Sodium in PDB 6xsn: Crystal Structure of Nhp VD20.5A4 Fab in Complex with 16055 V1V2 1FD6 Scaffold

The structure of Crystal Structure of Nhp VD20.5A4 Fab in Complex with 16055 V1V2 1FD6 Scaffold, PDB code: 6xsn was solved by S.Aljedani, M.Pancera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.24 / 2.87
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	106.565, 106.565, 128.926, 90, 90, 90
R / Rfree (%)	22.1 / 26.7

The binding sites of Sodium atom in the Crystal Structure of Nhp VD20.5A4 Fab in Complex with 16055 V1V2 1FD6 Scaffold (pdb code 6xsn). 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 Crystal Structure of Nhp VD20.5A4 Fab in Complex with 16055 V1V2 1FD6 Scaffold, PDB code: 6xsn:

Sodium binding site 1 out of 1 in the Crystal Structure of Nhp VD20.5A4 Fab in Complex with 16055 V1V2 1FD6 Scaffold


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Nhp VD20.5A4 Fab in Complex with 16055 V1V2 1FD6 Scaffold within 5.0Å range: probe atom residue distance (Å) B Occ L:Na606 b:36.1 occ:1.00 OE1 C:GLU186 2.2 43.8 1.0 OE2 L:GLU32 2.3 35.5 1.0 O H:TYR100 2.3 39.0 1.0 OD2 L:ASP91 2.3 43.1 1.0 O L:ASP91 2.5 45.9 1.0 O L:HOH714 2.8 38.6 1.0 CD C:GLU186 3.2 44.1 1.0 CD L:GLU32 3.4 38.6 1.0 C H:TYR100 3.4 41.2 1.0 CG L:ASP91 3.4 44.5 1.0 C L:ASP91 3.6 44.7 1.0 CG C:GLU186 3.7 41.0 1.0 CB L:ASP91 3.9 43.5 1.0 O C:GLU186A 3.9 49.8 1.0 OE1 L:GLU32 4.0 39.5 1.0 OH L:TYR96 4.1 33.4 1.0 OE2 C:GLU186 4.2 41.9 1.0 N H:PHE100A 4.3 41.0 1.0 CA H:TYR100 4.3 44.4 1.0 CB H:PHE100B 4.4 33.2 1.0 CA H:PHE100A 4.4 38.2 1.0 CA L:ASP91 4.4 44.8 1.0 CG L:GLU32 4.4 40.5 1.0 OD1 L:ASP91 4.5 44.8 1.0 N L:TYR92 4.5 41.1 1.0 C H:PHE100A 4.5 38.5 1.0 CA L:TYR92 4.6 41.3 1.0 N H:PHE100B 4.6 34.6 1.0 CB H:TYR100 4.6 45.0 1.0 CB L:GLU32 4.7 32.5 1.0 CZ L:TYR96 4.8 31.5 1.0 O L:TYR92 4.8 44.4 1.0 C L:TYR92 4.9 40.4 1.0

S.Aljedani, T.Liban, K.Tran, G.Phad, S.Singh, V.Dubrovskaya, P.Pushparaj, P.Martinez-Murillo, J.Rodarte, R.Kinzelman, K.Lee, L.Shapiro, G.Hedestam, R.Wyatt, M.Pancera. Structural Basis For Potent Tier 2 Autologous Neutralization Elicited By Vaccination To Be Published.