Sodium in PDB 3bov: Crystal Structure of the Receptor Binding Domain of Mouse Pd-L2

The structure of Crystal Structure of the Receptor Binding Domain of Mouse Pd-L2, PDB code: 3bov was solved by E.Lazar-Molnar, U.Ramagopal, E.Cao, R.Toro, S.G.Nathenson, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.13 / 1.77
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	45.173, 116.637, 45.108, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 22.3

The binding sites of Sodium atom in the Crystal Structure of the Receptor Binding Domain of Mouse Pd-L2 (pdb code 3bov). 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 Crystal Structure of the Receptor Binding Domain of Mouse Pd-L2, PDB code: 3bov:

Sodium binding site 1 out of 1 in the Crystal Structure of the Receptor Binding Domain of Mouse Pd-L2


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 Receptor Binding Domain of Mouse Pd-L2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1 b:33.2 occ:1.00 O A:HOH201 2.3 31.1 1.0 O A:HOH158 2.3 32.2 1.0 OG A:SER97 2.4 20.3 1.0 O A:SER97 2.5 18.0 1.0 O A:HOH161 2.6 32.0 1.0 C A:SER97 3.2 17.3 1.0 CB A:SER97 3.5 19.1 1.0 CA A:SER97 3.8 18.2 1.0 N A:GLY98 3.9 17.0 1.0 NZ A:LYS61 4.0 18.8 1.0 CA A:GLY98 4.1 17.2 1.0 N A:SER97 4.2 17.9 1.0 O A:VAL94 4.5 22.1 1.0 O A:ARG95 4.8 23.1 1.0 CE A:LYS61 4.9 18.7 1.0 O A:HOH176 5.0 40.4 1.0

E.Lazar-Molnar, Q.Yan, E.Cao, U.Ramagopal, S.G.Nathenson, S.C.Almo. Crystal Structure of the Complex Between Programmed Death-1 (Pd-1) and Its Ligand Pd-L2. Proc.Natl.Acad.Sci.Usa V. 105 10483 2008.
ISSN: ISSN 0027-8424
PubMed: 18641123
DOI: 10.1073/PNAS.0804453105