Zinc in PDB 7ndj: Crystal Structure of ZC3H12C Pin-Ccch Zn Finger Domain with Rna Heptamer

The structure of Crystal Structure of ZC3H12C Pin-Ccch Zn Finger Domain with Rna Heptamer, PDB code: 7ndj was solved by A.Garg, U.Heinemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.72 / 1.65
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	63.248, 63.248, 114.544, 90, 90, 90
R / Rfree (%)	17.5 / 20.8

The structure of Crystal Structure of ZC3H12C Pin-Ccch Zn Finger Domain with Rna Heptamer also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of ZC3H12C Pin-Ccch Zn Finger Domain with Rna Heptamer (pdb code 7ndj). 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 ZC3H12C Pin-Ccch Zn Finger Domain with Rna Heptamer, PDB code: 7ndj:

Zinc binding site 1 out of 1 in the Crystal Structure of ZC3H12C Pin-Ccch Zn Finger Domain with Rna Heptamer


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 ZC3H12C Pin-Ccch Zn Finger Domain with Rna Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn406 b:36.5 occ:1.00 NE2 B:HIS322 2.0 45.8 1.0 SG B:CYS318 2.3 50.5 1.0 SG B:CYS312 2.3 45.0 1.0 SG B:CYS306 2.4 40.2 1.0 CE1 B:HIS322 2.8 53.4 1.0 CD2 B:HIS322 3.1 57.1 1.0 CB B:CYS312 3.2 42.1 1.0 CB B:CYS306 3.3 43.5 1.0 CB B:CYS318 3.3 56.9 1.0 ND1 B:HIS322 4.0 50.4 1.0 CG B:HIS322 4.2 48.1 1.0 N6 C:A6 4.5 60.8 1.0 CA B:CYS312 4.6 43.8 1.0 CA B:CYS306 4.6 39.7 1.0 CB B:TYR320 4.7 49.1 1.0 CD2 B:TYR320 4.7 54.8 1.0 CA B:CYS318 4.7 57.5 1.0

A.Garg, Y.Roske, S.Yamada, T.Uehata, O.Takeuchi, U.Heinemann. Pin and Ccch Zn-Finger Domains Coordinate Rna Targeting in ZC3H12 Family Endoribonucleases. Nucleic Acids Res. 2021.
ISSN: ESSN 1362-4962
PubMed: 33950203
DOI: 10.1093/NAR/GKAB316