Zinc in PDB 5yz4: Structure of the Pin Domain Endonuclease UTP24

The structure of Structure of the Pin Domain Endonuclease UTP24, PDB code: 5yz4 was solved by Y.Du, W.An, K.Ye, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.59 / 2.14
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	48.740, 73.328, 74.262, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 28.7

The structure of Structure of the Pin Domain Endonuclease UTP24 also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Zinc atom in the Structure of the Pin Domain Endonuclease UTP24 (pdb code 5yz4). 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 Structure of the Pin Domain Endonuclease UTP24, PDB code: 5yz4:

Zinc binding site 1 out of 1 in the Structure of the Pin Domain Endonuclease UTP24


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Pin Domain Endonuclease UTP24 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:38.2 occ:1.00 NE2 A:HIS134 1.8 46.7 1.0 SG A:CYS142 2.2 29.3 1.0 SG A:CYS132 2.3 33.6 1.0 CE1 A:HIS134 2.3 49.2 1.0 SG A:CYS103 2.5 59.7 1.0 CD2 A:HIS134 3.1 48.9 1.0 CB A:CYS132 3.1 38.6 1.0 CB A:CYS142 3.2 32.9 1.0 ND1 A:HIS134 3.5 48.6 1.0 CB A:CYS103 3.8 40.6 1.0 CG A:HIS134 3.9 48.1 1.0 N A:CYS103 4.2 25.5 1.0 CA A:CYS132 4.3 35.5 1.0 CA A:CYS142 4.3 33.4 1.0 CB A:SER101 4.4 25.2 1.0 OG A:SER101 4.4 24.3 1.0 O A:HOH313 4.6 35.2 1.0 CA A:CYS103 4.7 33.1 1.0 N A:ASP102 5.0 32.3 1.0

W.An, Y.Du, K.Ye. Structural and Functional Analysis of UTP24, An Endonuclease For Processing 18S Ribosomal Rna. Plos One V. 13 95723 2018.
ISSN: ESSN 1932-6203
PubMed: 29641590
DOI: 10.1371/JOURNAL.PONE.0195723