Sodium in PDB 3jpy: Crystal Structure of the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B

The structure of Crystal Structure of the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B, PDB code: 3jpy was solved by E.Karakas, N.Simorowski, H.Furukawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.29 / 3.21
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	143.368, 143.368, 88.467, 90.00, 90.00, 120.00
R / Rfree (%)	20.4 / 23.3

The structure of Crystal Structure of the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B also contains other interesting chemical elements:

Chlorine	(Cl)	5 atoms
Zinc	(Zn)	5 atoms

The binding sites of Sodium atom in the Crystal Structure of the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B (pdb code 3jpy). 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 Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B, PDB code: 3jpy:

Sodium binding site 1 out of 1 in the Crystal Structure of the Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B


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 Zinc-Bound Amino Terminal Domain of the Nmda Receptor Subunit NR2B within 5.0Å range: probe atom residue distance (Å) B Occ A:Na701 b:0.1 occ:1.00 O A:SER131 2.3 1.0 1.0 O A:PHE146 2.5 0.7 1.0 C A:SER131 3.5 96.9 1.0 C A:PHE146 3.6 1.0 1.0 CA A:GLY147 3.6 0.7 1.0 OG A:SER131 3.8 98.1 1.0 C A:GLY147 3.8 0.7 1.0 CL A:CL601 3.8 0.1 1.0 CD A:PRO148 3.9 0.2 1.0 N A:GLY147 4.1 0.4 1.0 N A:PRO148 4.1 0.3 1.0 CB A:SER131 4.1 92.7 1.0 O A:GLY147 4.2 0.7 1.0 O A:PRO148 4.2 0.6 1.0 CA A:SER131 4.4 94.5 1.0 N A:MET132 4.4 95.1 1.0 CA A:MET132 4.5 94.0 1.0 N A:ILE133 4.5 0.0 1.0 C A:MET132 4.8 0.8 1.0 CA A:PHE146 4.9 0.8 1.0 CB A:GLN145 4.9 95.0 1.0 N A:PHE146 5.0 0.3 1.0

E.Karakas, N.Simorowski, H.Furukawa. Structure of the Zinc-Bound Amino-Terminal Domain of the Nmda Receptor NR2B Subunit. Embo J. V. 28 3910 2009.
ISSN: ISSN 0261-4189
PubMed: 19910922
DOI: 10.1038/EMBOJ.2009.338