Sodium in PDB 6vjn: Structure of Nhp D11A.B5FAB in Complex with 16055 V2B Peptide

The structure of Structure of Nhp D11A.B5FAB in Complex with 16055 V2B Peptide, PDB code: 6vjn was solved by S.Singh, T.J.Liban, M.Pancera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.98 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.78, 74.78, 101.45, 90, 90, 90
R / Rfree (%)	18 / 23.6

The binding sites of Sodium atom in the Structure of Nhp D11A.B5FAB in Complex with 16055 V2B Peptide (pdb code 6vjn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Structure of Nhp D11A.B5FAB in Complex with 16055 V2B Peptide, PDB code: 6vjn:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Structure of Nhp D11A.B5FAB in Complex with 16055 V2B Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Nhp D11A.B5FAB in Complex with 16055 V2B Peptide within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:64.1 occ:1.00 N H:ALA84 3.0 25.2 1.0 CB H:ALA84 3.7 32.5 1.0 CA H:THR83 3.8 28.7 1.0 C H:THR83 3.8 30.5 1.0 CA H:ALA84 3.8 33.7 1.0 CB H:PRO14 3.8 30.5 1.0 CB H:THR83 4.1 35.7 1.0 CG H:PRO14 4.6 34.3 1.0 CG1 H:VAL114 4.6 26.6 1.0 CA H:PRO14 4.9 31.9 1.0 OG1 H:THR83 4.9 31.4 1.0 O H:THR83 4.9 25.2 1.0

Sodium binding site 2 out of 6 in the Structure of Nhp D11A.B5FAB in Complex with 16055 V2B Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Nhp D11A.B5FAB in Complex with 16055 V2B Peptide within 5.0Å range: probe atom residue distance (Å) B Occ L:Na301 b:62.4 occ:1.00 O L:HOH507 2.5 59.0 1.0 OE1 L:GLN37 2.8 28.8 1.0 NH1 L:ARG39 2.9 33.2 1.0 NE L:ARG39 3.4 30.3 1.0 CZ L:ARG39 3.6 34.6 1.0 CD L:GLN37 3.7 28.6 1.0 NE2 L:GLN37 3.8 17.8 1.0 O L:HOH482 3.9 33.7 1.0 O L:HOH416 3.9 59.2 1.0 O L:HOH425 4.3 27.2 1.0 O L:HOH413 4.6 36.0 1.0 CD L:ARG39 4.7 30.9 1.0 NH2 L:ARG39 4.9 30.2 1.0

Sodium binding site 3 out of 6 in the Structure of Nhp D11A.B5FAB in Complex with 16055 V2B Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Nhp D11A.B5FAB in Complex with 16055 V2B Peptide within 5.0Å range: probe atom residue distance (Å) B Occ L:Na302 b:49.5 occ:1.00 OE2 L:GLU81 2.8 64.8 1.0 N L:GLU81 2.8 31.7 1.0 O L:HOH511 3.0 56.9 1.0 CB L:GLU81 3.2 34.1 1.0 CG L:GLU81 3.4 43.9 1.0 CD L:GLU81 3.6 57.5 1.0 N L:SER80 3.6 30.1 1.0 CA L:GLU81 3.6 27.5 1.0 CB L:LYS79 3.7 25.6 1.0 CB L:SER80 3.7 42.1 1.0 C L:SER80 3.8 38.3 1.0 CA L:SER80 3.9 37.6 1.0 C L:LYS79 4.1 24.4 1.0 OG L:SER80 4.3 53.9 1.0 O L:HOH483 4.4 45.1 1.0 CD L:LYS79 4.4 40.0 1.0 CA L:LYS79 4.5 29.2 1.0 CG L:LYS79 4.6 31.8 1.0 O L:LYS79 4.8 27.4 1.0 OE1 L:GLU81 4.8 57.8 1.0 C L:GLU81 4.8 23.5 1.0 O L:SER80 4.9 33.3 1.0

