Calcium in PDB 6e58: Crystal Structure of Streptococcus Pyogenes Endo-Beta-N- Acetylglucosaminidase (ENDOS2)

The structure of Crystal Structure of Streptococcus Pyogenes Endo-Beta-N- Acetylglucosaminidase (ENDOS2), PDB code: 6e58 was solved by E.H.Klontz, B.Trastoy, S.Gunther, 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)	38.89 / 2.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.169, 105.829, 259.275, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 26.4

The binding sites of Calcium atom in the Crystal Structure of Streptococcus Pyogenes Endo-Beta-N- Acetylglucosaminidase (ENDOS2) (pdb code 6e58). 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), PDB code: 6e58:
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)


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) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:53.6 occ:1.00 O A:LYS699 2.3 49.5 1.0 OD1 A:ASP702 2.5 61.5 1.0 OE2 A:GLU825 2.5 50.5 1.0 O A:GLU704 2.7 46.4 1.0 OD1 A:ASP707 2.8 44.2 1.0 OD2 A:ASP707 2.8 49.8 1.0 O A:THR824 2.8 37.1 1.0 CG A:ASP707 3.2 53.7 1.0 CG A:ASP702 3.4 57.8 1.0 C A:LYS699 3.5 44.1 1.0 C A:GLU704 3.6 43.3 1.0 OD2 A:ASP702 3.6 42.4 1.0 CD A:GLU825 3.8 49.9 1.0 CA A:ILE700 3.9 34.9 1.0 C A:THR824 4.0 33.2 1.0 N A:ILE700 4.2 35.6 1.0 CB A:GLU825 4.2 34.0 1.0 C A:ILE700 4.3 37.2 1.0 N A:GLU704 4.3 49.4 1.0 N A:LYS705 4.5 42.2 1.0 CA A:GLU704 4.5 51.2 1.0 CA A:GLU825 4.5 34.5 1.0 N A:ASP702 4.5 41.1 1.0 CA A:LYS705 4.5 35.2 1.0 CA A:LYS699 4.5 43.4 1.0 CG A:GLU825 4.6 38.9 1.0 N A:PHE701 4.7 41.9 1.0 OE1 A:GLU825 4.7 51.2 1.0 CB A:ASP707 4.7 43.4 1.0 CB A:ASP702 4.7 50.8 1.0 N A:GLU825 4.7 32.3 1.0 CB A:LYS699 4.8 39.0 1.0 O A:ILE700 4.8 32.8 1.0 N A:SER706 4.9 38.3 1.0 C A:ASP702 4.9 53.1 1.0 CB A:GLU704 4.9 61.0 1.0 CA A:THR824 4.9 33.8 1.0 CA A:ASP702 4.9 48.7 1.0 O A:ASP702 5.0 54.1 1.0

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


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) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca901 b:90.4 occ:1.00 OD1 B:ASP702 2.4 52.9 1.0 O B:GLU704 2.4 54.3 1.0 OE1 B:GLU825 2.4 60.5 1.0 O B:LYS699 2.5 50.0 1.0 O B:THR824 2.9 39.7 1.0 OD1 B:ASP707 3.3 47.1 1.0 OD2 B:ASP707 3.3 56.3 1.0 CG B:ASP702 3.5 57.3 1.0 C B:GLU704 3.5 48.3 1.0 CD B:GLU825 3.6 48.3 1.0 CG B:ASP707 3.6 51.6 1.0 C B:LYS699 3.7 46.7 1.0 CA B:ILE700 3.9 47.7 1.0 OD2 B:ASP702 3.9 50.2 1.0 CB B:GLU825 3.9 45.5 1.0 C B:THR824 4.0 39.6 1.0 N B:GLU704 4.1 55.6 1.0 C B:ILE700 4.1 44.9 1.0 N B:ASP702 4.2 54.3 1.0 O B:HOH1007 4.2 50.7 1.0 CA B:GLU825 4.3 41.2 1.0 O B:ASP702 4.3 64.6 1.0 N B:ILE700 4.3 49.3 1.0 CA B:GLU704 4.3 50.1 1.0 CG B:GLU825 4.4 45.2 1.0 N B:LYS705 4.4 43.4 1.0 C B:ASP702 4.5 63.8 1.0 N B:PHE701 4.5 47.4 1.0 O B:ILE700 4.5 39.9 1.0 CA B:LYS705 4.5 42.6 1.0 OE2 B:GLU825 4.5 48.4 1.0 N B:GLU825 4.6 36.5 1.0 CB B:ASP702 4.6 56.9 1.0 CA B:ASP702 4.7 60.2 1.0 CA B:LYS699 4.8 43.7 1.0 C B:GLY703 4.8 49.9 1.0 CB B:GLU704 5.0 53.1 1.0 N B:GLY703 5.0 55.1 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