Sodium in PDB 3pdv: Structure of the PDLIM2 Pdz Domain in Complex with the C-Terminal 6- Peptide Extension of NS1

The structure of Structure of the PDLIM2 Pdz Domain in Complex with the C-Terminal 6- Peptide Extension of NS1, PDB code: 3pdv was solved by X.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.31 / 2.20
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	81.917, 81.917, 81.917, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 24.9

The binding sites of Sodium atom in the Structure of the PDLIM2 Pdz Domain in Complex with the C-Terminal 6- Peptide Extension of NS1 (pdb code 3pdv). 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 Structure of the PDLIM2 Pdz Domain in Complex with the C-Terminal 6- Peptide Extension of NS1, PDB code: 3pdv:

Sodium binding site 1 out of 1 in the Structure of the PDLIM2 Pdz Domain in Complex with the C-Terminal 6- Peptide Extension of NS1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the PDLIM2 Pdz Domain in Complex with the C-Terminal 6- Peptide Extension of NS1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na90 b:42.9 occ:1.00 O A:HOH137 2.2 51.3 1.0 O A:SER72 2.7 24.9 1.0 O A:ARG70 2.7 24.4 1.0 CB A:ALA11 3.4 32.4 1.0 CZ2 A:TRP13 3.4 25.2 1.0 N A:SER72 3.5 25.3 1.0 C A:ARG70 3.5 24.4 1.0 NE1 A:TRP13 3.5 24.7 1.0 C A:SER72 3.7 24.9 1.0 CE2 A:TRP13 3.7 25.2 1.0 N A:ALA11 3.8 33.2 1.0 C A:GLN71 3.8 25.5 1.0 O A:ILE69 3.8 23.0 1.0 CA A:SER72 4.0 24.9 1.0 N A:GLN71 4.2 24.9 1.0 CA A:ALA11 4.2 32.3 1.0 CA A:GLN71 4.3 25.5 1.0 CA A:ARG70 4.3 24.3 1.0 O A:GLN71 4.4 26.1 1.0 CB A:SER72 4.4 25.1 1.0 CH2 A:TRP13 4.5 25.1 1.0 CD1 A:TRP13 4.7 24.9 1.0 C A:ILE69 4.8 22.8 1.0 C A:PRO10 4.8 34.1 1.0 N A:PRO73 4.9 25.0 1.0

J.Yu, X.Li, Y.Wang, B.Li, H.Li, Y.Li, W.Zhou, C.Zhang, Y.Wang, Z.Rao, M.Bartlam, Y.Cao. PDLIM2 Selectively Interacts with the Pdz Binding Motif of Highly Pathogenic Avian H5N1 Influenza A Virus NS1 Plos One V. 6 19511 2011.
ISSN: ESSN 1932-6203
PubMed: 21625420
DOI: 10.1371/JOURNAL.PONE.0019511