Atomistry » Sodium » PDB 6vf7-6w0r » 6vjn
Atomistry »
  Sodium »
    PDB 6vf7-6w0r »
      6vjn »

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

Protein crystallography data

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

Sodium Binding Sites:

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 6vjn

Go back to Sodium Binding Sites List in 6vjn
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 6vjn

Go back to Sodium Binding Sites List in 6vjn
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 6vjn

Go back to Sodium Binding Sites List in 6vjn
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 6vjn

Go back to Sodium Binding Sites List in 6vjn
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 6vjn

Go back to Sodium Binding Sites List in 6vjn
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 6vjn

Go back to Sodium Binding Sites List in 6vjn
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

Reference:

T.Liban, S.Aljedani, S.Singh, J.Rodarte. Structural Basis For Potent Tier 2 Autologous Neutralization Elicited By Vaccination To Be Published.
Page generated: Tue Oct 8 14:23:34 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy