Sodium in PDB 8sfs: High Affinity Nanobodies Against Gfp
Protein crystallography data
The structure of High Affinity Nanobodies Against Gfp, PDB code: 8sfs
was solved by
N.E.Ketaren,
M.P.Rout,
J.B.Bonnano,
S.C.Almo,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.80 /
2.37
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
131.772,
131.772,
153.58,
90,
90,
120
|
R / Rfree (%)
|
19 /
21.8
|
Other elements in 8sfs:
The structure of High Affinity Nanobodies Against Gfp also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the High Affinity Nanobodies Against Gfp
(pdb code 8sfs). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the
High Affinity Nanobodies Against Gfp, PDB code: 8sfs:
Jump to Sodium binding site number:
1;
2;
3;
Sodium binding site 1 out
of 3 in 8sfs
Go back to
Sodium Binding Sites List in 8sfs
Sodium binding site 1 out
of 3 in the High Affinity Nanobodies Against Gfp
![](/pictures/NA/pdb/sf/8sfs-NA-sphere_01.jpg) Mono view
![](/pictures/NA/pdb/sf/8sfs-NA-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of High Affinity Nanobodies Against Gfp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na309
b:77.6
occ:1.00
|
OD2
|
B:ASP19
|
3.1
|
83.5
|
1.0
|
O
|
B:ILE123
|
3.2
|
49.9
|
1.0
|
O
|
B:HOH403
|
3.3
|
72.2
|
1.0
|
O
|
B:HOH451
|
3.4
|
65.2
|
1.0
|
CG
|
B:ARG122
|
3.6
|
65.2
|
1.0
|
CG
|
B:ASP19
|
3.6
|
69.2
|
1.0
|
N
|
B:ASP19
|
3.8
|
51.8
|
1.0
|
CD
|
B:ARG122
|
3.8
|
68.9
|
1.0
|
CB
|
B:ASP19
|
3.9
|
57.4
|
1.0
|
CE1
|
C:PHE33
|
3.9
|
59.0
|
1.0
|
C
|
B:ILE123
|
4.1
|
51.0
|
1.0
|
N
|
B:ILE123
|
4.3
|
50.8
|
1.0
|
C
|
B:LEU18
|
4.3
|
54.2
|
1.0
|
O
|
B:GLU17
|
4.3
|
49.1
|
1.0
|
CA
|
B:LEU18
|
4.4
|
50.8
|
1.0
|
CA
|
B:ASP19
|
4.4
|
52.1
|
1.0
|
OD1
|
B:ASP19
|
4.5
|
64.9
|
1.0
|
C
|
B:GLU17
|
4.5
|
48.9
|
1.0
|
N
|
B:LEU18
|
4.6
|
45.8
|
1.0
|
CG
|
B:GLU124
|
4.6
|
63.2
|
1.0
|
CD1
|
C:PHE33
|
4.7
|
59.0
|
1.0
|
CB
|
B:GLU17
|
4.8
|
50.9
|
1.0
|
CZ
|
C:PHE33
|
4.8
|
55.7
|
1.0
|
CA
|
B:ILE123
|
4.9
|
47.8
|
1.0
|
CB
|
B:ARG122
|
4.9
|
53.5
|
1.0
|
N
|
B:GLU124
|
4.9
|
51.6
|
1.0
|
O
|
B:HOH439
|
5.0
|
63.9
|
1.0
|
C
|
B:ARG122
|
5.0
|
50.1
|
1.0
|
|
Sodium binding site 2 out
of 3 in 8sfs
Go back to
Sodium Binding Sites List in 8sfs
Sodium binding site 2 out
of 3 in the High Affinity Nanobodies Against Gfp
![](/pictures/NA/pdb/sf/8sfs-NA-sphere_02.jpg) Mono view
