Zinc in PDB 8gbn: Structure of Apo Human SIRT5 P114T Mutant

The structure of Structure of Apo Human SIRT5 P114T Mutant, PDB code: 8gbn 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)	41.02 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.017, 114.896, 56.265, 90, 90.14, 90
R / Rfree (%)	18.2 / 23.1

The binding sites of Zinc atom in the Structure of Apo Human SIRT5 P114T Mutant (pdb code 8gbn). 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 P114T Mutant, PDB code: 8gbn:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Apo Human SIRT5 P114T Mutant


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 P114T Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:35.6 occ:1.00 SG A:CYS212 2.2 45.7 1.0 SG A:CYS207 2.3 32.8 1.0 SG A:CYS166 2.4 32.5 1.0 SG A:CYS169 2.4 38.8 1.0 CB A:CYS166 3.0 28.0 1.0 CB A:CYS207 3.1 28.8 1.0 CB A:CYS169 3.2 33.9 1.0 CB A:CYS212 3.4 41.5 1.0 N A:CYS169 3.7 32.5 1.0 CA A:CYS169 4.0 32.3 1.0 OG A:SER168 4.5 53.6 1.0 CA A:CYS166 4.5 26.7 1.0 CA A:CYS207 4.5 28.5 1.0 CB A:GLU209 4.6 33.0 1.0 N A:GLY214 4.7 30.6 1.0 CG A:GLU209 4.8 44.8 1.0 C A:CYS169 4.8 33.7 1.0 CA A:CYS212 4.8 40.8 1.0 CB A:SER168 4.8 35.8 1.0 C A:SER168 4.9 36.1 1.0 N A:GLY170 4.9 30.2 1.0 CA A:GLY214 5.0 28.7 1.0

Zinc binding site 2 out of 2 in the Structure of Apo Human SIRT5 P114T Mutant


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 P114T Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:35.6 occ:1.00 SG B:CYS212 2.3 42.8 1.0 SG B:CYS166 2.3 30.0 1.0 SG B:CYS207 2.4 30.0 1.0 SG B:CYS169 2.5 45.3 1.0 CB B:CYS166 2.9 26.2 1.0 CB B:CYS207 3.0 26.4 1.0 CB B:CYS169 3.2 40.6 1.0 CB B:CYS212 3.4 38.4 1.0 N B:CYS169 3.7 37.2 1.0 CA B:CYS169 4.0 39.1 1.0 OG B:SER168 4.4 49.6 1.0 CA B:CYS166 4.4 25.9 1.0 CA B:CYS207 4.5 26.6 1.0 N B:GLY214 4.7 27.7 1.0 CB B:GLU209 4.7 36.6 1.0 C B:CYS169 4.7 42.9 1.0 CB B:SER168 4.8 37.2 1.0 CA B:CYS212 4.8 37.4 1.0 C B:SER168 4.8 37.6 1.0 CG B:GLU209 4.8 46.0 1.0 N B:GLY170 4.9 38.0 1.0 CA B:GLY214 4.9 26.3 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