Zinc in PDB 5onk: Native Yndl

The structure of Native Yndl, PDB code: 5onk was solved by S.Ramaswamy, M.Rasheed, C.Morelli, C.Calvio, B.Sutton, A.Pastore, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.20 / 1.03
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.670, 46.860, 100.070, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 18.7

The binding sites of Zinc atom in the Native Yndl (pdb code 5onk). 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 Native Yndl, PDB code: 5onk:

Zinc binding site 1 out of 1 in the Native Yndl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Native Yndl within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:8.6 occ:1.00 OA1 A:FLC304 2.0 10.0 0.8 OA1 A:FLC304 2.0 11.2 0.2 ND1 A:HIS41 2.0 8.2 1.0 OE1 A:GLU46 2.0 8.0 1.0 ND1 A:HIS102 2.1 8.2 1.0 OE2 A:GLU46 2.5 9.5 1.0 OA2 A:FLC304 2.6 12.8 0.2 CD A:GLU46 2.6 8.4 1.0 OA2 A:FLC304 2.7 14.0 0.8 CAC A:FLC304 2.7 12.2 0.2 CAC A:FLC304 2.7 11.3 0.8 CE1 A:HIS41 3.0 8.8 1.0 CE1 A:HIS102 3.0 8.8 1.0 CG A:HIS41 3.1 8.3 1.0 CG A:HIS102 3.1 8.4 1.0 CB A:HIS41 3.5 7.9 1.0 CB A:HIS102 3.5 8.2 1.0 CA A:HIS102 4.1 8.1 1.0 NE2 A:HIS41 4.1 8.4 1.0 CG A:GLU46 4.1 8.8 1.0 NE2 A:HIS77 4.1 11.5 1.0 CA A:FLC304 4.1 13.4 0.2 NE2 A:HIS102 4.1 9.1 1.0 CA A:FLC304 4.1 16.9 0.8 CD2 A:HIS41 4.2 8.0 1.0 CD2 A:HIS102 4.2 8.9 1.0 CD2 A:HIS77 4.3 9.9 1.0 CBC A:FLC304 4.4 20.3 0.8 N A:GLY103 4.4 8.2 1.0 OB1 A:FLC304 4.5 16.8 0.8 CBC A:FLC304 4.5 14.0 0.2 O A:GLY103 4.5 10.4 1.0 OHB A:FLC304 4.6 14.2 0.2 OB1 A:FLC304 4.6 16.3 0.2 OB2 A:FLC304 4.6 25.3 0.8 CB A:FLC304 4.7 18.3 0.8 OB2 A:FLC304 4.7 17.4 0.2 CB A:FLC304 4.7 13.6 0.2 OE1 A:GLU165 4.8 14.4 1.0 OHB A:FLC304 4.9 16.9 0.8 C A:HIS102 4.9 7.8 1.0 CB A:GLU46 4.9 8.2 1.0 CA A:HIS41 4.9 7.7 1.0 O A:LEU101 5.0 8.2 1.0

S.Ramaswamy, M.Rasheed, C.F.Morelli, C.Calvio, B.J.Sutton, A.Pastore. The Structure of Pghl Hydrolase Bound to Its Substrate Poly-Gamma-Glutamate. Febs J. V. 285 4575 2018.
ISSN: ISSN 1742-4658
PubMed: 30387270
DOI: 10.1111/FEBS.14688