Sodium in PDB 4i9x: Crystal Structure of Human Cytomegalovirus Glycoprotein UL141 Targeting the Death Receptor Trail-R2

The structure of Crystal Structure of Human Cytomegalovirus Glycoprotein UL141 Targeting the Death Receptor Trail-R2, PDB code: 4i9x was solved by I.Nemcovicova, D.M.Zajonc, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.83 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.916, 97.043, 141.422, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 27.4

The structure of Crystal Structure of Human Cytomegalovirus Glycoprotein UL141 Targeting the Death Receptor Trail-R2 also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Human Cytomegalovirus Glycoprotein UL141 Targeting the Death Receptor Trail-R2 (pdb code 4i9x). 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 Human Cytomegalovirus Glycoprotein UL141 Targeting the Death Receptor Trail-R2, PDB code: 4i9x:

Sodium binding site 1 out of 1 in the Crystal Structure of Human Cytomegalovirus Glycoprotein UL141 Targeting the Death Receptor Trail-R2


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 Human Cytomegalovirus Glycoprotein UL141 Targeting the Death Receptor Trail-R2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:64.3 occ:1.00 O B:TRP116 3.5 40.6 1.0 N B:TRP116 3.5 43.0 1.0 O B:HOH418 3.6 61.9 1.0 CD2 B:TRP116 3.7 41.0 1.0 CE2 B:TRP116 3.8 40.8 1.0 CE3 B:TRP116 4.0 48.4 1.0 CA B:THR115 4.0 47.6 1.0 CG B:TRP116 4.1 41.1 1.0 CB B:THR115 4.1 47.6 1.0 NE1 B:TRP116 4.2 37.2 1.0 CZ2 B:TRP116 4.2 47.0 1.0 C B:THR115 4.3 45.6 1.0 C B:TRP116 4.3 42.7 1.0 CD1 B:TRP116 4.3 40.2 1.0 CZ3 B:TRP116 4.4 50.2 1.0 CA B:TRP116 4.4 43.1 1.0 CH2 B:TRP116 4.4 46.7 1.0 CG2 B:THR115 4.7 46.2 1.0 CB B:TRP116 4.8 40.8 1.0 O B:HOH466 4.9 58.7 1.0

I.Nemcovicova, C.A.Benedict, D.M.Zajonc. Structure of Human Cytomegalovirus UL141 Binding to Trail-R2 Reveals Novel, Non-Canonical Death Receptor Interactions. Plos Pathog. V. 9 03224 2013.
ISSN: ISSN 1553-7366
PubMed: 23555243
DOI: 10.1371/JOURNAL.PPAT.1003224