Calcium in PDB 6tcw: Crystal Structure of Bacteroides Thetaiotamicron Endobt-3987 with MAN5GLCNAC Product

The structure of Crystal Structure of Bacteroides Thetaiotamicron Endobt-3987 with MAN5GLCNAC Product, PDB code: 6tcw 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)	20.00 / 1.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	76.250, 133.440, 49.460, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 18.9

The binding sites of Calcium atom in the Crystal Structure of Bacteroides Thetaiotamicron Endobt-3987 with MAN5GLCNAC Product (pdb code 6tcw). 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 with MAN5GLCNAC Product, PDB code: 6tcw:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Bacteroides Thetaiotamicron Endobt-3987 with MAN5GLCNAC Product


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 with MAN5GLCNAC Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca908 b:14.4 occ:1.00 O A:ASN182 2.3 16.6 1.0 O A:HOH1144 2.5 20.2 1.0 OD1 A:ASN182 2.5 18.0 1.0 O A:HOH1119 2.7 18.8 1.0 C A:ASN182 3.4 17.3 1.0 CG A:ASN182 3.5 17.5 1.0 CA A:ASN182 3.9 14.3 1.0 CB A:ASN182 4.3 14.7 1.0 ND2 A:ASN182 4.3 16.0 1.0 O A:HOH1058 4.4 30.1 1.0 O A:HOH1106 4.5 16.8 1.0 OD1 A:ASP185 4.5 18.8 0.9 N A:ALA183 4.5 16.2 1.0 OD2 A:ASP185 4.7 19.2 0.9 N A:GLY184 4.7 19.1 1.0 CA A:ALA183 4.9 17.3 1.0 CG A:ASP185 5.0 17.6 0.9

Calcium binding site 2 out of 2 in the Crystal Structure of Bacteroides Thetaiotamicron Endobt-3987 with MAN5GLCNAC Product


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 with MAN5GLCNAC Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca909 b:21.1 occ:0.68 O2 A:GOL901 2.3 34.7 1.0 O6 A:NAG902 2.4 23.8 1.0 O A:HOH1249 2.4 35.6 1.0 O1 A:NAG902 2.5 23.4 1.0 O3 A:GOL901 2.5 33.8 1.0 O5 A:NAG902 2.6 18.6 1.0 O A:HOH1160 2.6 28.8 1.0 O A:HOH1125 2.7 32.9 1.0 HO2 A:GOL901 2.7 41.7 1.0 C1 A:NAG902 3.1 19.9 1.0 HO3 A:GOL901 3.1 40.6 1.0 C2 A:GOL901 3.2 37.3 1.0 C3 A:GOL901 3.3 37.0 1.0 C6 A:NAG902 3.3 20.4 1.0 C5 A:NAG902 3.4 18.5 1.0 H12 A:GOL901 3.4 47.9 1.0 H31 A:GOL901 3.6 44.4 1.0 C1 A:GOL901 3.8 39.9 1.0 C4 A:NAG902 3.8 17.6 1.0 H2 A:GOL901 4.0 44.7 1.0 HO1 A:GOL901 4.1 49.2 1.0 H32 A:GOL901 4.1 44.4 1.0 O1 A:GOL901 4.2 41.0 1.0 C2 A:NAG902 4.4 18.5 1.0 OE2 A:GLU314 4.6 20.5 1.0 H11 A:GOL901 4.6 47.9 1.0 C3 A:NAG902 4.7 16.3 1.0 OH A:TYR315 4.7 19.0 1.0 O4 A:NAG902 4.9 18.2 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