Chlorine 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
Sodium	(Na)	1 atom

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine where determined in the The Native Crystal Structure of 7SK 5'-Hairpin, PDB code: 5lyu:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the The Native Crystal Structure of 7SK 5'-Hairpin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl102 b:74.2 occ:1.00 C4 A:C62 3.5 60.8 1.0 N3 A:C62 3.7 61.2 1.0 O6 A:G64 3.7 53.8 1.0 C5 A:C62 3.7 60.9 1.0 O4' A:U63 3.8 54.4 1.0 N4 A:C62 3.8 60.8 1.0 O A:HOH247 3.8 57.2 1.0 N7 A:G64 3.8 57.0 1.0 C5 A:U40 3.9 56.8 1.0 O A:HOH221 4.0 52.2 1.0 C2 A:C62 4.0 61.3 1.0 O A:HOH226 4.0 42.5 1.0 C6 A:C62 4.1 61.1 1.0 C4' A:U63 4.2 55.4 1.0 C5' A:U63 4.2 57.0 1.0 N1 A:C62 4.2 61.6 1.0 C6 A:G64 4.5 54.5 1.0 C5 A:G64 4.5 56.3 1.0 C6 A:U40 4.6 57.8 1.0 O2 A:C62 4.8 61.6 1.0 C4 A:U40 4.8 56.4 1.0 O4 A:U40 4.9 56.9 1.0 C2' A:C62 5.0 62.1 1.0 C8 A:G64 5.0 56.6 1.0 O5' A:U63 5.0 59.2 1.0

Chlorine binding site 2 out of 2 in the The Native Crystal Structure of 7SK 5'-Hairpin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Native Crystal Structure of 7SK 5'-Hairpin within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl102 b:74.8 occ:1.00 C4 B:C62 3.5 55.0 1.0 O4' B:U63 3.7 52.4 1.0 N3 B:C62 3.7 55.2 1.0 N7 B:G64 3.7 51.5 1.0 C5 B:C62 3.7 54.1 1.0 O6 B:G64 3.8 47.7 1.0 N4 B:C62 3.9 55.0 1.0 O B:HOH208 4.0 39.0 1.0 C2 B:C62 4.0 54.6 1.0 C4' B:U63 4.0 53.5 1.0 C6 B:C62 4.0 54.5 1.0 C5' B:U63 4.1 55.9 1.0 C5 B:U40 4.1 50.0 0.5 C5 B:U40 4.2 46.8 0.5 N1 B:C62 4.2 55.7 1.0 C5 B:G64 4.5 50.8 1.0 C6 B:G64 4.5 48.9 1.0 O2 B:C62 4.7 53.3 1.0 C6 B:U40 4.7 51.2 0.5 C8 B:G64 4.8 52.4 1.0 O5' B:U63 4.8 58.1 1.0 C2' B:C62 4.8 57.5 1.0 C6 B:U40 4.9 47.9 0.5 C1' B:U63 5.0 50.8 1.0 C4 B:U40 5.0 46.1 0.5 C4 B:U40 5.0 49.3 0.5 O4 B:U40 5.0 44.7 0.5

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