU202 4.1 8.6 1.0 C B:PRO201 4.1 7.2 1.0 O B:CYS243 4.2 7.1 1.0 CA B:ALA245 4.2 7.2 1.0 CD1 B:TYR242 4.3 6.8 1.0 CB B:GLU200 4.4 7.5 1.0 CG2 B:THR244 4.4 7.3 1.0 CA B:PRO201 4.4 6.8 1.0 CG B:PRO201 4.4 6.8 1.0 CG B:LEU202 4.4 8.6 1.0 O B:HOH1075 4.6 8.5 1.0 CB B:THR244 4.6 6.9 1.0 N B:THR244 4.7 6.7 1.0 O B:HOH837 4.7 14.7 1.0 C B:CYS243 4.8 6.9 1.0 N B:GLU200 4.8 6.4 1.0 CA B:TRP203 4.8 9.7 1.0 CB B:TRP203 4.8 10.6 1.0 CG B:GLU200 5.0 7.9 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of BUGH86E322Q in Complex with Neoagarooctaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of BUGH86E322Q in Complex with Neoagarooctaose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca724 b:11.6 occ:1.00 O B:HOH1228 3.1 11.2 1.0 O B:HOH1075 3.1 8.5 1.0 NE B:ARG256 3.2 11.1 1.0 N B:ASP248 3.4 9.3 1.0 O B:PHE246 3.6 8.6 1.0 CA B:PRO247 3.6 8.1 1.0 CG B:ARG256 3.8 10.7 1.0 OH B:TYR242 3.9 7.8 1.0 C B:PRO247 4.0 8.7 1.0 CD B:ARG256 4.0 11.0 1.0 CD1 B:PHE249 4.0 9.1 1.0 CD B:ARG260 4.0 9.0 1.0 NH1 B:ARG256 4.0 11.8 1.0 CZ B:ARG256 4.1 11.3 1.0 CE1 B:PHE249 4.1 8.9 1.0 C B:ASP248 4.3 9.5 1.0 CA B:ASP248 4.4 9.8 1.0 CB B:ARG260 4.4 8.7 1.0 C B:PHE246 4.4 8.5 1.0 O B:ASP248 4.4 10.2 1.0 CG2 B:THR244 4.5 7.3 1.0 CD1 B:TRP261 4.5 8.3 1.0 N B:PRO247 4.5 8.0 1.0 CB B:PRO247 4.7 8.3 1.0 N B:PHE249 4.8 9.4 1.0 CG B:ARG260 4.8 9.0 1.0 O B:ARG256 4.8 10.0 1.0 CB B:ASP248 4.9 10.9 1.0 NH1 B:ARG260 5.0 9.5 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