Sodium in PDB 8sfs: High Affinity Nanobodies Against Gfp

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

The structure of High Affinity Nanobodies Against Gfp also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

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 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 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 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

N.E.Ketaren, M.P.Rout, S.Almo. High Affinity Nanobodies Against Gfp To Be Published.