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
|