Sodium in PDB 4d79: Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Atp at 1.768 Angstroem Resolution

The structure of Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Atp at 1.768 Angstroem Resolution, PDB code: 4d79 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)	41.128 / 1.77
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 (%)	14.16 / 18.33

The structure of Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Atp at 1.768 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 Atp at 1.768 Angstroem Resolution (pdb code 4d79). 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 Atp at 1.768 Angstroem Resolution, PDB code: 4d79:
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 Atp at 1.768 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 Atp at 1.768 Angstroem Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:23.3 occ:1.00 O B:THR162 2.3 18.2 1.0 O A:THR162 2.4 18.6 1.0 O A:HOH2095 2.4 32.0 1.0 O A:HOH2098 2.5 24.6 1.0 O B:HOH2092 2.5 20.8 1.0 O A:HOH2094 2.6 18.6 1.0 C B:THR162 3.2 20.6 1.0 C A:THR162 3.2 23.1 1.0 CA B:THR162 3.6 18.0 1.0 CA A:THR162 3.6 20.3 1.0 O A:HOH2096 4.0 30.8 1.0 O A:ILE164 4.1 20.1 1.0 CB A:THR162 4.1 20.2 1.0 O B:ILE164 4.1 21.8 1.0 CB B:THR162 4.1 18.1 1.0 N B:GLN163 4.3 18.9 1.0 O A:HOH2097 4.3 35.8 1.0 N A:GLN163 4.3 19.9 1.0 CA B:GLN163 4.7 18.4 1.0 O B:PRO161 4.7 19.6 1.0 N B:ILE164 4.8 17.7 1.0 CA A:GLN163 4.8 18.1 1.0 N A:ILE164 4.8 16.6 1.0 O A:PRO161 4.8 18.1 1.0 C B:GLN163 5.0 17.9 1.0 N B:THR162 5.0 16.4 1.0 N A:THR162 5.0 17.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Atp at 1.768 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 Atp at 1.768 Angstroem Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Na302 b:24.7 occ:0.99 O C:HOH2112 2.2 43.8 1.0 O D:THR162 2.4 23.9 1.0 O D:HOH2075 2.4 23.3 1.0 O C:THR162 2.4 23.7 1.0 O C:HOH2109 2.5 27.0 1.0 O C:HOH2110 2.6 34.2 1.0 O C:HOH2111 2.9 38.2 1.0 C D:THR162 3.2 22.3 1.0 C C:THR162 3.2 24.8 1.0 CA C:THR162 3.6 23.8 1.0 CA D:THR162 3.7 19.5 1.0 CB C:THR162 4.1 25.0 1.0 CB D:THR162 4.2 23.9 1.0 O D:HOH2076 4.2 51.2 1.0 O D:ILE164 4.2 22.9 1.0 N D:GLN163 4.3 21.6 1.0 O C:ILE164 4.3 25.4 1.0 N C:GLN163 4.3 21.7 1.0 CA D:GLN163 4.7 22.8 1.0 N D:ILE164 4.8 20.7 1.0 CA C:GLN163 4.8 19.7 1.0 O D:PRO161 4.9 26.4 1.0 O C:PRO161 4.9 28.0 1.0 N C:ILE164 4.9 21.6 1.0 N C:THR162 5.0 22.9 1.0 OG1 C:THR162 5.0 24.0 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