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Zinc in PDB 5yqm: Crystal Structure of SIRT2 in Complex with Selective Inhibitor A29

Protein crystallography data

The structure of Crystal Structure of SIRT2 in Complex with Selective Inhibitor A29, PDB code: 5yqm was solved by H.Wang, Y.Yu, G.Li, Q.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.51 / 1.74
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.748, 73.952, 55.947, 90.00, 94.96, 90.00
R / Rfree (%) 18.3 / 22

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of SIRT2 in Complex with Selective Inhibitor A29 (pdb code 5yqm). 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 SIRT2 in Complex with Selective Inhibitor A29, PDB code: 5yqm:

Zinc binding site 1 out of 1 in 5yqm

Go back to Zinc Binding Sites List in 5yqm
Zinc binding site 1 out of 1 in the Crystal Structure of SIRT2 in Complex with Selective Inhibitor A29


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 SIRT2 in Complex with Selective Inhibitor A29 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:15.3
occ:1.00
SG A:CYS200 2.3 15.3 1.0
SG A:CYS224 2.3 14.7 1.0
SG A:CYS221 2.3 15.4 1.0
SG A:CYS195 2.3 14.9 1.0
HB3 A:CYS200 2.9 12.3 1.0
HB3 A:CYS221 3.0 18.0 1.0
HB2 A:CYS195 3.0 15.0 1.0
H A:CYS224 3.1 23.3 1.0
CB A:CYS221 3.1 15.0 1.0
CB A:CYS200 3.1 10.2 1.0
HB2 A:CYS221 3.1 18.0 1.0
CB A:CYS195 3.2 12.5 1.0
HB3 A:CYS195 3.4 15.0 1.0
HB3 A:CYS224 3.4 29.3 1.0
HB2 A:CYS200 3.4 12.3 1.0
CB A:CYS224 3.5 24.4 1.0
HB2 A:ASP223 3.5 24.1 1.0
HB2 A:SER197 3.8 24.9 0.7
N A:CYS224 3.8 19.4 1.0
HB2 A:SER226 3.8 19.9 1.0
H A:HIS202 3.9 18.5 1.0
HB3 A:SER197 3.9 24.7 0.3
HB3 A:HIS202 4.0 25.4 1.0
HB2 A:HIS202 4.0 25.4 1.0
H A:SER226 4.1 20.0 1.0
CA A:CYS224 4.2 20.7 1.0
HB2 A:CYS224 4.2 29.3 1.0
H A:ARG201 4.3 12.8 1.0
CB A:HIS202 4.4 21.2 1.0
CB A:ASP223 4.5 20.0 1.0
HH A:TYR204 4.5 25.9 1.0
CA A:CYS221 4.5 17.7 1.0
CA A:CYS200 4.6 13.6 1.0
H A:ASP223 4.6 21.8 1.0
CA A:CYS195 4.6 14.9 1.0
HB3 A:ASP223 4.7 24.1 1.0
HB2 A:SER197 4.7 24.7 0.3
CB A:SER197 4.7 20.7 0.7
N A:ARG201 4.7 10.7 1.0
H A:SER197 4.7 20.2 0.3
H A:SER197 4.7 20.2 0.7
N A:HIS202 4.7 15.4 1.0
H A:GLN225 4.7 17.0 1.0
O A:HOH775 4.7 22.7 1.0
CB A:SER226 4.7 16.6 1.0
CB A:SER197 4.8 20.6 0.3
HG A:SER197 4.8 34.6 0.7
HG A:SER226 4.8 25.2 1.0
C A:CYS224 4.8 20.1 1.0
HA A:CYS195 4.8 17.8 1.0
C A:ASP223 4.8 19.4 1.0
HA A:CYS221 4.9 21.2 1.0
C A:CYS200 4.9 10.8 1.0
N A:SER226 4.9 16.7 1.0
N A:GLN225 5.0 14.2 1.0
HA A:CYS200 5.0 16.3 1.0
HA A:CYS224 5.0 24.8 1.0

Reference:

L.L.Yang, H.L.Wang, L.Zhong, C.Yuan, S.Y.Liu, Z.J.Yu, S.Liu, Y.H.Yan, C.Wu, Y.Wang, Z.Wang, Y.Yu, Q.Chen, G.B.Li. X-Ray Crystal Structure Guided Discovery of New Selective, Substrate-Mimicking Sirtuin 2 Inhibitors That Exhibit Activities Against Non-Small Cell Lung Cancer Cells. Eur J Med Chem V. 155 806 2018.
ISSN: ISSN 1768-3254
PubMed: 29957526
DOI: 10.1016/J.EJMECH.2018.06.041
Page generated: Wed Dec 16 11:24:23 2020

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