Sodium in PDB 8s6e: Monoclonal Antibody Menw Targeting Serogroup W of Neisseria Meningitidis

The structure of Monoclonal Antibody Menw Targeting Serogroup W of Neisseria Meningitidis, PDB code: 8s6e was solved by G.P.Pietri, S.Bertuzzi, K.Karnicar, L.Unione, B.Lisnic, S.Malic, K.Miklic, M.Novak, I.Calloni, L.Santini, A.Usenik, M.Rosaria Romano, R.Adamo, S.Jonjic, D.Turk, J.Jimenez-Barbero, T.Lenac Rovis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.27 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.87, 69.16, 128.98, 90, 90, 90
R / Rfree (%)	20.1 / 22.3

The binding sites of Sodium atom in the Monoclonal Antibody Menw Targeting Serogroup W of Neisseria Meningitidis (pdb code 8s6e). 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 Monoclonal Antibody Menw Targeting Serogroup W of Neisseria Meningitidis, PDB code: 8s6e:

Sodium binding site 1 out of 1 in the Monoclonal Antibody Menw Targeting Serogroup W of Neisseria Meningitidis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Monoclonal Antibody Menw Targeting Serogroup W of Neisseria Meningitidis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:29.7 occ:1.00 H B:GLY376 2.3 20.0 0.0 HG1 B:THR417 2.9 20.0 0.0 HB3 B:SER415 2.9 20.0 0.0 OG1 B:THR417 3.0 31.8 1.0 N B:GLY376 3.0 25.3 1.0 H B:ASP375 3.2 20.0 0.0 OG B:SER415 3.3 37.4 1.0 HB B:THR417 3.3 20.0 0.0 HB3 B:LYS373 3.4 20.0 0.0 N B:ASP375 3.5 34.8 1.0 HA B:ASP375 3.5 20.0 0.0 HB2 B:LYS373 3.5 20.0 0.0 O B:SER415 3.5 24.9 1.0 HA2 B:GLY376 3.6 20.0 0.0 CB B:SER415 3.6 31.8 1.0 O B:LYS373 3.6 27.7 1.0 HA B:TYR416 3.6 20.0 0.0 C B:SER415 3.7 29.3 1.0 CB B:THR417 3.7 30.3 1.0 CA B:ASP375 3.8 34.4 1.0 C B:ASP375 3.8 33.4 1.0 HA B:ILE374 3.9 20.0 0.0 N B:THR417 3.9 25.4 1.0 C B:LYS373 3.9 31.4 1.0 HG B:SER415 3.9 20.0 0.0 H B:THR417 3.9 20.0 0.0 CA B:GLY376 3.9 29.1 1.0 N B:TYR416 3.9 27.1 1.0 CB B:LYS373 3.9 27.6 1.0 H1 B:HOH640 4.0 20.0 0.0 C B:TYR416 4.0 21.3 1.0 CA B:TYR416 4.1 24.9 1.0 C B:ILE374 4.1 28.2 1.0 H1 B:HOH674 4.1 20.0 0.0 H2 B:HOH640 4.2 20.0 0.0 N B:ILE374 4.2 27.6 1.0 O B:HOH674 4.3 54.0 1.0 H2 B:HOH674 4.3 20.0 0.0 CA B:ILE374 4.3 30.2 1.0 CA B:SER415 4.3 38.6 1.0 CA B:THR417 4.5 21.6 1.0 HB2 B:SER415 4.5 20.0 0.0 O B:HOH640 4.5 32.8 1.0 H B:TYR416 4.5 20.0 0.0 HA3 B:GLY376 4.6 20.0 0.0 CA B:LYS373 4.6 30.4 1.0 HE2 B:LYS373 4.6 20.0 0.0 O B:TYR416 4.7 25.9 1.0 H B:SER377 4.8 20.0 0.0 HB2 B:SER432 4.8 20.0 0.0 HG21 B:THR417 4.9 20.0 0.0 HD3 B:LYS373 4.9 20.0 0.0 O B:ILE374 4.9 28.2 1.0 H B:ILE374 5.0 20.0 0.0 O B:ASP375 5.0 29.1 1.0 HA B:SER415 5.0 20.0 0.0 CG2 B:THR417 5.0 32.2 1.0

G.P.Pietri, S.Bertuzzi, K.Karnicar, L.Unione, B.Lisnic, S.Malic, K.Miklic, M.Novak, I.Calloni, L.Santini, A.Usenik, M.R.Romano, R.Adamo, S.Jonjic, D.Turk, J.Jimenez-Barbero, T.Lenac Rovis. Antigenic Determinants Driving Serogroup-Specific Antibody Response to Neisseria Meningitidis C, W, and Y Capsular Polysaccharides: Insights For Rational Vaccine Design. Carbohydr Polym V. 341 22349 2024.
ISSN: ESSN 1879-1344
PubMed: 38876728
DOI: 10.1016/J.CARBPOL.2024.122349