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

Protein crystallography data

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

Other elements in 5omi:

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

Chlorine Binding Sites:

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 5omi

Go back to Chlorine Binding Sites List in 5omi
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 5omi

Go back to Chlorine Binding Sites List in 5omi
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

Reference:

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
Page generated: Sat Dec 12 12:12:55 2020

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