Atomistry » Sodium » PDB 5llu-5m0e » 5lys
Atomistry »
  Sodium »
    PDB 5llu-5m0e »
      5lys »

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

Protein crystallography data

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

Other elements in 5lys:

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

Sodium Binding Sites:

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 5lys

Go back to Sodium Binding Sites List in 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

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: Tue Dec 15 11:14:29 2020

Last articles

Zn in 7NA9
Zn in 7LZP
Zn in 7M1H
Zn in 7L6V
Zn in 7CM0
V in 7P8R
Ni in 7L19
Na in 7T88
Na in 7MJ5
Na in 7L00
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy