Sodium in PDB 5lys: The Crystal Structure of 7SK 5'-Hairpin - Gold Derivative

The structure of The Crystal Structure of 7SK 5'-Hairpin - Gold Derivative, PDB code: 5lys was solved by D.Martinez-Zapien, P.Legrand, A.G.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)	40.00 / 2.32
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.320, 47.830, 69.230, 90.00, 105.54, 90.00
R / Rfree (%)	18.5 / 22.7

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

Gold	(Au)	2 atoms
Magnesium	(Mg)	1 atom

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

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of 7SK 5'-Hairpin - Gold Derivative within 5.0Å range: probe atom residue distance (Å) B Occ B:Na103 b:66.6 occ:1.00 OP2 B:G64 2.6 51.5 1.0 OP2 B:A65 2.6 46.6 1.0 O B:HOH234 2.8 38.5 1.0 O B:HOH263 3.2 60.9 1.0 O3' B:U63 3.4 51.7 1.0 P B:G64 3.6 52.0 1.0 O2' B:U63 3.7 48.5 1.0 P B:A65 4.1 47.2 1.0 O5' B:G64 4.4 50.9 1.0 C2' B:U63 4.4 48.2 1.0 C3' B:U63 4.5 51.0 1.0 C1' B:U63 4.5 46.4 1.0 O B:HOH275 4.5 41.6 1.0 N7 B:A65 4.6 35.4 1.0 C3' B:G64 4.7 47.8 1.0 O2 B:U63 4.8 42.4 1.0 O5' B:A65 4.8 46.7 1.0 O3' B:G64 4.8 48.0 1.0 O4 B:U66 4.8 34.2 1.0 O B:HOH220 4.9 36.3 1.0 OP1 B:G64 4.9 53.0 1.0 C8 B:A65 4.9 37.1 1.0

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