Sodium in PDB 4l8b: Crystal Structure of the H2DB in Complex with the Np-N5H Peptide

The structure of Crystal Structure of the H2DB in Complex with the Np-N5H Peptide, PDB code: 4l8b was solved by J.Rossjohn, S.Gras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.49 / 2.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	90.990, 132.138, 47.038, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 23.2

The binding sites of Sodium atom in the Crystal Structure of the H2DB in Complex with the Np-N5H Peptide (pdb code 4l8b). 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 H2DB in Complex with the Np-N5H Peptide, PDB code: 4l8b:

Sodium binding site 1 out of 1 in the Crystal Structure of the H2DB in Complex with the Np-N5H 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 the H2DB in Complex with the Np-N5H Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:68.1 occ:1.00 O B:HOH226 3.2 58.3 1.0 O B:HOH233 3.4 73.8 1.0 N B:LYS58 3.6 34.8 1.0 CB B:LYS58 3.7 40.4 1.0 CB B:SER57 3.7 39.1 1.0 CA B:LYS58 4.3 36.0 1.0 CA B:SER57 4.4 33.2 1.0 OG B:SER57 4.5 53.8 1.0 C B:SER57 4.5 37.1 1.0 CE B:LYS58 4.6 92.8 1.0 CG B:LYS58 4.9 66.4 1.0 CD B:LYS58 5.0 82.4 0.8

S.A.Valkenburg, S.Quinones-Parra, S.Gras, N.Komadina, J.Mcvernon, Z.Wang, H.Halim, P.Iannello, C.Cole, K.Laurie, A.Kelso, J.Rossjohn, P.C.Doherty, S.J.Turner, K.Kedzierska. Acute Emergence and Reversion of Influenza A Virus Quasispecies Within CD8(+) T Cell Antigenic Peptides. Nat Commun V. 4 2663 2013.
ISSN: ESSN 2041-1723
PubMed: 24173108
DOI: 10.1038/NCOMMS3663