Sodium in PDB 4g0r: 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: 4g0r was solved by S.Halder, M.Agbandje-Mckenna, H.-J.Nam, L.Govindasamy, M.Vogel, C.Dinsart, N.Salome, R.Mckenna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	255.400, 350.400, 271.600, 90.00, 90.34, 90.00
R / Rfree (%)	21.6 / 21.7

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

Magnesium	(Mg)	2 atoms
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 4g0r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structural Characterization of H-1 Parvovirus: Comparison of Infectious Virions to Replication Defective Particles, PDB code: 4g0r:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 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:Na605 b:19.8 occ:1.00 O A:HOH756 3.2 28.2 1.0 O1 A:EDO601 3.3 45.2 1.0 N A:ARG299 3.3 24.6 1.0 CA A:PRO298 3.8 23.9 1.0 CG A:ARG319 3.9 32.0 1.0 C A:PRO298 4.0 23.6 1.0 C1 A:EDO601 4.1 47.2 1.0 CB A:PRO298 4.1 23.3 1.0 CB A:ARG299 4.2 28.0 1.0 CD A:ARG319 4.2 33.6 1.0 CA A:ARG299 4.3 26.6 1.0 O A:PHE320 4.5 26.7 1.0 O A:ARG299 4.7 26.9 1.0 N A:PHE320 5.0 28.4 1.0

Sodium binding site 2 out of 2 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 2 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:Na607 b:25.8 occ:1.00 OD1 A:ASP367 2.8 31.6 1.0 O A:ASP408 2.9 34.4 1.0 O A:ILE407 3.1 32.1 1.0 O A:ALA406 3.2 28.5 1.0 O A:HOH803 3.3 33.0 1.0 C A:ILE407 3.6 31.5 1.0 C A:ASP408 3.7 33.0 1.0 CG A:ASP367 3.7 30.9 1.0 CB A:SER409 4.1 33.7 1.0 CA A:SER409 4.1 33.5 1.0 N A:SER409 4.2 32.0 1.0 N A:ASP408 4.3 32.5 1.0 CA A:ILE407 4.3 30.1 1.0 C A:ALA406 4.3 28.6 1.0 OD2 A:ASP367 4.4 33.0 1.0 CB A:ASP367 4.4 28.4 1.0 CA A:ASP408 4.6 32.6 1.0 CA A:ASP367 4.7 27.7 1.0 N A:ILE407 4.8 29.1 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