Sodium in PDB 5lyu: The Native Crystal Structure of 7SK 5'-Hairpin

The structure of The Native Crystal Structure of 7SK 5'-Hairpin, PDB code: 5lyu was solved by D.Martinez-Zapien, P.Legrand, A.C.Mcewen, S.Pasquali, A.-C.Dock-Bregeon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.32 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.790, 47.780, 68.670, 90.00, 99.05, 90.00
R / Rfree (%)	19.1 / 24

The structure of The Native Crystal Structure of 7SK 5'-Hairpin also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the The Native Crystal Structure of 7SK 5'-Hairpin (pdb code 5lyu). 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 The Native Crystal Structure of 7SK 5'-Hairpin, PDB code: 5lyu:

Sodium binding site 1 out of 1 in the The Native Crystal Structure of 7SK 5'-Hairpin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Native Crystal Structure of 7SK 5'-Hairpin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:57.9 occ:1.00 OP1 A:A34 2.3 44.3 0.4 O A:HOH288 2.5 52.8 1.0 O A:HOH297 2.6 55.6 1.0 OP2 A:A34 2.8 46.2 0.6 O A:HOH230 2.8 48.8 1.0 O A:HOH233 2.9 42.5 1.0 P A:A34 3.4 42.0 0.4 O A:HOH263 3.6 54.9 1.0 OP2 A:A34 3.7 42.3 0.4 N7 A:A34 3.7 41.0 0.4 N7 A:A34 3.8 43.5 0.6 C5 A:A34 3.8 43.9 0.6 P A:A34 3.8 44.5 0.6 C5 A:A34 3.9 41.1 0.4 OP1 A:A34 4.1 43.7 0.6 O A:HOH203 4.1 37.1 1.0 C6 A:A34 4.1 44.6 0.6 O5' A:A34 4.2 40.7 0.4 C8 A:A34 4.2 43.1 0.6 C8 A:A34 4.2 40.5 0.4 C6 A:A34 4.3 41.6 0.4 C4 A:A34 4.3 43.4 0.6 N6 A:A34 4.4 42.8 0.4 N6 A:A34 4.4 46.0 0.6 O A:HOH231 4.4 41.7 1.0 O5' A:A34 4.4 42.7 0.6 O A:HOH251 4.5 44.2 1.0 N9 A:A34 4.5 43.0 0.6 C4 A:A34 4.6 40.6 0.4 O A:HOH282 4.6 63.0 1.0 O3' A:C33 4.7 41.1 0.4 O A:HOH222 4.7 83.1 1.0 N9 A:A34 4.7 40.5 0.4 N1 A:A34 4.8 44.2 0.6 O B:HOH247 4.9 65.4 1.0 O4' A:A34 4.9 42.9 0.6 N3 A:A34 5.0 43.2 0.6

D.Martinez-Zapien, P.Legrand, A.G.Mcewen, F.Proux, T.Cragnolini, S.Pasquali, A.C.Dock-Bregeon. The Crystal Structure of the 5 Functional Domain of the Transcription Riboregulator 7SK. Nucleic Acids Res. V. 45 3568 2017.
ISSN: ESSN 1362-4962
PubMed: 28082395
DOI: 10.1093/NAR/GKW1351