Sodium in PDB 3ecq: Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus Pneumoniae: Semet Structure

All present enzymatic activity of Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus Pneumoniae: Semet Structure:
3.2.1.97;

The structure of Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus Pneumoniae: Semet Structure, PDB code: 3ecq was solved by M.E.C.Caines, H.Zhu, M.Vuckovic, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	112.51 / 2.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	210.611, 158.209, 112.436, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 23.5

The structure of Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus Pneumoniae: Semet Structure also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Sodium atom in the Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus Pneumoniae: Semet Structure (pdb code 3ecq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus Pneumoniae: Semet Structure, PDB code: 3ecq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus Pneumoniae: Semet Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus Pneumoniae: Semet Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2002 b:20.8 occ:1.00 OE1 A:GLU703 1.9 54.6 1.0 NE2 A:HIS1258 2.5 36.0 1.0 OD2 A:ASP728 2.9 55.7 1.0 OD1 A:ASP728 3.1 56.6 1.0 CD A:GLU703 3.1 53.8 1.0 CD2 A:HIS1258 3.3 35.2 1.0 CG A:ASP728 3.3 55.7 1.0 CE1 A:HIS1258 3.5 36.5 1.0 OE2 A:GLU703 3.7 55.3 1.0 CA A:SER1260 4.2 32.0 1.0 CG A:GLU703 4.3 51.0 1.0 O A:LEU1259 4.3 31.4 1.0 CB A:SER1260 4.5 32.2 1.0 CG A:HIS1258 4.5 33.3 1.0 CB A:GLU703 4.5 50.5 1.0 ND1 A:HIS1258 4.6 36.1 1.0 N A:GLU1261 4.7 34.1 1.0 CB A:ASP728 4.8 54.7 1.0 C A:SER1260 5.0 33.0 1.0

Sodium binding site 2 out of 2 in the Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus Pneumoniae: Semet Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Endo-Alpha-N-Acetylgalactosaminidase From Streptococcus Pneumoniae: Semet Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2002 b:41.2 occ:1.00 OE1 B:GLU703 2.3 73.8 1.0 NE2 B:HIS1258 2.4 47.0 1.0 OD2 B:ASP728 2.5 78.0 1.0 CD B:GLU703 2.9 71.9 1.0 CD2 B:HIS1258 3.2 45.4 1.0 OE2 B:GLU703 3.2 71.3 1.0 CG B:ASP728 3.4 79.5 1.0 CE1 B:HIS1258 3.5 47.5 1.0 OD1 B:ASP728 3.6 82.6 1.0 CG B:GLU703 4.0 69.2 1.0 CA B:SER1260 4.4 39.8 1.0 CG B:HIS1258 4.4 43.0 1.0 ND1 B:HIS1258 4.5 46.5 1.0 O B:LEU1259 4.6 38.5 1.0 CB B:GLU703 4.6 69.3 1.0 CB B:SER1260 4.7 40.5 1.0 CB B:ASP728 4.8 78.2 1.0 N B:GLU1261 4.9 41.4 1.0

M.E.Caines, H.Zhu, M.Vuckovic, L.M.Willis, S.G.Withers, W.W.Wakarchuk, N.C.Strynadka. The Structural Basis For T-Antigen Hydrolysis By Streptococcus Pneumoniae: A Target For Structure-Based Vaccine Design. J.Biol.Chem. V. 283 31279 2008.
ISSN: ISSN 0021-9258
PubMed: 18784084
DOI: 10.1074/JBC.C800150200