Sodium in PDB 5omi: Crystal Structure of GP2 From Lassa Virus in A Post Fusion Conformation

The structure of Crystal Structure of GP2 From Lassa Virus in A Post Fusion Conformation, PDB code: 5omi was solved by A.Shulman, R.Diskin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.52 / 2.56
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	58.318, 103.433, 171.551, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 28.7

The structure of Crystal Structure of GP2 From Lassa Virus in A Post Fusion Conformation also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of GP2 From Lassa Virus in A Post Fusion Conformation (pdb code 5omi). 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 GP2 From Lassa Virus in A Post Fusion Conformation, PDB code: 5omi:

Sodium binding site 1 out of 1 in the Crystal Structure of GP2 From Lassa Virus in A Post Fusion Conformation


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 GP2 From Lassa Virus in A Post Fusion Conformation within 5.0Å range: probe atom residue distance (Å) B Occ C:Na501 b:86.3 occ:1.00 CL A:CL502 3.9 76.2 1.0 O C:MET312 3.9 76.2 1.0 O A:MET312 4.0 71.5 1.0 O B:MET312 4.2 99.9 1.0 CB C:LEU315 4.4 67.9 1.0 N C:PHE316 4.4 87.5 1.0 CB A:LEU315 4.5 77.5 1.0 N A:PHE316 4.6 77.8 1.0 N B:PHE316 4.7 76.4 1.0 CB B:LEU315 4.7 75.6 1.0 CB C:MET312 4.7 75.2 1.0 CA C:PHE316 4.8 73.2 1.0 C C:MET312 4.8 99.7 1.0 CB C:PHE316 4.8 76.2 1.0 CB A:MET312 4.8 72.3 1.0 CA A:PHE316 4.9 71.2 1.0 CA C:MET312 4.9 88.6 1.0 C A:MET312 4.9 86.1 1.0 CB B:MET312 4.9 78.6 1.0 CB B:PHE316 4.9 74.5 1.0 CA B:PHE316 4.9 76.2 1.0 CB A:PHE316 4.9 68.6 1.0 CA A:MET312 4.9 79.5 1.0 C C:LEU315 4.9 83.2 1.0 C B:MET312 5.0 88.4 1.0

A.Shulman, M.Katz, H.Cohen-Dvashi, H.M.Greenblatt, Y.Levy, R.Diskin. Variations in Core Packing of GP2 From Old World Mammarenaviruses in Their Post-Fusion Conformations Affect Membrane-Fusion Efficiencies. J.Mol.Biol. V. 431 2095 2019.
ISSN: ESSN 1089-8638
PubMed: 31004664
DOI: 10.1016/J.JMB.2019.04.012