Zinc in PDB 5ytk: Crystal Structure of SIRT3 Bound to A Leucylated ACECS2

The structure of Crystal Structure of SIRT3 Bound to A Leucylated ACECS2, PDB code: 5ytk was solved by J.Li, W.Gong, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.80 / 2.70
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	108.906, 108.906, 340.564, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 23.7

The binding sites of Zinc atom in the Crystal Structure of SIRT3 Bound to A Leucylated ACECS2 (pdb code 5ytk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of SIRT3 Bound to A Leucylated ACECS2, PDB code: 5ytk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of SIRT3 Bound to A Leucylated ACECS2


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 SIRT3 Bound to A Leucylated ACECS2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:45.0 occ:1.00 SG A:CYS280 2.6 66.0 1.0 SG A:CYS259 2.6 48.1 1.0 SG A:CYS256 2.6 47.8 1.0 SG A:CYS283 2.7 49.6 1.0 CB A:CYS280 3.0 48.4 1.0 CB A:CYS256 3.4 46.1 1.0 CB A:CYS259 3.4 47.5 1.0 CB A:CYS283 3.7 48.1 1.0 N A:CYS283 3.9 49.8 1.0 N A:CYS259 3.9 45.5 1.0 CA A:CYS259 4.2 46.5 1.0 CA A:CYS283 4.3 48.9 1.0 CA A:CYS280 4.5 49.2 1.0 CB A:VAL282 4.6 51.7 1.0 N A:GLY285 4.7 46.3 1.0 CB A:VAL258 4.8 44.4 1.0 N A:THR284 4.8 48.5 1.0 NH2 A:ARG261 4.8 66.2 1.0 C A:CYS283 4.8 48.2 1.0 C A:CYS259 4.9 46.6 1.0 CA A:CYS256 4.9 45.3 1.0 CB A:ARG261 4.9 51.1 1.0 C A:VAL282 5.0 51.0 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of SIRT3 Bound to A Leucylated ACECS2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of SIRT3 Bound to A Leucylated ACECS2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:45.0 occ:1.00 SG B:CYS259 2.6 40.9 1.0 SG B:CYS280 2.6 36.2 1.0 SG B:CYS283 2.6 36.6 1.0 SG B:CYS256 2.7 36.8 1.0 CB B:CYS280 3.1 35.3 1.0 CB B:CYS259 3.2 34.2 1.0 CB B:CYS256 3.4 34.4 1.0 CB B:CYS283 3.7 33.5 1.0 N B:CYS259 3.8 32.7 1.0 N B:CYS283 3.9 35.0 1.0 CA B:CYS259 4.1 33.5 1.0 CA B:CYS283 4.3 34.0 1.0 CA B:CYS280 4.6 36.2 1.0 N B:GLY285 4.6 32.7 1.0 CB B:VAL282 4.7 44.5 1.0 C B:CYS259 4.7 34.2 1.0 N B:THR284 4.8 33.9 1.0 C B:CYS283 4.8 33.4 1.0 CB B:VAL258 4.8 31.2 1.0 NH2 B:ARG261 4.8 37.4 1.0 CA B:CYS256 4.9 34.1 1.0 C B:VAL258 4.9 31.9 1.0 N B:GLN260 5.0 33.9 1.0 C B:VAL282 5.0 37.5 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of SIRT3 Bound to A Leucylated ACECS2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of SIRT3 Bound to A Leucylated ACECS2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:45.0 occ:1.00 SG C:CYS256 2.6 45.1 1.0 SG C:CYS280 2.6 44.5 1.0 SG C:CYS259 2.6 43.4 1.0 SG C:CYS283 2.7 43.4 1.0 CB C:CYS280 3.1 44.0 1.0 CB C:CYS259 3.3 42.7 1.0 CB C:CYS256 3.3 40.8 1.0 N C:CYS259 3.7 45.8 1.0 CB C:CYS283 3.7 45.0 1.0 N C:CYS283 4.0 46.3 1.0 CA C:CYS259 4.1 41.5 1.0 CA C:CYS283 4.4 46.0 1.0 CA C:CYS280 4.6 44.8 1.0 N C:GLY285 4.6 33.6 1.0 CB C:VAL258 4.6 40.7 1.0 C C:CYS259 4.8 41.1 1.0 CB C:VAL282 4.8 47.3 1.0 CA C:CYS256 4.8 