Sodium in PDB 4d7a: Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Amp at 1.801 Angstroem Resolution

The structure of Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Amp at 1.801 Angstroem Resolution, PDB code: 4d7a was solved by M.Lopez-Estepa, A.Arda, M.Savko, A.Round, W.Shepard, M.Bruix, M.Coll, F.J.Fernandez, J.Jimenez-Barbero, M.C.Vega, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.138 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.690, 97.160, 83.190, 90.00, 111.61, 90.00
R / Rfree (%)	13.92 / 17.66

The structure of Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Amp at 1.801 Angstroem Resolution also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Amp at 1.801 Angstroem Resolution (pdb code 4d7a). 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 E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Amp at 1.801 Angstroem Resolution, PDB code: 4d7a:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Amp at 1.801 Angstroem Resolution


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 E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Amp at 1.801 Angstroem Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:22.3 occ:0.96 O B:THR162 2.3 16.0 1.0 O A:HOH2125 2.4 36.2 1.0 O A:THR162 2.4 16.6 1.0 O A:HOH2126 2.4 24.0 1.0 O B:HOH2122 2.5 21.2 1.0 O A:HOH2122 2.5 18.1 1.0 C B:THR162 3.2 14.3 1.0 C A:THR162 3.3 16.8 1.0 CA B:THR162 3.6 13.6 1.0 CA A:THR162 3.7 13.0 1.0 O A:HOH2124 3.9 29.4 1.0 O A:ILE164 4.0 18.0 1.0 CB B:THR162 4.1 15.1 1.0 CB A:THR162 4.2 14.7 1.0 O B:ILE164 4.2 17.8 1.0 N A:GLN163 4.3 15.0 1.0 O A:HOH2123 4.3 26.2 1.0 N B:GLN163 4.3 12.8 1.0 O D:HOH2040 4.6 45.5 1.0 N A:ILE164 4.7 12.8 1.0 CA A:GLN163 4.7 15.9 1.0 CA B:GLN163 4.7 13.0 1.0 O B:PRO161 4.8 16.8 1.0 O A:HOH2127 4.8 40.4 1.0 O A:PRO161 4.8 16.6 1.0 O B:HOH2123 4.8 44.4 1.0 N B:ILE164 4.8 13.2 1.0 C A:GLN163 4.9 16.9 1.0 N B:THR162 5.0 13.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Amp at 1.801 Angstroem Resolution


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 E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Amp at 1.801 Angstroem Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Na302 b:26.0 occ:1.00 O C:THR162 2.4 29.2 1.0 O C:HOH2150 2.5 37.6 1.0 O D:THR162 2.5 27.9 1.0 O C:HOH2148 2.5 38.6 1.0 O C:HOH2180 2.6 26.4 1.0 O C:HOH2147 2.6 27.3 1.0 C C:THR162 3.3 34.1 1.0 C D:THR162 3.4 25.6 1.0 CA C:THR162 3.8 24.2 1.0 CA D:THR162 3.9 17.2 1.0 CB C:THR162 4.1 26.1 1.0 CB D:THR162 4.3 24.9 1.0 O C:ILE164 4.4 27.4 1.0 N C:GLN163 4.4 25.0 1.0 O D:ILE164 4.4 29.4 1.0 N D:GLN163 4.5 22.2 1.0 CA C:GLN163 4.8 23.0 1.0 CA D:GLN163 4.8 22.4 1.0 N C:ILE164 4.9 23.6 1.0 O C:HOH2149 4.9 44.8 1.0 N D:ILE164 5.0 23.6 1.0

M.Lopez-Estepa, A.Arda, M.Savko, A.Round, W.E.Shepard, M.Bruix, M.Coll, F.J.Fernandez, J.Jimenez-Barbero, M.C.Vega. The Crystal Structure and Small-Angle X-Ray Analysis of Csdl/Tcda Reveal A New Trna Binding Motif in the Moeb/E1 Superfamily. Plos One V. 10 18606 2015.
ISSN: ISSN 1932-6203
PubMed: 25897750
DOI: 10.1371/JOURNAL.PONE.0118606