Sodium in PDB 6xyf: Nanobody 22

The structure of Nanobody 22, PDB code: 6xyf was solved by G.Pompidor, S.Zimmermann, C.Loew, T.Schneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.01 / 1.11
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	30.322, 38.685, 44.873, 90, 98.27, 90
R / Rfree (%)	12.5 / 15.3

The binding sites of Sodium atom in the Nanobody 22 (pdb code 6xyf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Nanobody 22, PDB code: 6xyf:

Sodium binding site 1 out of 1 in the Nanobody 22


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Nanobody 22 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:24.2 occ:1.00 H A:LYS118 2.3 10.4 1.0 HG3 A:LYS118 2.5 22.6 1.0 HD2 A:LYS118 2.6 27.4 1.0 O A:LEU4 2.7 8.7 1.0 O A:HOH345 2.8 32.5 1.0 HB2 A:LYS118 2.9 16.8 1.0 HA A:GLN5 3.0 8.5 1.0 N A:LYS118 3.0 8.6 1.0 CG A:LYS118 3.1 18.8 1.0 CD A:LYS118 3.2 22.8 1.0 HA2 A:GLY117 3.2 8.3 1.0 CB A:LYS118 3.4 14.0 1.0 HE3 A:LYS118 3.6 30.1 1.0 HG3 A:GLN5 3.7 19.8 1.0 CA A:LYS118 3.8 9.6 1.0 C A:LEU4 3.8 6.5 1.0 CA A:GLY117 3.9 6.9 1.0 C A:GLY117 3.9 7.0 1.0 CA A:GLN5 3.9 7.1 1.0 CE A:LYS118 4.0 25.1 1.0 OE1 A:GLU6 4.0 8.6 1.0 HA3 A:GLY117 4.0 8.3 1.0 HD3 A:LYS118 4.0 27.4 1.0 HG2 A:LYS118 4.0 22.6 1.0 HB2 A:GLN5 4.1 12.1 1.0 H A:GLU6 4.3 9.1 1.0 HB3 A:LYS118 4.3 16.8 1.0 HA A:LYS118 4.3 11.5 1.0 N A:GLN5 4.3 7.0 1.0 CB A:GLN5 4.4 10.1 1.0 CG A:GLN5 4.5 16.5 1.0 HE21 A:GLN5 4.5 26.2 1.0 HE2 A:LYS118 4.6 30.1 1.0 O A:HOH301 4.7 20.3 1.0 H A:LEU4 4.7 12.1 1.0 H A:GLY119 4.7 9.7 1.0 HZ2 A:LYS118 4.8 31.8 1.0 OE1 A:GLN3 4.8 28.8 1.0 N A:GLU6 4.9 7.6 1.0 NZ A:LYS118 5.0 26.5 1.0 C A:GLN5 5.0 6.4 1.0 C A:LYS118 5.0 8.7 1.0 O A:GLY117 5.0 9.4 1.0 HE22 A:GLN3 5.0 36.4 1.0

G.Pompidor, S.Zimmermann, C.Loew, T.Schneider. Engineered Nanobodies with A Lanthanide Binding Motif For Crystallographic Phasing To Be Published.