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

Protein crystallography data

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

Other elements in 6ljk:

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

Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Human SIRT5 in Complex with An Internally Quenched Fluorescent Substrate Gluiqf, PDB code: 6ljk:

Zinc binding site 1 out of 1 in 6ljk

Go back to Zinc Binding Sites List in 6ljk
Zinc 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 Zinc with other atoms in the Zn 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:Zn401

b:11.0
occ:1.00
SG A:CYS169 2.3 11.3 1.0
SG A:CYS212 2.3 11.3 1.0
SG A:CYS207 2.4 10.7 1.0
SG A:CYS166 2.4 10.2 1.0
HB2 A:CYS207 3.0 12.6 1.0
HB3 A:CYS169 3.0 14.8 1.0
H A:CYS169 3.1 14.3 1.0
CB A:CYS207 3.1 10.5 1.0
HB3 A:CYS207 3.1 12.6 1.0
HB2 A:CYS166 3.1 11.4 1.0
CB A:CYS166 3.1 9.5 1.0
HB3 A:CYS166 3.1 11.4 1.0
HB3 A:CYS212 3.2 13.5 1.0
CB A:CYS169 3.2 12.3 1.0
CB A:CYS212 3.3 11.2 1.0
HB2 A:CYS212 3.5 13.5 1.0
HG12 A:VAL171 3.5 22.2 1.0
N A:CYS169 3.7 11.9 1.0
H A:GLY214 3.7 15.1 1.0
HB3 A:SER168 3.8 15.9 0.7
HB2 A:SER168 3.8 13.4 0.3
HB2 A:GLU209 3.9 16.8 1.0
HB2 A:CYS169 4.0 14.8 1.0
CA A:CYS169 4.0 12.6 1.0
HA3 A:GLY214 4.2 13.8 1.0
HG11 A:VAL171 4.3 22.2 1.0
O A:HOH835 4.3 24.8 1.0
CG1 A:VAL171 4.3 18.5 1.0
HG3 A:GLU209 4.3 19.9 1.0
H A:SER168 4.4 13.3 0.3
H A:SER168 4.4 13.5 0.7
H A:VAL171 4.5 15.2 1.0
N A:GLY214 4.5 12.5 1.0
CA A:CYS207 4.5 10.5 1.0
H A:GLY170 4.6 14.6 1.0
CA A:CYS166 4.6 8.8 1.0
CA A:CYS212 4.7 10.7 1.0
H A:GLY213 4.7 17.3 1.0
CB A:SER168 4.7 13.2 0.7
CB A:SER168 4.7 11.2 0.3
HG2 A:GLU209 4.7 19.9 1.0
H A:GLU209 4.7 14.5 1.0
CB A:GLU209 4.8 14.0 1.0
C A:SER168 4.8 12.8 0.7
C A:SER168 4.8 11.9 0.3
C A:CYS169 4.8 13.3 1.0
HA A:CYS207 4.8 12.6 1.0
CG A:GLU209 4.8 16.6 1.0
HA A:CYS169 4.8 15.1 1.0
HG13 A:VAL171 4.8 22.2 1.0
CA A:GLY214 4.9 11.5 1.0
O A:HOH832 4.9 14.1 1.0
HB3 A:SER168 4.9 13.4 0.3
HA A:CYS166 4.9 10.5 1.0
HD21 A:LEU216 4.9 11.9 1.0
N A:GLY170 4.9 12.2 1.0
N A:GLY213 5.0 14.4 1.0
HA A:CYS212 5.0 12.9 1.0

Reference:

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
Page generated: Mon Jan 25 16:32:55 2021

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