Zinc in PDB 8gbl: Structure of Apo Human SIRT5

The structure of Structure of Apo Human SIRT5, PDB code: 8gbl was solved by E.M.Petrunak, J.A.Stuckey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.62 / 2.24
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.624, 112.528, 56.083, 90, 90.03, 90
R / Rfree (%)	21.5 / 25.6

The binding sites of Zinc atom in the Structure of Apo Human SIRT5 (pdb code 8gbl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Apo Human SIRT5, PDB code: 8gbl:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Apo Human SIRT5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Apo Human SIRT5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn600 b:21.9 occ:1.00 SG A:CYS169 2.2 24.9 1.0 SG A:CYS207 2.3 20.3 1.0 SG A:CYS166 2.3 20.6 1.0 SG A:CYS212 2.4 28.8 1.0 CB A:CYS166 3.0 17.2 1.0 CB A:CYS207 3.1 16.2 1.0 CB A:CYS169 3.2 21.6 1.0 CB A:CYS212 3.4 25.0 1.0 N A:CYS169 3.7 20.8 1.0 CA A:CYS169 4.0 21.1 1.0 N A:GLY214 4.5 22.5 1.0 CA A:CYS166 4.5 16.5 1.0 CA A:CYS207 4.5 17.3 1.0 CB A:GLU209 4.5 24.4 1.0 CG A:GLU209 4.6 32.7 1.0 CB A:SER168 4.7 26.5 1.0 CA A:CYS212 4.8 25.2 1.0 C A:CYS169 4.8 25.8 1.0 C A:SER168 4.8 24.5 1.0 CA A:GLY214 4.8 21.1 1.0 N A:GLY213 4.9 27.8 1.0 N A:GLY170 5.0 23.2 1.0 O A:HOH762 5.0 15.1 1.0

Zinc binding site 2 out of 2 in the Structure of Apo Human SIRT5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Apo Human SIRT5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn600 b:22.0 occ:1.00 SG B:CYS169 2.3 24.7 1.0 SG B:CYS212 2.3 27.3 1.0 SG B:CYS207 2.3 22.3 1.0 SG B:CYS166 2.3 23.4 1.0 CB B:CYS166 3.1 19.1 1.0 CB B:CYS207 3.1 17.7 1.0 CB B:CYS169 3.2 22.2 1.0 CB B:CYS212 3.3 24.3 1.0 N B:CYS169 3.7 24.1 1.0 CA B:CYS169 4.0 23.9 1.0 N B:GLY214 4.5 23.8 1.0 CB B:GLU209 4.5 27.9 1.0 CA B:CYS166 4.6 19.2 1.0 CG B:GLU209 4.6 35.5 1.0 CA B:CYS207 4.6 17.3 1.0 CB B:SER168 4.7 28.1 1.0 CA B:CYS212 4.7 25.7 1.0 C B:CYS169 4.8 29.3 1.0 C B:SER168 4.8 27.0 1.0 CA B:GLY214 4.8 22.6 1.0 N B:GLY213 4.9 29.5 1.0 N B:GLY170 4.9 26.2 1.0 O B:HOH751 5.0 20.9 1.0

T.Yuan, S.Kumar, M.E.Skinner, R.Victor-Joseph, M.Abuaita, J.Keijer, J.Zhang, T.J.Kunkel, Y.Liu, E.M.Petrunak, T.L.Saunders, A.P.Lieberman, J.A.Stuckey, N.Neamati, F.Al-Murshedi, M.Alfadhel, J.N.Spelbrink, R.Rodenburg, V.C.De Boer, D.B.Lombard. Human SIRT5 Variants with Reduced Stability and Activity Do Not Cause Neuropathology in Mice Iscience V. 27 09991 2024.
ISSN: ESSN 2589-0042
DOI: 10.1016/J.ISCI.2024.109991