Zinc in PDB 6ljm: Crystal Structure of Human SIRT5 in Complex with the Fluorogenic Tetrapeptide Substrate P13

Protein crystallography data

The structure of Crystal Structure of Human SIRT5 in Complex with the Fluorogenic Tetrapeptide Substrate P13, PDB code: 6ljm 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) 41.34 / 1.78
Space group P 21 2 21
Cell size a, b, c (Å), α, β, γ (°) 42.200, 55.275, 124.524, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 19.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human SIRT5 in Complex with the Fluorogenic Tetrapeptide Substrate P13 (pdb code 6ljm). 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 the Fluorogenic Tetrapeptide Substrate P13, PDB code: 6ljm:

Zinc binding site 1 out of 1 in 6ljm

Go back to Zinc Binding Sites List in 6ljm
Zinc binding site 1 out of 1 in the Crystal Structure of Human SIRT5 in Complex with the Fluorogenic Tetrapeptide Substrate P13


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 the Fluorogenic Tetrapeptide Substrate P13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:16.8
occ:1.00
SG A:CYS169 2.3 17.4 1.0
SG A:CYS166 2.3 14.6 1.0
SG A:CYS212 2.3 17.5 1.0
SG A:CYS207 2.4 16.1 1.0
HB2 A:CYS166 3.0 13.6 1.0
HB2 A:CYS207 3.0 23.6 1.0
HB3 A:CYS169 3.0 25.5 1.0
CB A:CYS166 3.0 11.3 1.0
HB3 A:CYS166 3.0 13.6 1.0
HB3 A:CYS212 3.0 22.4 1.0
HB3 A:CYS207 3.0 23.6 1.0
CB A:CYS207 3.0 19.6 1.0
H A:CYS169 3.1 20.6 1.0
CB A:CYS212 3.1 18.6 1.0
CB A:CYS169 3.2 21.2 1.0
HB2 A:CYS212 3.3 22.4 1.0
H A:GLY214 3.7 20.9 1.0
N A:CYS169 3.7 17.2 1.0
HB2 A:SER168 3.9 30.1 1.0
HB2 A:GLU209 3.9 21.9 1.0
HB2 A:CYS169 4.0 25.5 1.0
CA A:CYS169 4.1 20.0 1.0
HG3 A:GLU209 4.2 27.0 1.0
HA3 A:GLY214 4.3 25.6 1.0
HB A:VAL171 4.4 17.0 1.0
H A:VAL171 4.4 16.7 1.0
H A:SER168 4.4 18.3 1.0
HG2 A:GLU209 4.5 27.0 1.0
N A:GLY214 4.5 17.4 1.0
CA A:CYS166 4.5 14.2 1.0
CA A:CYS207 4.5 14.3 1.0
CA A:CYS212 4.6 16.7 1.0
CG A:GLU209 4.7 22.5 1.0
H A:GLY170 4.7 16.5 1.0
H A:GLY213 4.7 31.9 1.0
CB A:GLU209 4.7 18.2 1.0
CB A:SER168 4.7 25.1 1.0
H A:GLU209 4.8 20.7 1.0
HA A:CYS166 4.8 17.1 1.0
C A:CYS169 4.8 23.0 1.0
HG23 A:VAL171 4.8 36.3 1.0
HA A:CYS169 4.8 24.0 1.0
HA A:CYS207 4.9 17.2 1.0
HA A:CYS212 4.9 20.0 1.0
C A:SER168 4.9 21.5 1.0
HD21 A:LEU216 4.9 16.8 1.0
CA A:GLY214 4.9 21.3 1.0
N A:GLY213 4.9 26.6 1.0
C A:CYS212 4.9 25.3 1.0
N A:GLY170 5.0 13.7 1.0
HB3 A:SER168 5.0 30.1 1.0
O A:HOH755 5.0 15.9 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: Wed Dec 16 12:16:00 2020

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