39.8 1.0 NH2 C:ARG261 4.8 52.6 1.0 C C:VAL258 4.8 40.3 1.0 N C:THR284 4.8 45.7 1.0 C C:CYS283 4.8 45.6 1.0 N C:GLN260 5.0 40.2 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of SIRT3 Bound to A Leucylated ACECS2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of SIRT3 Bound to A Leucylated ACECS2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:45.0 occ:1.00 SG D:CYS283 2.6 46.8 1.0 SG D:CYS256 2.6 44.9 1.0 SG D:CYS280 2.6 62.7 1.0 SG D:CYS259 2.7 46.0 1.0 CB D:CYS280 3.1 48.5 1.0 CB D:CYS256 3.4 44.8 1.0 CB D:CYS259 3.4 45.4 1.0 CB D:CYS283 3.7 48.1 1.0 N D:CYS259 3.9 43.9 1.0 N D:CYS283 4.0 49.9 1.0 CA D:CYS259 4.2 44.2 1.0 CA D:CYS283 4.3 49.4 1.0 CA D:CYS280 4.6 50.0 1.0 N D:GLY285 4.7 47.8 1.0 CB D:VAL282 4.7 51.1 1.0 C D:CYS283 4.8 49.4 1.0 N D:THR284 4.8 49.9 1.0 CB D:VAL258 4.8 44.4 1.0 CA D:CYS256 4.8 44.0 1.0 C D:CYS259 4.8 43.8 1.0 NH2 D:ARG261 5.0 48.2 1.0 C D:VAL258 5.0 43.5 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of SIRT3 Bound to A Leucylated ACECS2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of SIRT3 Bound to A Leucylated ACECS2 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn401 b:49.0 occ:1.00 SG E:CYS256 2.6 57.4 1.0 SG E:CYS259 2.6 69.0 1.0 SG E:CYS280 2.6 63.5 1.0 SG E:CYS283 2.7 68.7 1.0 CB E:CYS280 3.1 61.7 1.0 CB E:CYS259 3.2 59.9 1.0 CB E:CYS256 3.4 56.0 1.0 N E:CYS259 3.6 55.4 1.0 CB E:CYS283 3.8 62.7 1.0 CA E:CYS259 4.0 57.3 1.0 N E:CYS283 4.0 66.0 1.0 CA E:CYS283 4.4 64.6 1.0 CA E:CYS280 4.6 63.1 1.0 CB E:VAL258 4.6 53.4 1.0 N E:GLY285 4.6 49.7 1.0 CB E:VAL282 4.7 69.4 1.0 C E:CYS259 4.7 57.0 1.0 C E:VAL258 4.7 53.7 1.0 CA E:CYS256 4.9 53.5 1.0 N E:THR284 4.9 63.5 1.0 C E:CYS283 4.9 63.2 1.0 N E:GLN260 4.9 55.2 1.0 NH2 E:ARG261 4.9 68.2 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of SIRT3 Bound to A Leucylated ACECS2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of SIRT3 Bound to A Leucylated ACECS2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn401 b:45.0 occ:1.00 SG F:CYS259 2.6 43.4 1.0 SG F:CYS280 2.6 46.7 1.0 SG F:CYS283 2.7 48.7 1.0 SG F:CYS256 2.7 41.6 1.0 CB F:CYS280 3.0 45.7 1.0 CB F:CYS259 3.4 43.0 1.0 CB F:CYS256 3.4 41.5 1.0 CB F:CYS283 3.7 50.8 1.0 N F:CYS259 3.9 41.4 1.0 N F:CYS283 3.9 50.6 1.0 CA F:CYS259 4.2 41.9 1.0 CA F:CYS283 4.3 51.3 1.0 CA F:CYS280 4.5 45.7 1.0 CB F:VAL282 4.5 50.4 1.0 N F:GLY285 4.6 47.2 1.0 N F:THR284 4.7 49.7 1.0 CB F:VAL258 4.7 41.1 1.0 C F:CYS283 4.8 50.8 1.0 C F:CYS259 4.8 41.6 1.0 NH2 F:ARG261 4.9 54.9 1.0 CA F:CYS256 4.9 40.7 1.0 C F:VAL282 4.9 52.3 1.0 C F:VAL258 4.9 40.8 1.0

X.D.He, W.Gong, J.N.Zhang, J.Nie, C.F.Yao, F.S.Guo, Y.Lin, X.H.Wu, F.Li, J.Li, W.C.Sun, E.D.Wang, Y.P.An, H.R.Tang, G.Q.Yan, P.Y.Yang, Y.Wei, Y.Z.Mao, P.C.Lin, J.Y.Zhao, Y.Xu, W.Xu, S.M.Zhao. Sensing and Transmitting Intracellular Amino Acid Signals Through Reversible Lysine Aminoacylations Cell Metab. V. 27 151 2018.
ISSN: ESSN 1932-7420
PubMed: 29198988
DOI: 10.1016/J.CMET.2017.10.015