Sodium in PDB 3tnd: Crystal Structure of Shigella Flexneri Vapbc Toxin-Antitoxin Complex

The structure of Crystal Structure of Shigella Flexneri Vapbc Toxin-Antitoxin Complex, PDB code: 3tnd was solved by C.Dienemann, A.Boggild, K.S.Winther, K.Gerdes, D.E.Brodersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.62 / 2.70
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	91.403, 91.403, 549.090, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 23.8

The binding sites of Sodium atom in the Crystal Structure of Shigella Flexneri Vapbc Toxin-Antitoxin Complex (pdb code 3tnd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Shigella Flexneri Vapbc Toxin-Antitoxin Complex, PDB code: 3tnd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Shigella Flexneri Vapbc Toxin-Antitoxin Complex


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 Shigella Flexneri Vapbc Toxin-Antitoxin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na82 b:56.6 occ:1.00 O B:HOH121 2.8 77.2 1.0 O A:HOH171 3.2 69.8 1.0 O B:HOH120 3.3 71.8 1.0 O A:HOH138 3.5 57.5 1.0 NH1 B:ARG64 4.0 44.0 1.0 NE2 B:GLN66 4.0 43.8 1.0 O B:HOH109 4.1 52.0 1.0 O B:HOH122 4.1 64.1 1.0 CD B:ARG64 4.4 43.3 1.0 OD1 A:ASN9 4.5 68.8 1.0 ND2 A:ASN9 4.6 60.8 1.0 OD2 A:ASP98 4.8 59.0 1.0 CZ B:ARG64 4.9 44.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Shigella Flexneri Vapbc Toxin-Antitoxin Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Shigella Flexneri Vapbc Toxin-Antitoxin Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Na82 b:79.0 occ:1.00 O D:HOH124 3.0 73.9 1.0 O C:HOH149 3.1 91.2 1.0 O D:HOH108 3.4 58.2 1.0 NE2 D:GLN66 3.6 60.7 1.0 O D:HOH93 3.9 65.5 1.0 CB D:GLN66 4.4 66.7 1.0 O C:HOH139 4.7 47.8 1.0 CD D:GLN66 4.8 54.0 1.0 NH1 D:ARG64 4.8 63.3 1.0 CB D:ARG64 4.9 66.9 1.0 O D:GLN66 4.9 81.7 1.0

C.Dienemann, A.Boggild, K.S.Winther, K.Gerdes, D.E.Brodersen. Crystal Structure of the Vapbc Toxin-Antitoxin Complex From Shigella Flexneri Reveals A Hetero-Octameric Dna-Binding Assembly. J.Mol.Biol. V. 414 713 2011.
ISSN: ISSN 0022-2836
PubMed: 22037005
DOI: 10.1016/J.JMB.2011.10.024