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Sodium 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

Protein crystallography data

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

Other elements in 2ygm:

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:

Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2ygm

Go back to Sodium Binding Sites List in 2ygm
Sodium 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 Sodium with other atoms in the Na 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:Na1418

b:43.5
occ:1.00
OD1 A:ASP400 2.6 43.4 1.0
O A:ASP343 2.8 37.5 1.0
OG1 A:THR397 3.1 48.8 1.0
O A:THR397 3.1 47.9 1.0
O A:ALA399 3.1 45.0 1.0
CG A:ASP400 3.6 43.6 1.0
N A:GLY394 3.6 41.8 1.0
C A:THR397 3.6 47.8 1.0
N A:LYS395 3.7 44.6 1.0
C A:ALA399 3.7 44.9 1.0
C A:ASP343 3.8 37.6 1.0
CA A:GLY394 3.9 43.0 1.0
N A:THR397 4.0 47.6 1.0
CB A:THR397 4.0 48.0 1.0
N A:ALA399 4.1 46.4 1.0
CA A:THR397 4.1 47.9 1.0
CA A:ASP343 4.1 38.1 1.0
OD2 A:ASP400 4.1 44.9 1.0
C A:GLY394 4.2 43.9 1.0
C A:TRP398 4.3 47.2 1.0
N A:TRP398 4.3 47.9 1.0
N A:ASP400 4.4 44.1 1.0
CA A:ALA399 4.5 45.5 1.0
CA A:ASP400 4.5 43.3 1.0
O A:ALA342 4.6 39.0 1.0
C A:SER393 4.6 40.8 1.0
CA A:TRP398 4.6 47.9 1.0
CB A:ASP400 4.6 43.3 1.0
O A:TRP398 4.7 47.3 1.0
CA A:LYS395 4.7 45.6 1.0
CB A:SER393 4.7 40.0 1.0
N A:HIS396 4.7 46.5 1.0
CA A:SER393 4.8 40.1 1.0
CB A:ASP343 4.9 38.2 1.0
C A:LYS395 5.0 46.1 1.0

Sodium binding site 2 out of 2 in 2ygm

Go back to Sodium Binding Sites List in 2ygm
Sodium 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 Sodium with other atoms in the Na 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:Na1417

b:34.6
occ:1.00
O B:GLY394 2.5 48.0 1.0
OD1 B:ASP400 2.6 45.2 1.0
O B:THR397 2.6 48.3 1.0
O B:ASP343 2.9 45.7 1.0
O B:ALA399 2.9 46.2 1.0
OG1 B:THR397 3.0 48.8 1.0
C B:THR397 3.4 48.3 1.0
CG B:ASP400 3.5 45.6 1.0
OG B:SER393 3.6 46.7 1.0
C B:GLY394 3.6 48.0 1.0
C B:ALA399 3.7 46.2 1.0
C B:ASP343 3.8 45.6 1.0
N B:GLY394 3.8 47.2 1.0
CA B:GLY394 4.0 47.6 1.0
CA B:ASP343 4.0 45.8 1.0
OD2 B:ASP400 4.0 45.1 1.0
C B:TRP398 4.0 47.8 1.0
CA B:THR397 4.1 48.4 1.0
CB B:THR397 4.1 48.3 1.0
N B:THR397 4.1 48.5 1.0
N B:ALA399 4.1 47.1 1.0
O B:TRP398 4.2 47.9 1.0
N B:TRP398 4.3 48.3 1.0
N B:ASP400 4.4 45.8 1.0
CA B:ASP400 4.4 45.5 1.0
CA B:ALA399 4.5 46.7 1.0
O B:ALA342 4.5 46.2 1.0
CA B:TRP398 4.5 48.1 1.0
CB B:ASP400 4.5 45.5 1.0
C B:SER393 4.8 46.8 1.0
N B:LYS395 4.8 48.3 1.0
OD1 B:ASP343 4.8 46.7 1.0
CB B:ASP343 4.8 45.9 1.0
CB B:SER393 4.8 46.5 1.0

Reference:

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
Page generated: Tue Dec 15 06:00:38 2020

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