Sodium in PDB 4gbt: Structural Characterization of H-1 Parvovirus: Comparison of Infectious Virions to Replication Defective Particles

The structure of Structural Characterization of H-1 Parvovirus: Comparison of Infectious Virions to Replication Defective Particles, PDB code: 4gbt was solved by S.Halder, H.-J.Nam, L.Govindasamy, M.Vogel, C.Dinsart, N.Salome, R.Mckenna, M.Agbandje-Mckenna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 3.20
Space group	P 1 21 1 1
Cell size a, b, c (Å), α, β, γ (°)	255.200, 350.100, 272.100, 90.00, 90.12, 90.00
R / Rfree (%)	25.6 / 25.9

The structure of Structural Characterization of H-1 Parvovirus: Comparison of Infectious Virions to Replication Defective Particles also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Structural Characterization of H-1 Parvovirus: Comparison of Infectious Virions to Replication Defective Particles (pdb code 4gbt). 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 Structural Characterization of H-1 Parvovirus: Comparison of Infectious Virions to Replication Defective Particles, PDB code: 4gbt:

Sodium binding site 1 out of 1 in the Structural Characterization of H-1 Parvovirus: Comparison of Infectious Virions to Replication Defective Particles


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Characterization of H-1 Parvovirus: Comparison of Infectious Virions to Replication Defective Particles within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:28.5 occ:1.00 CB A:HIS374 3.1 75.0 1.0 N A:HIS374 3.1 77.1 1.0 N A:ASP375 3.1 75.4 1.0 CA A:HIS374 3.4 75.4 1.0 OD2 A:ASP375 3.5 86.9 1.0 C A:HIS374 3.8 75.0 1.0 CG A:ASP375 3.8 84.5 1.0 CG A:HIS374 4.0 74.0 1.0 C A:ASP373 4.0 78.5 1.0 CB A:ASP375 4.1 79.8 1.0 CD2 A:HIS374 4.2 74.3 1.0 CA A:ASP375 4.2 74.8 1.0 CA A:ASP373 4.4 80.0 1.0 OD1 A:ASP375 4.5 87.1 1.0 O A:GLU372 4.5 79.3 1.0 O A:ASP373 4.9 78.3 1.0

S.Halder, H.J.Nam, L.Govindasamy, M.Vogel, C.Dinsart, N.Salome, R.Mckenna, M.Agbandje-Mckenna. Structural Characterization of H-1 Parvovirus: Comparison of Infectious Virions to Empty Capsids. J.Virol. V. 87 5128 2013.
ISSN: ISSN 0022-538X
PubMed: 23449783
DOI: 10.1128/JVI.03416-12