Calcium in PDB 6mds: Crystal Structure of Streptococcus Pyogenes Endo-Beta-N- Acetylglucosaminidase (ENDOS2) with Complex Biantennary Glycan

The structure of Crystal Structure of Streptococcus Pyogenes Endo-Beta-N- Acetylglucosaminidase (ENDOS2) with Complex Biantennary Glycan, PDB code: 6mds was solved by E.H.Klontz, B.Trastoy, J.Orwenyo, L.X.Wang, M.E.Guerin, E.J.Sundberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.71 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.378, 105.514, 259.768, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 24.2

The binding sites of Calcium atom in the Crystal Structure of Streptococcus Pyogenes Endo-Beta-N- Acetylglucosaminidase (ENDOS2) with Complex Biantennary Glycan (pdb code 6mds). 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 Streptococcus Pyogenes Endo-Beta-N- Acetylglucosaminidase (ENDOS2) with Complex Biantennary Glycan, PDB code: 6mds:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Streptococcus Pyogenes Endo-Beta-N- Acetylglucosaminidase (ENDOS2) with Complex Biantennary Glycan


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 Streptococcus Pyogenes Endo-Beta-N- Acetylglucosaminidase (ENDOS2) with Complex Biantennary Glycan within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca909 b:65.2 occ:1.00 O A:LYS699 2.3 53.3 1.0 O A:THR824 2.4 46.7 1.0 OD2 A:ASP707 2.6 54.2 1.0 O A:GLU704 2.7 54.6 1.0 OD1 A:ASP702 2.7 64.1 1.0 OD1 A:ASP707 2.8 54.2 1.0 OE1 A:GLU825 2.8 48.0 1.0 CG A:ASP707 3.1 55.6 1.0 C A:LYS699 3.5 53.4 1.0 C A:THR824 3.6 43.1 1.0 C A:GLU704 3.6 48.1 1.0 CG A:ASP702 3.7 61.6 1.0 CB A:GLU825 3.7 41.5 1.0 CA A:ILE700 3.8 44.0 1.0 OD2 A:ASP702 3.9 52.0 1.0 CD A:GLU825 4.0 51.5 1.0 N A:ILE700 4.1 47.8 1.0 CA A:GLU825 4.1 41.3 1.0 C A:ILE700 4.2 47.1 1.0 N A:GLU825 4.3 42.4 1.0 N A:GLU704 4.4 55.5 1.0 N A:LYS705 4.5 42.5 1.0 CA A:GLU704 4.5 54.4 1.0 CG A:GLU825 4.5 47.6 1.0 O A:ILE700 4.5 42.9 1.0 CA A:LYS705 4.5 45.6 1.0 CA A:THR824 4.6 39.6 1.0 CB A:ASP707 4.6 47.0 1.0 CA A:LYS699 4.6 53.9 1.0 N A:ASP702 4.7 48.0 1.0 N A:PHE701 4.7 48.3 1.0 CB A:LYS699 4.7 55.5 1.0 CB A:THR824 4.8 42.5 1.0 CB A:GLU704 4.9 59.1 1.0 CB A:ILE700 5.0 41.6 1.0 CB A:ASP702 5.0 57.7 1.0 OE2 A:GLU825 5.0 57.7 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Streptococcus Pyogenes Endo-Beta-N- Acetylglucosaminidase (ENDOS2) with Complex Biantennary Glycan


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 Streptococcus Pyogenes Endo-Beta-N- Acetylglucosaminidase (ENDOS2) with Complex Biantennary Glycan within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca901 b:74.0 occ:1.00 OE1 B:GLU825 2.4 58.7 1.0 O B:GLU704 2.5 58.6 1.0 O B:LYS699 2.5 57.4 1.0 O B:THR824 2.6 48.5 1.0 OD2 B:ASP707 2.7 60.8 1.0 OD1 B:ASP702 2.8 58.7 1.0 OD1 B:ASP707 3.3 60.3 1.0 CG B:ASP707 3.3 63.8 1.0 C B:GLU704 3.5 57.6 1.0 CD B:GLU825 3.6 62.6 1.0 C B:LYS699 3.6 56.3 1.0 CB B:GLU825 3.7 54.5 1.0 C B:THR824 3.8 46.6 1.0 CG B:ASP702 3.8 61.9 1.0 O B:HOH1035 3.9 59.3 1.0 CA B:ILE700 4.0 56.9 1.0 N B:GLU704 4.0 60.2 1.0 CA B:GLU825 4.1 51.9 1.0 C B:ILE700 4.2 52.6 1.0 CA B:GLU704 4.2 64.4 1.0 OD2 B:ASP702 4.3 58.8 1.0 CG B:GLU825 4.3 58.8 1.0 N B:ILE700 4.3 53.1 1.0 O B:ILE700 4.4 45.7 1.0 N B:GLU825 4.4 47.3 1.0 N B:LYS705 4.5 54.0 1.0 OE2 B:GLU825 4.6 68.3 1.0 N B:ASP702 4.6 62.7 1.0 CA B:LYS705 4.6 55.1 1.0 N B:PHE701 4.7 54.5 1.0 CA B:LYS699 4.8 58.3 1.0 CB B:GLU704 4.8 60.6 1.0 O B:ASP702 4.8 69.2 1.0 CA B:THR824 4.8 45.7 1.0 CB B:ASP707 4.9 58.6 1.0 C B:ASP702 4.9 66.7 1.0 C B:GLY703 4.9 60.5 1.0 CB B:LYS699 5.0 61.3 1.0

E.H.Klontz, B.Trastoy, D.Deredge, J.K.Fields, C.Li, J.Orwenyo, A.Marina, R.Beadenkopf, S.Gunther, J.Flores, P.L.Wintrode, L.X.Wang, M.E.Guerin, E.J.Sundberg. Molecular Basis of Broad Spectrumn-Glycan Specificity and Processing of Therapeutic Igg Monoclonal Antibodies By Endoglycosidase S2. Acs Cent Sci V. 5 524 2019.
ISSN: ESSN 2374-7943
PubMed: 30937380
DOI: 10.1021/ACSCENTSCI.8B00917