Zinc in PDB 5onj: Yndl in Complex with 5 Amino Acid (Pga) Complex

The structure of Yndl in Complex with 5 Amino Acid (Pga) Complex, PDB code: 5onj 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)	15.75 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.592, 47.651, 99.328, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 20.4

The binding sites of Zinc atom in the Yndl in Complex with 5 Amino Acid (Pga) Complex (pdb code 5onj). 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 Yndl in Complex with 5 Amino Acid (Pga) Complex, PDB code: 5onj:

Zinc binding site 1 out of 1 in the Yndl in Complex with 5 Amino Acid (Pga) Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Yndl in Complex with 5 Amino Acid (Pga) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:10.3 occ:0.49 ND1 A:HIS41 2.0 10.7 1.0 OE1 A:GLU46 2.0 9.4 1.0 OE1 D:GGL4 2.1 17.9 1.0 ND1 A:HIS102 2.2 9.1 1.0 OE2 A:GLU46 2.6 10.3 1.0 CD A:GLU46 2.6 14.6 1.0 CE1 A:HIS41 2.9 11.3 1.0 CG A:HIS41 3.0 9.4 1.0 CD D:GGL4 3.1 21.4 1.0 CG A:HIS102 3.1 10.4 1.0 CE1 A:HIS102 3.2 9.1 1.0 CB A:HIS102 3.3 11.5 1.0 CB A:HIS41 3.4 8.4 1.0 CA A:HIS102 3.9 10.4 1.0 CG D:GGL4 3.9 24.7 1.0 N D:GGL5 3.9 17.4 1.0 NE2 A:HIS41 4.0 10.4 1.0 CD2 A:HIS41 4.1 8.4 1.0 CG A:GLU46 4.1 13.1 1.0 NE2 A:HIS77 4.2 11.9 1.0 CA D:GGL5 4.2 17.1 1.0 CD2 A:HIS102 4.2 9.6 1.0 NE2 A:HIS102 4.2 8.9 1.0 N A:GLY103 4.3 8.9 1.0 C D:GGL5 4.3 12.8 1.0 CD2 A:HIS77 4.3 9.0 1.0 O D:GGL5 4.3 11.9 1.0 O A:GLY103 4.5 12.8 1.0 CB D:GGL4 4.6 17.1 1.0 C A:HIS102 4.7 9.5 1.0 O A:LEU101 4.8 10.2 1.0 CA A:HIS41 4.9 9.0 1.0 CB A:GLU46 4.9 9.6 1.0 O A:HOH482 4.9 8.1 1.0 OXT D:GGL5 4.9 18.2 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 1742-464X
PubMed: 30387270
DOI: 10.1111/FEBS.14688