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

The structure of Crystal Structure of T-Cell Lymphoma Invasion and Metastasis-1 Pdz in Complex with SYNDECAN1 Peptide, PDB code: 4gvd 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)	50.95 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	26.517, 58.106, 50.948, 90.00, 90.50, 90.00
R / Rfree (%)	19.6 / 24.3

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

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of T-Cell Lymphoma Invasion and Metastasis-1 Pdz in Complex with SYNDECAN1 Peptide (pdb code 4gvd). 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 T-Cell Lymphoma Invasion and Metastasis-1 Pdz in Complex with SYNDECAN1 Peptide, PDB code: 4gvd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of T-Cell Lymphoma Invasion and Metastasis-1 Pdz in Complex with 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 SYNDECAN1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1002 b:45.8 occ:1.00 CL A:CL1003 2.5 65.3 1.0 CG A:MET839 3.5 33.1 1.0 O A:HOH1124 4.1 29.3 1.0 SD A:MET839 4.3 39.8 1.0 CB A:MET839 4.7 28.6 1.0 CE A:MET839 4.8 37.9 1.0 O A:ALA838 4.9 23.7 1.0 O A:HOH1122 4.9 23.2 1.0 CA A:MET839 4.9 22.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of T-Cell Lymphoma Invasion and Metastasis-1 Pdz in Complex with SYNDECAN1 Peptide


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 T-Cell Lymphoma Invasion and Metastasis-1 Pdz in Complex with SYNDECAN1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1001 b:40.9 occ:1.00 CL B:CL1002 2.6 35.3 1.0 O B:HOH1139 2.8 27.6 1.0 O B:HOH1136 2.9 36.9 1.0 O B:VAL878 3.8 19.1 1.0 CB B:ALA891 3.8 23.1 1.0 N B:VAL878 4.3 18.6 1.0 N B:ALA891 4.4 21.5 1.0 CB B:VAL878 4.4 17.4 1.0 C B:VAL878 4.7 20.8 1.0 CA B:VAL878 4.7 17.6 1.0 CA B:ALA891 4.8 19.6 1.0 O B:HOH1148 4.9 32.5 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