Sodium in PDB 6ljk: Crystal Structure of Human SIRT5 in Complex with An Internally Quenched Fluorescent Substrate Gluiqf

The structure of Crystal Structure of Human SIRT5 in Complex with An Internally Quenched Fluorescent Substrate Gluiqf, PDB code: 6ljk was solved by Q.Chen, Y.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.10 / 1.39
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	33.997, 72.754, 55.876, 90.00, 97.06, 90.00
R / Rfree (%)	12.2 / 15.8

The structure of Crystal Structure of Human SIRT5 in Complex with An Internally Quenched Fluorescent Substrate Gluiqf also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Human SIRT5 in Complex with An Internally Quenched Fluorescent Substrate Gluiqf (pdb code 6ljk). 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 Crystal Structure of Human SIRT5 in Complex with An Internally Quenched Fluorescent Substrate Gluiqf, PDB code: 6ljk:

Sodium binding site 1 out of 1 in the Crystal Structure of Human SIRT5 in Complex with An Internally Quenched Fluorescent Substrate Gluiqf


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human SIRT5 in Complex with An Internally Quenched Fluorescent Substrate Gluiqf within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:9.2 occ:1.00 H A:ALA59 2.4 7.2 1.0 H A:SER251 2.6 11.2 0.3 H A:SER251 2.6 11.3 0.7 HA A:THR250 2.8 10.4 0.7 HA A:THR250 2.8 12.3 0.3 HG A:SER251 2.9 15.9 0.7 O A:HOH694 3.1 18.5 1.0 O A:HOH712 3.1 16.3 1.0 HA3 A:GLY58 3.2 6.8 1.0 O A:HOH742 3.2 13.0 1.0 N A:ALA59 3.3 6.0 1.0 HB3 A:ALA59 3.3 8.4 1.0 N A:SER251 3.4 9.3 0.3 N A:SER251 3.4 9.5 0.7 OG1 A:THR250 3.5 10.4 0.7 OE1 A:GLN140 3.5 15.3 1.0 O A:HOH667 3.6 12.3 1.0 CA A:THR250 3.6 8.7 0.7 HB2 A:ALA59 3.6 8.4 1.0 OG A:SER251 3.7 13.2 0.7 HB2 A:SER251 3.7 11.6 0.3 CA A:THR250 3.7 10.2 0.3 HB A:THR250 3.7 12.3 0.7 CB A:ALA59 3.8 7.0 1.0 CB A:THR250 3.8 10.3 0.7 HB A:THR250 3.8 14.9 0.3 CA A:GLY58 3.9 5.6 1.0 HG1 A:THR250 4.0 12.5 0.7 C A:THR250 4.1 8.5 0.7 C A:THR250 4.1 9.4 0.3 HA2 A:GLY58 4.1 6.8 1.0 C A:GLY58 4.1 5.8 1.0 O A:GLY249 4.1 10.1 1.0 CA A:ALA59 4.2 6.5 1.0 HH11 A:ARG71 4.3 12.7 1.0 HB3 A:SER251 4.3 14.3 0.7 CB A:THR250 4.3 12.5 0.3 H A:GLY60 4.3 7.7 1.0 CB A:SER251 4.3 9.7 0.3 H A:SER252 4.4 10.8 1.0 CB A:SER251 4.4 11.9 0.7 HG22 A:THR250 4.4 13.8 0.3 OG A:SER251 4.4 10.2 0.3 CA A:SER251 4.5 9.1 0.3 CA A:SER251 4.5 10.0 0.7 NH1 A:ARG71 4.7 10.6 1.0 HB1 A:ALA59 4.7 8.4 1.0 CD A:GLN140 4.8 13.1 1.0 N A:THR250 4.8 8.1 0.7 N A:THR250 4.8 9.0 0.3 HD2 A:ARG71 4.8 12.8 1.0 HH12 A:ARG71 4.8 12.7 1.0 HA A:ALA59 4.9 7.8 1.0 O B:HOH201 4.9 31.3 1.0 C A:GLY249 4.9 7.8 1.0 O A:HOH607 4.9 13.4 1.0 CG2 A:THR250 4.9 11.5 0.3 N A:GLY60 5.0 6.4 1.0

L.L.Yang, H.L.Wang, Y.H.Yan, S.Liu, Z.J.Yu, M.Y.Huang, Y.Luo, X.Zheng, Y.Yu, G.B.Li. Sensitive Fluorogenic Substrates For Sirtuin Deacylase Inhibitor Discovery. Eur.J.Med.Chem. V. 192 12201 2020.
ISSN: ISSN 0223-5234
PubMed: 32163813
DOI: 10.1016/J.EJMECH.2020.112201