Chlorine 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:

Sodium

(Na)

1 atom

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of GP2 From Lassa Virus in A Post Fusion Conformation, PDB code: 5omi:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of GP2 From Lassa Virus in A Post Fusion Conformation


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 A:Cl501 b:63.5 occ:1.00 CG C:GLN348 3.3 72.1 1.0 CG A:GLN348 3.3 81.3 1.0 CG B:GLN348 3.4 70.5 1.0 NE2 A:GLN348 3.4 73.0 1.0 NE2 C:GLN348 3.6 89.4 1.0 NE2 B:GLN348 3.6 89.4 1.0 CD A:GLN348 3.9 77.0 1.0 CE A:MET351 4.0 69.6 1.0 CD C:GLN348 4.0 73.5 1.0 CD B:GLN348 4.0 74.8 1.0 SD A:MET351 4.0 82.5 1.0 SD C:MET351 4.1 91.4 1.0 CB C:GLN348 4.2 67.9 1.0 CB B:GLN348 4.2 67.2 1.0 CB A:GLN348 4.2 84.3 1.0 SD B:MET351 4.2 0.8 1.0 CE C:MET351 4.4 85.8 1.0 CE B:MET351 4.6 95.9 1.0 CA C:GLN348 4.6 73.5 1.0 CA B:GLN348 4.6 85.2 1.0 CA A:GLN348 4.8 83.5 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of GP2 From Lassa Virus in A Post Fusion Conformation


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of GP2 From Lassa Virus in A Post Fusion Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:76.2 occ:1.00 ND2 C:ASN319 3.0 79.3 1.0 ND2 B:ASN319 3.2 71.6 1.0 ND2 A:ASN319 3.3 84.0 1.0 NA C:NA501 3.9 86.3 1.0 CB B:ASN319 3.9 64.5 1.0 CB C:ASN319 4.0 74.7 1.0 CG C:ASN319 4.0 75.0 1.0 CB A:ASN319 4.0 68.0 1.0 CG B:ASN319 4.1 78.0 1.0 CG A:ASN319 4.1 70.0 1.0 CA B:PHE316 4.3 76.2 1.0 CA A:PHE316 4.4 71.2 1.0 CA C:PHE316 4.5 73.2 1.0 O B:LEU315 4.5 82.3 1.0 CD1 A:PHE316 4.6 83.6 1.0 O C:LEU315 4.7 76.9 1.0 O A:LEU315 4.7 82.7 1.0 CD1 B:PHE316 4.8 70.0 1.0 CD1 C:PHE316 4.8 77.1 1.0 N B:PHE316 4.8 76.4 1.0 N A:PHE316 4.9 77.8 1.0 N C:PHE316 4.9 87.5 1.0 C B:LEU315 4.9 79.7 1.0 O B:PHE316 4.9 74.2 1.0 O A:PHE316 5.0 73.7 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