Sodium binding site 4 out of 6 in the Structure of Nhp D11A.B5FAB in Complex with 16055 V2B Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Nhp D11A.B5FAB in Complex with 16055 V2B Peptide within 5.0Å range: probe atom residue distance (Å) B Occ L:Na303 b:44.7 occ:1.00 OG1 L:THR5 2.9 26.4 1.0 CG2 L:THR5 3.7 22.9 1.0 CB L:THR5 3.8 22.4 1.0 CG2 L:THR26 4.0 32.5 1.0 CG2 L:THR24 4.3 25.7 1.0 CB L:THR24 4.4 28.0 1.0 O L:HOH523 4.5 39.0 1.0 O L:THR24 4.9 22.6 1.0

Sodium binding site 5 out of 6 in the Structure of Nhp D11A.B5FAB in Complex with 16055 V2B Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Nhp D11A.B5FAB in Complex with 16055 V2B Peptide within 5.0Å range: probe atom residue distance (Å) B Occ G:Na201 b:68.2 occ:1.00 O G:HOH303 3.2 26.1 1.0 OE2 G:GLU185 3.3 41.5 1.0 O G:HOH310 3.4 54.1 1.0 O G:HOH306 3.5 58.2 1.0 CD G:GLU185 3.5 43.5 1.0 OE1 G:GLU185 3.7 48.9 1.0 CG G:ARG186B 3.9 29.4 1.0 CD G:ARG186B 3.9 31.7 1.0 CE2 L:TYR95 3.9 47.5 1.0 O G:SER188 3.9 55.1 1.0 CB G:SER189 4.3 35.7 1.0 CG G:GLU185 4.3 38.3 1.0 CA G:SER189 4.4 38.7 1.0 CD2 L:TYR95 4.5 42.0 1.0 CZ L:TYR95 4.6 47.4 1.0 O H:HOH490 4.6 28.0 1.0 OH L:TYR95 4.7 53.5 1.0 O G:GLU186 4.7 29.1 1.0 C G:SER188 4.9 53.2 1.0

Sodium binding site 6 out of 6 in the Structure of Nhp D11A.B5FAB in Complex with 16055 V2B Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Nhp D11A.B5FAB in Complex with 16055 V2B Peptide within 5.0Å range: probe atom residue distance (Å) B Occ F:Na201 b:58.1 occ:1.00 OH G:TYR191 2.5 42.2 1.0 O G:HOH305 2.7 35.1 1.0 N F:SER189 3.2 80.9 1.0 N F:LYS190 3.2 74.6 1.0 O F:LYS190 3.4 57.8 1.0 CB F:SER189 3.5 82.4 1.0 CA F:SER189 3.7 80.8 1.0 CZ G:TYR191 3.7 40.1 1.0 OG G:SER189 3.8 38.8 1.0 C F:SER189 3.9 81.5 1.0 OE1 G:GLU186A 4.0 48.8 1.0 CE1 G:TYR191 4.0 33.9 1.0 C F:LYS190 4.1 62.4 1.0 CA F:LYS190 4.2 69.5 1.0 CG G:GLU186A 4.2 43.3 1.0 CB G:GLU186A 4.2 34.6 1.0 OG F:SER189 4.3 82.7 1.0 O G:ASN187 4.5 49.1 1.0 CD G:GLU186A 4.6 52.7 1.0 CD F:LYS190 4.6 65.2 1.0 O G:ARG186B 4.6 31.5 1.0 CB F:LYS190 4.7 68.9 1.0 N G:ARG186B 4.8 30.5 1.0 CA G:GLU186A 4.9 31.9 1.0 CE2 G:TYR191 4.9 34.7 1.0

T.Liban, S.Aljedani, S.Singh, J.Rodarte. Structural Basis For Potent Tier 2 Autologous Neutralization Elicited By Vaccination To Be Published.