Sodium in PDB 5kw9: Structural Basis For Norovirus Neutralization By A Hbga Blocking Human Iga Antibody

The structure of Structural Basis For Norovirus Neutralization By A Hbga Blocking Human Iga Antibody, PDB code: 5kw9 was solved by S.Shanker, B.V.V.Prasad, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	81.00 / 2.30
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	162.000, 162.000, 146.810, 90.00, 90.00, 120.00
R / Rfree (%)	18.6 / 21.2

The structure of Structural Basis For Norovirus Neutralization By A Hbga Blocking Human Iga Antibody also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Sodium atom in the Structural Basis For Norovirus Neutralization By A Hbga Blocking Human Iga Antibody (pdb code 5kw9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structural Basis For Norovirus Neutralization By A Hbga Blocking Human Iga Antibody, PDB code: 5kw9:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Structural Basis For Norovirus Neutralization By A Hbga Blocking Human Iga Antibody


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Basis For Norovirus Neutralization By A Hbga Blocking Human Iga Antibody within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:66.1 occ:1.00 O A:HOH870 2.4 43.7 1.0 O A:HOH778 3.3 39.9 1.0 NE2 A:HIS337 3.6 37.3 1.0 CE1 A:HIS337 4.0 39.3 1.0 CA A:GLY367 4.2 30.1 1.0 CD2 A:HIS337 4.6 35.8 1.0 NE2 A:GLN334 4.8 28.7 1.0 O A:HOH877 4.9 53.4 1.0 O A:SER366 4.9 30.1 1.0 N A:ASN368 4.9 30.0 1.0 O A:HOH832 5.0 43.2 1.0

Sodium binding site 2 out of 3 in the Structural Basis For Norovirus Neutralization By A Hbga Blocking Human Iga Antibody


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structural Basis For Norovirus Neutralization By A Hbga Blocking Human Iga Antibody within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:44.8 occ:1.00 O A:HOH731 3.7 33.2 1.0 O A:HOH763 3.9 65.9 1.0 NE2 A:GLN342 4.1 27.9 1.0 CZ2 A:TRP375 4.1 28.6 1.0 CH2 A:TRP375 4.3 28.8 1.0 OE1 A:GLN342 4.8 28.0 1.0 CD A:GLN342 4.9 28.7 1.0

Sodium binding site 3 out of 3 in the Structural Basis For Norovirus Neutralization By A Hbga Blocking Human Iga Antibody


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structural Basis For Norovirus Neutralization By A Hbga Blocking Human Iga Antibody within 5.0Å range: probe atom residue distance (Å) B Occ L:Na301 b:48.7 occ:1.00 OH L:TYR38 2.5 34.8 1.0 NE2 A:HIS381 2.7 37.0 1.0 CD2 L:TYR31 3.1 30.9 1.0 CE2 L:TYR31 3.2 33.8 1.0 CZ L:TYR38 3.3 33.5 1.0 CE1 A:HIS381 3.5 36.8 1.0 CD2 A:HIS381 3.6 34.4 1.0 CE2 L:TYR38 3.9 34.2 1.0 OD2 L:ASP34 3.9 41.7 1.0 CG L:TYR31 4.2 29.6 1.0 CE1 L:TYR38 4.2 32.3 1.0 CZ L:TYR31 4.2 33.7 1.0 O H:HOH419 4.3 37.4 1.0 CG A:PRO382 4.5 30.4 1.0 O H:HOH442 4.5 50.9 1.0 CB A:PRO382 4.6 30.9 1.0 ND1 A:HIS381 4.6 35.0 1.0 CG A:HIS381 4.7 33.2 1.0 CG L:ASP34 4.7 40.7 1.0 OD2 H:ASP108 4.8 35.3 1.0 CB L:TYR31 4.9 29.4 1.0 OH L:TYR31 4.9 31.4 1.0 O L:HOH449 4.9 54.6 1.0 O L:HOH430 5.0 42.0 1.0

S.Shanker, R.Czako, G.Sapparapu, G.Alvarado, M.Viskovska, B.Sankaran, R.L.Atmar, J.E.Crowe, M.K.Estes, B.V.Prasad. Structural Basis For Norovirus Neutralization By An Hbga Blocking Human Iga Antibody. Proc.Natl.Acad.Sci.Usa V. 113 E5830 2016.
ISSN: ESSN 1091-6490
PubMed: 27647885
DOI: 10.1073/PNAS.1609990113