Calcium in PDB 6mdv: Crystal Structure of Streptococcus Pyogenes Endo-Beta-N- Acetylglucosaminidase (ENDOS2) with High-Mannose Glycan

The structure of Crystal Structure of Streptococcus Pyogenes Endo-Beta-N- Acetylglucosaminidase (ENDOS2) with High-Mannose Glycan, PDB code: 6mdv 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)	29.63 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.966, 105.353, 257.298, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 24.8

The binding sites of Calcium atom in the Crystal Structure of Streptococcus Pyogenes Endo-Beta-N- Acetylglucosaminidase (ENDOS2) with High-Mannose Glycan (pdb code 6mdv). 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 High-Mannose Glycan, PDB code: 6mdv:
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 High-Mannose 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 High-Mannose Glycan within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:70.4 occ:1.00 O A:LYS699 2.3 59.1 1.0 O A:GLU704 2.5 59.4 1.0 OD1 A:ASP702 2.5 63.5 1.0 O A:THR824 2.6 52.2 1.0 OE1 A:GLU825 2.7 54.6 1.0 OD2 A:ASP707 2.8 67.9 1.0 OD1 A:ASP707 2.8 58.7 1.0 CG A:ASP707 3.2 64.7 1.0 CG A:ASP702 3.4 61.8 1.0 C A:LYS699 3.5 59.3 1.0 C A:GLU704 3.5 60.7 1.0 OD2 A:ASP702 3.6 58.5 1.0 C A:THR824 3.7 53.6 1.0 CA A:ILE700 3.9 53.5 1.0 CD A:GLU825 3.9 56.2 1.0 CB A:GLU825 4.1 49.4 1.0 N A:ILE700 4.1 51.9 1.0 N A:GLU704 4.2 62.4 1.0 C A:ILE700 4.3 53.9 1.0 CA A:GLU825 4.3 49.9 1.0 CA A:GLU704 4.4 60.4 1.0 N A:LYS705 4.4 54.8 1.0 N A:GLU825 4.5 50.9 1.0 N A:ASP702 4.5 53.6 1.0 CA A:LYS699 4.5 60.0 1.0 CA A:LYS705 4.5 53.6 1.0 N A:PHE701 4.6 52.3 1.0 CG A:GLU825 4.6 50.1 1.0 O A:ASP702 4.7 69.0 1.0 CB A:ASP707 4.7 57.7 1.0 CB A:ASP702 4.7 64.3 1.0 CB A:LYS699 4.7 56.5 1.0 CA A:THR824 4.7 51.5 1.0 C A:ASP702 4.8 64.7 1.0 O A:ILE700 4.8 50.2 1.0 OE2 A:GLU825 4.8 55.2 1.0 CA A:ASP702 4.9 62.6 1.0 CB A:THR824 4.9 52.4 1.0 CB A:GLU704 4.9 65.2 1.0 N A:SER706 5.0 56.7 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Streptococcus Pyogenes Endo-Beta-N- Acetylglucosaminidase (ENDOS2) with High-Mannose 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 High-Mannose Glycan within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca901 b:75.3 occ:1.00 O B:LYS699 2.4 55.9 1.0 O B:GLU704 2.4 59.9 1.0 OE1 B:GLU825 2.4 57.5 1.0 OD1 B:ASP702 2.5 56.0 1.0 O B:THR824 2.8 49.4 1.0 OD2 B:ASP707 2.9 63.0 1.0 OD1 B:ASP707 3.2 56.6 1.0 C B:GLU704 3.4 60.3 1.0 CG B:ASP707 3.4 62.8 1.0 C B:LYS699 3.6 52.0 1.0 CG B:ASP702 3.6 62.3 1.0 CD B:GLU825 3.6 59.5 1.0 CB B:GLU825 3.8 58.1 1.0 N B:GLU704 3.8 65.8 1.0 C B:THR824 3.9 50.6 1.0 CA B:ILE700 3.9 60.9 1.0 CA B:GLU704 4.1 63.8 1.0 OD2 B:ASP702 4.1 58.8 1.0 CA B:GLU825 4.1 54.3 1.0 C B:ILE700 4.2 55.3 1.0 O B:ASP702 4.2 67.5 1.0 N B:ILE700 4.2 55.6 1.0 CG B:GLU825 4.3 56.0 1.0 N B:ASP702 4.4 68.4 1.0 N B:LYS705 4.4 54.3 1.0 C B:ASP702 4.5 62.9 1.0 N B:PHE701 4.5 56.1 1.0 N B:GLU825 4.5 51.1 1.0 CB B:GLU704 4.6 63.5 1.0 OE2 B:GLU825 4.6 66.6 1.0 O B:ILE700 4.6 51.4 1.0 CA B:LYS699 4.7 59.8 1.0 CA B:LYS705 4.7 56.5 1.0 C B:GLY703 4.8 64.5 1.0 CB B:ASP702 4.8 65.9 1.0 CA B:ASP702 4.8 63.2 1.0 CB B:ASP707 4.9 58.4 1.0 CA B:THR824 4.9 52.1 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