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:

Chlorine (Cl) 4 atoms

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


Mono view


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


Mono view


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


Mono view


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

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