Calcium in PDB 6t8k: Crystal Structure of Bacteroides Thetaiotamicron Endobt-3987 in Complex with MAN9GLCNAC Product in P1

The structure of Crystal Structure of Bacteroides Thetaiotamicron Endobt-3987 in Complex with MAN9GLCNAC Product in P1, PDB code: 6t8k was solved by B.Trastoy, J.J.Du, E.H.Klontz, J.O.Cifuente, E.J.Sundberg, M.E.Guerin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.28 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.898, 59.633, 76.061, 97.31, 90.14, 92.29
R / Rfree (%)	16.2 / 19.7

The binding sites of Calcium atom in the Crystal Structure of Bacteroides Thetaiotamicron Endobt-3987 in Complex with MAN9GLCNAC Product in P1 (pdb code 6t8k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Bacteroides Thetaiotamicron Endobt-3987 in Complex with MAN9GLCNAC Product in P1, PDB code: 6t8k:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Bacteroides Thetaiotamicron Endobt-3987 in Complex with MAN9GLCNAC Product in P1


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 Bacteroides Thetaiotamicron Endobt-3987 in Complex with MAN9GLCNAC Product in P1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca511 b:16.3 occ:1.00 OD1 A:ASN182 2.3 15.2 1.0 O A:ASN182 2.4 20.3 1.0 O A:HOH613 2.5 13.4 1.0 O A:HOH700 2.5 16.2 1.0 CG A:ASN182 3.4 16.6 1.0 C A:ASN182 3.4 18.7 1.0 CA A:ASN182 3.9 16.8 1.0 ND2 A:ASN182 4.2 16.5 1.0 CB A:ASN182 4.2 15.9 1.0 OD1 A:ASP185 4.3 23.8 1.0 O A:HOH680 4.4 18.8 1.0 O A:HOH685 4.5 25.4 1.0 OD2 A:ASP185 4.5 22.7 1.0 N A:ALA183 4.5 17.9 1.0 O A:ARG264 4.7 15.9 1.0 CG A:ASP185 4.7 22.3 1.0 N A:GLY184 4.8 19.9 1.0 CA A:ALA183 4.9 18.6 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Bacteroides Thetaiotamicron Endobt-3987 in Complex with MAN9GLCNAC Product in P1


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 Bacteroides Thetaiotamicron Endobt-3987 in Complex with MAN9GLCNAC Product in P1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca511 b:16.2 occ:1.00 O B:ASN182 2.4 20.1 1.0 O A:GLY356 2.4 16.8 1.0 O A:HOH675 2.4 14.9 1.0 O B:HOH778 2.5 18.5 1.0 OD1 B:ASN182 2.5 17.8 1.0 O B:HOH751 2.6 12.9 1.0 O A:HOH634 2.6 16.7 1.0 O A:HOH722 2.7 9.6 1.0 C B:ASN182 3.4 18.5 1.0 CG B:ASN182 3.4 19.5 1.0 C A:GLY356 3.6 16.9 1.0 CA B:ASN182 3.9 18.9 1.0 OD1 A:ASP354 4.2 14.1 1.0 ND2 B:ASN182 4.3 14.6 1.0 CB B:ASN182 4.3 19.5 1.0 O A:HOH638 4.3 18.1 1.0 OD1 B:ASP185 4.4 23.7 1.0 CA A:GLN357 4.4 16.0 1.0 O A:TYR359 4.4 17.1 1.0 O B:HOH693 4.4 19.5 1.0 N A:GLN357 4.5 15.6 1.0 N A:GLY356 4.5 14.6 1.0 N B:ALA183 4.5 17.8 1.0 OD2 B:ASP185 4.5 23.3 1.0 O B:HOH776 4.5 21.0 1.0 C A:TRP355 4.6 14.1 1.0 CA A:GLY356 4.6 16.2 1.0 O A:TRP355 4.6 13.6 1.0 N B:GLY184 4.7 16.8 1.0 O B:ARG264 4.7 14.4 1.0 CG B:ASP185 4.8 21.6 1.0 CA B:ALA183 4.9 17.5 1.0

B.Trastoy, J.J.Du, E.H.Klontz, C.Li, J.O.Cifuente, L.X.Wang, E.J.Sundberg, M.E.Guerin. Structural Basis of Mammalian High-Mannose N-Glycan Processing By Human Gut Bacteroides. Nat Commun V. 11 899 2020.
ISSN: ESSN 2041-1723
PubMed: 32060313
DOI: 10.1038/S41467-020-14754-7