![](/pictures/NA/pdb/sf/8sfs-NA-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of High Affinity Nanobodies Against Gfp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na310
b:77.1
occ:1.00
|
OE1
|
B:GLU124
|
2.7
|
85.7
|
1.0
|
NH1
|
B:ARG109
|
2.9
|
80.9
|
1.0
|
CD
|
B:ARG109
|
3.0
|
82.2
|
1.0
|
CG
|
B:ARG109
|
3.3
|
67.4
|
1.0
|
CD
|
B:GLU124
|
3.7
|
77.5
|
1.0
|
O2
|
C:SO4201
|
3.8
|
117.9
|
1.0
|
CZ
|
B:ARG109
|
3.8
|
76.8
|
1.0
|
NE
|
B:ARG109
|
3.8
|
78.7
|
1.0
|
CD2
|
C:PHE33
|
3.9
|
52.8
|
1.0
|
CG
|
C:PHE33
|
4.0
|
57.5
|
1.0
|
CE2
|
C:PHE33
|
4.1
|
55.0
|
1.0
|
CB
|
B:ARG109
|
4.1
|
55.1
|
1.0
|
OE2
|
B:GLU124
|
4.3
|
88.0
|
1.0
|
CD1
|
C:PHE33
|
4.4
|
59.0
|
1.0
|
CZ
|
C:PHE33
|
4.5
|
55.7
|
1.0
|
O4
|
C:SO4201
|
4.5
|
85.2
|
1.0
|
CB
|
C:PHE33
|
4.6
|
59.4
|
1.0
|
CE1
|
C:PHE33
|
4.6
|
59.0
|
1.0
|
CB
|
B:GLU124
|
4.7
|
51.2
|
1.0
|
S
|
C:SO4201
|
4.7
|
131.0
|
1.0
|
CG
|
B:GLU124
|
4.7
|
63.2
|
1.0
|
|
Sodium binding site 3 out
of 3 in 8sfs
Go back to
Sodium Binding Sites List in 8sfs
Sodium binding site 3 out
of 3 in the High Affinity Nanobodies Against Gfp
![](/pictures/NA/pdb/sf/8sfs-NA-sphere_03.jpg) Mono view
![](/pictures/NA/pdb/sf/8sfs-NA-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of High Affinity Nanobodies Against Gfp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na209
b:79.0
occ:1.00
|
HO1
|
C:GOL204
|
2.3
|
73.3
|
1.0
|
O1
|
C:GOL204
|
3.0
|
61.0
|
1.0
|
O
|
B:HOH423
|
3.1
|
60.0
|
1.0
|
NE1
|
C:TRP57
|
3.3
|
48.4
|
1.0
|
H12
|
C:GOL204
|
3.3
|
73.6
|
1.0
|
C1
|
C:GOL204
|
3.7
|
61.3
|
1.0
|
O
|
C:THR32
|
3.9
|
54.4
|
1.0
|
CD1
|
C:TRP57
|
3.9
|
49.6
|
1.0
|
OD1
|
C:ASN81
|
4.1
|
57.8
|
1.0
|
H11
|
C:GOL204
|
4.2
|
73.6
|
1.0
|
CD
|
C:ARG78
|
4.3
|
53.2
|
1.0
|
O
|
C:ARG78
|
4.4
|
61.0
|
1.0
|
CE2
|
C:TRP57
|
4.5
|
48.6
|
1.0
|
CB
|
C:ARG78
|
4.6
|
54.6
|
1.0
|
NE
|
B:ARG122
|
4.7
|
79.3
|
1.0
|
C
|
C:THR32
|
4.7
|
53.2
|
1.0
|
NH2
|
B:ARG122
|
4.7
|
89.5
|
1.0
|
CG
|
C:ARG78
|
4.7
|
54.0
|
1.0
|
C2
|
C:GOL204
|
4.8
|
70.2
|
1.0
|
HO2
|
C:GOL204
|
4.8
|
92.9
|
1.0
|
CA
|
C:PHE33
|
4.8
|
55.6
|
1.0
|
O
|
C:PHE33
|
4.9
|
54.4
|
1.0
|
O2
|
C:GOL204
|
4.9
|
77.4
|
1.0
|
H2
|
C:GOL204
|
4.9
|
84.2
|
1.0
|
CG
|
C:ASN81
|
5.0
|
55.9
|
1.0
|
CZ
|
B:ARG122
|
5.0
|
87.0
|
1.0
|
|
Reference:
N.E.Ketaren,
M.P.Rout,
S.Almo.
High Affinity Nanobodies Against Gfp To Be Published.
Page generated: Wed Oct 9 13:27:20 2024
|