Zinc in PDB 8z58: Crystal Structure of Human N141V-SIRT5 in Complex with Succinylated PRX1 Fragment

The structure of Crystal Structure of Human N141V-SIRT5 in Complex with Succinylated PRX1 Fragment, PDB code: 8z58 was solved by T.Yokoyama, Y.Takayama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.69 / 2.41
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	43.916, 73.43, 163.774, 90, 90, 90
R / Rfree (%)	21.2 / 25.8

The structure of Crystal Structure of Human N141V-SIRT5 in Complex with Succinylated PRX1 Fragment also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Human N141V-SIRT5 in Complex with Succinylated PRX1 Fragment (pdb code 8z58). 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 N141V-SIRT5 in Complex with Succinylated PRX1 Fragment, PDB code: 8z58:

Zinc binding site 1 out of 1 in the Crystal Structure of Human N141V-SIRT5 in Complex with Succinylated PRX1 Fragment


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 N141V-SIRT5 in Complex with Succinylated PRX1 Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:43.0 occ:1.00 SG A:CYS166 2.2 44.1 1.0 SG A:CYS212 2.3 43.8 1.0 SG A:CYS207 2.3 39.6 1.0 SG A:CYS169 2.4 39.1 1.0 CB A:CYS207 3.0 39.1 1.0 CB A:CYS166 3.1 38.6 1.0 CB A:CYS212 3.3 45.3 1.0 CB A:CYS169 3.4 37.1 1.0 N A:CYS169 3.8 35.7 1.0 CA A:CYS169 4.1 37.4 1.0 N A:GLY214 4.4 41.4 1.0 CA A:CYS207 4.5 40.8 1.0 CG1 A:VAL171 4.5 45.9 1.0 O A:HOH532 4.5 39.4 1.0 CB A:GLU209 4.5 52.4 1.0 CA A:CYS166 4.5 34.5 1.0 CA A:CYS212 4.7 48.1 1.0 CB A:SER168 4.7 39.1 1.0 C A:CYS169 4.8 37.0 1.0 CA A:GLY214 4.8 37.6 1.0 C A:SER168 4.9 42.4 1.0 N A:GLY213 4.9 43.3 1.0 N A:GLY170 4.9 36.5 1.0 C A:CYS212 5.0 45.8 1.0

T.Yokoyama, Y.Takayama, M.Mizuguchi, Y.Nabeshima, K.Kusaka. SIRT5 Mutants Reveal the Role of Conserved Asparagine and Glutamine Residues in the Nad + -Binding Pocket. Febs Lett. V. 598 2269 2024.
ISSN: ISSN 0014-5793
PubMed: 39031546
DOI: 10.1002/1873-3468.14961