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

Protein crystallography data

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

Other elements in 5lyu:

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

Chlorine Binding Sites:

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 5lyu

Go back to Chlorine Binding Sites List in 5lyu
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 5lyu

Go back to Chlorine Binding Sites List in 5lyu
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

Reference:

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
Page generated: Sat Dec 12 12:04:42 2020

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