Sodium in PDB 3dzd: Crystal Structure of SIGMA54 Activator NTRC4 in the Inactive State

The structure of Crystal Structure of SIGMA54 Activator NTRC4 in the Inactive State, PDB code: 3dzd was solved by J.D.Batchelor, M.Doucleff, C.-J.Lee, K.Matsubara, S.De Carlo, J.Heideker, M.M.Lamers, J.G.Pelton, D.E.Wemmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.04 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.897, 93.105, 114.163, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 26.2

The binding sites of Sodium atom in the Crystal Structure of SIGMA54 Activator NTRC4 in the Inactive State (pdb code 3dzd). 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 Crystal Structure of SIGMA54 Activator NTRC4 in the Inactive State, PDB code: 3dzd:

Sodium binding site 1 out of 1 in the Crystal Structure of SIGMA54 Activator NTRC4 in the Inactive State


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 SIGMA54 Activator NTRC4 in the Inactive State within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1 b:45.2 occ:1.00 OG1 B:THR271 3.1 45.5 1.0 OE1 B:GLU231 3.2 78.9 1.0 CD B:GLU231 3.4 83.9 1.0 N B:GLY233 3.4 53.4 1.0 CE B:LYS273 3.5 60.3 1.0 CA B:GLU231 3.5 68.0 1.0 OE2 B:GLU231 3.5 83.8 1.0 C B:GLU231 3.6 69.9 1.0 NZ B:LYS273 3.6 60.7 1.0 CA B:GLY233 3.7 56.0 1.0 CG B:LYS273 3.7 54.4 1.0 CA B:THR271 3.8 41.8 1.0 CB B:THR271 3.8 44.4 1.0 CB B:GLU231 3.9 70.2 1.0 O B:GLU231 3.9 74.8 1.0 N B:ASN272 4.0 45.3 1.0 CD B:LYS273 4.0 60.4 1.0 N B:VAL232 4.0 44.1 1.0 OD1 B:ASN272 4.1 64.4 1.0 N B:GLU234 4.1 64.4 1.0 CG B:GLU231 4.2 80.6 1.0 C B:GLY233 4.2 61.8 1.0 O B:ALA270 4.3 39.0 1.0 C B:THR271 4.4 39.3 1.0 C B:VAL232 4.6 44.7 1.0 CG B:GLU234 4.6 76.7 1.0 N B:LYS273 4.6 42.4 1.0 CB B:LYS273 4.7 48.3 1.0 N B:GLU231 4.8 63.1 1.0 N B:THR271 4.9 39.0 1.0 CA B:VAL232 4.9 39.9 1.0

J.D.Batchelor, M.Doucleff, C.J.Lee, K.Matsubara, S.De Carlo, J.Heideker, M.H.Lamers, J.G.Pelton, D.E.Wemmer. Structure and Regulatory Mechanism of Aquifex Aeolicus NTRC4: Variability and Evolution in Bacterial Transcriptional Regulation. J.Mol.Biol. V. 384 1058 2008.
ISSN: ISSN 0022-2836
PubMed: 18955063
DOI: 10.1016/J.JMB.2008.10.024