Sodium in PDB 4gvc: Crystal Structure of T-Cell Lymphoma Invasion and Metastasis-1 Pdz in Complex with Phosphorylated SYNDECAN1 Peptide

The structure of Crystal Structure of T-Cell Lymphoma Invasion and Metastasis-1 Pdz in Complex with Phosphorylated SYNDECAN1 Peptide, PDB code: 4gvc was solved by X.Liu, T.R.Shepherd, A.M.Murray, Z.Xu, E.J.Fuentes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.85 / 1.54
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	26.717, 50.135, 57.712, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 20

The structure of Crystal Structure of T-Cell Lymphoma Invasion and Metastasis-1 Pdz in Complex with Phosphorylated SYNDECAN1 Peptide also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of T-Cell Lymphoma Invasion and Metastasis-1 Pdz in Complex with Phosphorylated SYNDECAN1 Peptide (pdb code 4gvc). 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 T-Cell Lymphoma Invasion and Metastasis-1 Pdz in Complex with Phosphorylated SYNDECAN1 Peptide, PDB code: 4gvc:

Sodium binding site 1 out of 1 in the Crystal Structure of T-Cell Lymphoma Invasion and Metastasis-1 Pdz in Complex with Phosphorylated SYNDECAN1 Peptide


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 T-Cell Lymphoma Invasion and Metastasis-1 Pdz in Complex with Phosphorylated SYNDECAN1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na103 b:18.6 occ:1.00 CL B:CL102 2.7 12.9 1.0 CE B:LYS2 3.7 16.0 1.0 NZ B:LYS2 3.8 16.1 1.0 C3 B:ANS101 3.9 15.0 1.0 CD B:LYS2 4.1 14.8 1.0 C2 B:ANS101 4.2 14.6 1.0 CG B:LYS2 4.6 14.6 1.0

X.Liu, T.R.Shepherd, A.M.Murray, Z.Xu, E.J.Fuentes. The Structure of the TIAM1 Pdz Domain/ Phospho-SYNDECAN1 Complex Reveals A Ligand Conformation That Modulates Protein Dynamics. Structure V. 21 342 2013.
ISSN: ISSN 0969-2126
PubMed: 23395182
DOI: 10.1016/J.STR.2013.01.004