Sodium in PDB 5cxb: Structure of YTM1 Bound to the C-Terminal Domain of ERB1 in P21 21 2 Space Group

The structure of Structure of YTM1 Bound to the C-Terminal Domain of ERB1 in P21 21 2 Space Group, PDB code: 5cxb was solved by M.Wegrecki, J.Bravo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.53 / 2.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	86.443, 108.149, 108.618, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 21.3

The structure of Structure of YTM1 Bound to the C-Terminal Domain of ERB1 in P21 21 2 Space Group also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Structure of YTM1 Bound to the C-Terminal Domain of ERB1 in P21 21 2 Space Group (pdb code 5cxb). 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 Structure of YTM1 Bound to the C-Terminal Domain of ERB1 in P21 21 2 Space Group, PDB code: 5cxb:

Sodium binding site 1 out of 1 in the Structure of YTM1 Bound to the C-Terminal Domain of ERB1 in P21 21 2 Space Group


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of YTM1 Bound to the C-Terminal Domain of ERB1 in P21 21 2 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:54.8 occ:1.00 O A:HOH829 2.4 57.7 1.0 OE1 A:GLU442 2.5 47.3 1.0 N A:ARG443 3.1 42.4 1.0 NH1 A:ARG454 3.2 0.3 1.0 CE3 A:TRP446 3.6 57.4 1.0 CA A:GLU442 3.6 40.1 1.0 CB A:GLU442 3.7 39.8 1.0 CD A:GLU442 3.7 52.6 1.0 CB A:ARG443 3.7 44.2 1.0 O A:GLY411 3.8 37.7 1.0 C A:GLU442 3.9 42.2 1.0 CA A:ARG443 3.9 43.0 1.0 CG2 A:THR412 4.0 31.6 1.0 CZ3 A:TRP446 4.2 61.6 1.0 C A:GLY411 4.2 37.6 1.0 CG A:GLU442 4.3 44.1 1.0 CD2 A:TRP446 4.3 51.1 1.0 O A:ARG443 4.3 43.3 1.0 CZ A:ARG454 4.5 97.5 1.0 CG A:ARG454 4.6 89.3 1.0 CB A:TRP446 4.6 47.3 1.0 C A:ARG443 4.6 39.1 1.0 CD A:ARG454 4.7 98.8 1.0 OE2 A:GLU442 4.7 53.7 1.0 CG A:TRP446 4.8 52.5 1.0 N A:THR412 4.8 31.1 1.0 CA A:GLY411 4.8 33.3 1.0 CA A:THR412 4.9 28.6 1.0 O A:ASP410 5.0 37.1 1.0

M.Wegrecki, O.Rodriguez-Galan, J.De La Cruz, J.Bravo. The Structure of ERB1-YTM1 Complex Reveals the Functional Importance of A High-Affinity Binding Between Two Beta-Propellers During the Assembly of Large Ribosomal Subunits in Eukaryotes. Nucleic Acids Res. V. 43 11017 2015.
ISSN: ESSN 1362-4962
PubMed: 26476442
DOI: 10.1093/NAR/GKV1043