Calcium in PDB 2ygm: The X-Ray Crystal Structure of Tandem CBM51 Modules of SP3GH98, the Family 98 Glycoside Hydrolase From Streptococcus Pneumoniae SP3-BS71, in Complex with the Blood Group B Antigen

The structure of The X-Ray Crystal Structure of Tandem CBM51 Modules of SP3GH98, the Family 98 Glycoside Hydrolase From Streptococcus Pneumoniae SP3-BS71, in Complex with the Blood Group B Antigen, PDB code: 2ygm was solved by M.A.Higgins, E.Ficko-Blean, C.Wright, P.J.Meloncelli, T.L.Lowary, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.700, 78.500, 131.580, 90.00, 90.00, 90.00
R / Rfree (%)	24.521 / 29.728

The structure of The X-Ray Crystal Structure of Tandem CBM51 Modules of SP3GH98, the Family 98 Glycoside Hydrolase From Streptococcus Pneumoniae SP3-BS71, in Complex with the Blood Group B Antigen also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Calcium atom in the The X-Ray Crystal Structure of Tandem CBM51 Modules of SP3GH98, the Family 98 Glycoside Hydrolase From Streptococcus Pneumoniae SP3-BS71, in Complex with the Blood Group B Antigen (pdb code 2ygm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the The X-Ray Crystal Structure of Tandem CBM51 Modules of SP3GH98, the Family 98 Glycoside Hydrolase From Streptococcus Pneumoniae SP3-BS71, in Complex with the Blood Group B Antigen, PDB code: 2ygm:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the The X-Ray Crystal Structure of Tandem CBM51 Modules of SP3GH98, the Family 98 Glycoside Hydrolase From Streptococcus Pneumoniae SP3-BS71, in Complex with the Blood Group B Antigen


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The X-Ray Crystal Structure of Tandem CBM51 Modules of SP3GH98, the Family 98 Glycoside Hydrolase From Streptococcus Pneumoniae SP3-BS71, in Complex with the Blood Group B Antigen within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1417 b:44.8 occ:1.00 O A:HIS214 2.2 43.7 1.0 O A:HOH2022 2.3 44.0 1.0 OD2 A:ASP218 2.3 41.3 1.0 O A:ALA211 2.4 41.7 1.0 O A:VAL161 2.4 41.6 1.0 OD1 A:ASP218 3.0 42.6 1.0 CG A:ASP218 3.0 42.3 1.0 C A:HIS214 3.3 43.6 1.0 C A:ALA211 3.5 41.8 1.0 C A:VAL161 3.5 41.7 1.0 CA A:ALA211 4.0 41.6 1.0 N A:VAL161 4.0 42.6 1.0 CA A:VAL161 4.1 42.1 1.0 N A:HIS214 4.1 44.1 1.0 CB A:VAL161 4.1 42.0 1.0 CB A:ALA211 4.1 41.4 1.0 CA A:HIS214 4.2 43.9 1.0 N A:THR215 4.2 43.4 1.0 CA A:THR215 4.3 43.1 1.0 C A:THR215 4.5 43.2 1.0 CB A:ASP218 4.5 42.4 1.0 N A:VAL162 4.6 41.3 1.0 N A:GLY212 4.6 42.3 1.0 N A:TRP216 4.6 43.1 1.0 O A:TRP216 4.6 43.7 1.0 CB A:HIS214 4.7 43.9 1.0 CG1 A:VAL161 4.8 41.9 1.0 CA A:VAL162 4.9 40.9 1.0 CA A:GLY212 4.9 43.0 1.0 N A:GLU213 4.9 44.0 1.0 O A:ASP158 4.9 46.1 1.0 C A:GLY212 5.0 43.6 1.0

Calcium binding site 2 out of 2 in the The X-Ray Crystal Structure of Tandem CBM51 Modules of SP3GH98, the Family 98 Glycoside Hydrolase From Streptococcus Pneumoniae SP3-BS71, in Complex with the Blood Group B Antigen


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The X-Ray Crystal Structure of Tandem CBM51 Modules of SP3GH98, the Family 98 Glycoside Hydrolase From Streptococcus Pneumoniae SP3-BS71, in Complex with the Blood Group B Antigen within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1418 b:53.6 occ:1.00 O B:HIS214 2.2 46.8 1.0 O B:VAL161 2.3 50.5 1.0 O B:ALA211 2.5 45.4 1.0 OD2 B:ASP218 2.5 43.9 1.0 OD1 B:ASP218 3.0 43.1 1.0 CG B:ASP218 3.1 42.7 1.0 C B:VAL161 3.4 50.6 1.0 C B:HIS214 3.4 47.0 1.0 C B:ALA211 3.6 45.2 1.0 CB B:VAL161 3.7 51.0 1.0 CA B:VAL161 3.9 50.9 1.0 N B:VAL161 4.0 51.2 1.0 N B:HIS214 4.0 47.7 1.0 CA B:ALA211 4.2 44.6 1.0 CA B:HIS214 4.2 47.3 1.0 CB B:ALA211 4.3 44.5 1.0 N B:THR215 4.4 46.8 1.0 O B:TRP216 4.4 45.1 1.0 CG1 B:VAL161 4.5 50.9 1.0 CA B:THR215 4.5 46.5 1.0 N B:VAL162 4.5 50.5 1.0 C B:THR215 4.6 46.2 1.0 O B:ASP158 4.6 52.2 1.0 N B:GLY212 4.6 45.9 1.0 CB B:ASP218 4.6 42.5 1.0 N B:GLU213 4.6 47.8 1.0 N B:TRP216 4.6 45.9 1.0 CB B:HIS214 4.7 47.2 1.0 CG2 B:VAL161 4.8 50.9 1.0 CA B:GLY212 4.8 46.6 1.0 CA B:VAL162 4.9 50.3 1.0

M.A.Higgins, E.Ficko-Blean, C.Wright, P.J.Meloncelli, T.L.Lowary, A.B.Boraston. The Overall Architecture and Receptor Binding of Pneumococcal Carbohydrate Antigen Hydrolyzing Enzymes. J.Mol.Biol. V. 411 1017 2011.
ISSN: ISSN 0022-2836
PubMed: 21767550
DOI: 10.1016/J.JMB.2011.06.035