Sodium in PDB 5f7k: Blood Group Antigen Binding Adhesin Baba of Helicobacter Pylori Strain 17875 in Complex with Nanobody Nb-ER19

The structure of Blood Group Antigen Binding Adhesin Baba of Helicobacter Pylori Strain 17875 in Complex with Nanobody Nb-ER19, PDB code: 5f7k was solved by K.Moonens, P.Gideonsson, S.Subedi, E.Romao, S.Oscarson, S.Muyldermans, T.Boren, H.Remaut, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.04 / 2.17
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.990, 131.660, 123.460, 90.00, 94.77, 90.00
R / Rfree (%)	17.1 / 20.7

The binding sites of Sodium atom in the Blood Group Antigen Binding Adhesin Baba of Helicobacter Pylori Strain 17875 in Complex with Nanobody Nb-ER19 (pdb code 5f7k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Blood Group Antigen Binding Adhesin Baba of Helicobacter Pylori Strain 17875 in Complex with Nanobody Nb-ER19, PDB code: 5f7k:

Sodium binding site 1 out of 1 in the Blood Group Antigen Binding Adhesin Baba of Helicobacter Pylori Strain 17875 in Complex with Nanobody Nb-ER19


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Blood Group Antigen Binding Adhesin Baba of Helicobacter Pylori Strain 17875 in Complex with Nanobody Nb-ER19 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na201 b:48.4 occ:1.00 O C:HOH315 2.9 54.8 1.0 N C:TRP48 3.0 42.0 1.0 CA C:GLU47 3.7 45.6 1.0 CB C:TRP48 3.8 40.0 1.0 CB A:GLN445 3.8 42.2 1.0 C C:GLU47 3.8 43.6 1.0 CA C:TRP48 3.9 38.8 1.0 CA A:THR442 4.0 42.6 1.0 CG2 A:THR442 4.0 44.0 1.0 CG A:GLN445 4.0 43.9 1.0 O A:THR442 4.2 42.1 1.0 O C:TRP48 4.3 40.8 1.0 CB C:GLU47 4.3 54.2 1.0 CG C:GLU47 4.3 64.8 1.0 CB A:THR442 4.4 44.5 1.0 OG1 A:THR442 4.4 47.0 1.0 O C:ARG46 4.5 43.5 1.0 C A:THR442 4.6 42.7 1.0 C C:TRP48 4.6 42.2 1.0 N C:GLU47 4.8 44.3 1.0

K.Moonens, P.Gideonsson, S.Subedi, J.Bugaytsova, E.Romao, M.Mendez, J.Norden, M.Fallah, L.Rakhimova, A.Shevtsova, M.Lahmann, G.Castaldo, K.Brannstrom, F.Coppens, A.W.Lo, T.Ny, J.V.Solnick, G.Vandenbussche, S.Oscarson, L.Hammarstrom, A.Arnqvist, D.E.Berg, S.Muyldermans, T.Boren, H.Remaut. Structural Insights Into Polymorphic Abo Glycan Binding By Helicobacter Pylori. Cell Host Microbe V. 19 55 2016.
ISSN: ESSN 1934-6069
PubMed: 26764597
DOI: 10.1016/J.CHOM.2015.12.004