Sodium in PDB 8oju: Crystal Structure of the Human Igd Fab - Structure FAB3

The structure of Crystal Structure of the Human Igd Fab - Structure FAB3, PDB code: 8oju was solved by A.M.Davies, R.L.Beavil, J.M.Mcdonnell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.25 / 1.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.893, 74.198, 70.915, 90, 92.15, 90
R / Rfree (%)	15.7 / 18.9

The binding sites of Sodium atom in the Crystal Structure of the Human Igd Fab - Structure FAB3 (pdb code 8oju). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Human Igd Fab - Structure FAB3, PDB code: 8oju:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Human Igd Fab - Structure FAB3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Human Igd Fab - Structure FAB3 within 5.0Å range: probe atom residue distance (Å) B Occ L:Na307 b:62.7 occ:1.00 CE1 L:TYR33 3.9 30.9 1.0 CZ L:TYR33 4.0 32.3 1.0 O L:GLY32 4.1 31.1 1.0 O L:ALA31 4.1 34.3 1.0 C L:GLY32 4.2 28.9 1.0 CD1 L:TYR33 4.2 29.8 1.0 OH L:TYR33 4.4 37.1 1.0 CE2 L:TYR33 4.4 30.1 1.0 CA L:GLY32 4.6 31.1 1.0 CG L:TYR33 4.6 27.4 1.0 CD2 L:TYR33 4.7 28.1 1.0 N L:TYR33 4.7 25.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Human Igd Fab - Structure FAB3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Human Igd Fab - Structure FAB3 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na305 b:63.0 occ:1.00 NZ H:LYS204 3.9 30.4 1.0 CD2 H:PHE219 4.1 24.4 1.0 CD H:LYS204 4.1 28.0 1.0 CG H:PHE219 4.2 22.3 1.0 CE2 H:PHE219 4.5 25.4 1.0 CB H:PHE219 4.5 20.7 1.0 OE1 H:GLU217 4.6 37.4 1.0 CD1 H:PHE219 4.6 24.9 1.0 CE H:LYS204 4.6 29.8 1.0 CZ H:PHE219 4.9 26.5 1.0 CE1 H:PHE219 5.0 25.9 1.0

A.M.Davies, R.L.Beavil, M.Barbolov, B.S.Sandhar, H.J.Gould, A.J.Beavil, B.J.Sutton, J.M.Mcdonnell. Crystal Structures of the Human Igd Fab Reveal Insights Into C H 1 Domain Diversity. Mol.Immunol. V. 159 28 2023.
ISSN: ISSN 0161-5890
PubMed: 37267832
DOI: 10.1016/J.MOLIMM.2023.05.006