Zinc in PDB 4ykl: HNT3 in Complex with Dna and Guanosine

The structure of HNT3 in Complex with Dna and Guanosine, PDB code: 4ykl was solved by A.Jacewicz, M.Chauleau, S.Shuman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.54 / 2.25
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	119.083, 119.083, 36.564, 90.00, 90.00, 120.00
R / Rfree (%)	18 / 24

The structure of HNT3 in Complex with Dna and Guanosine also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the HNT3 in Complex with Dna and Guanosine (pdb code 4ykl). 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 HNT3 in Complex with Dna and Guanosine, PDB code: 4ykl:

Zinc binding site 1 out of 1 in the HNT3 in Complex with Dna and Guanosine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of HNT3 in Complex with Dna and Guanosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:36.8 occ:1.00 OE1 B:GLU221 2.0 32.9 1.0 NE2 B:HIS217 2.0 35.2 1.0 SG B:CYS200 2.3 34.8 1.0 SG B:CYS203 2.3 39.8 1.0 CD B:GLU221 2.9 35.2 1.0 CD2 B:HIS217 3.0 34.3 1.0 CB B:CYS200 3.0 31.4 1.0 CE1 B:HIS217 3.0 37.1 1.0 CG B:GLU221 3.2 33.1 1.0 CB B:CYS203 3.3 37.2 1.0 N B:CYS203 3.7 34.4 1.0 CA B:CYS203 4.1 36.5 1.0 OE2 B:GLU221 4.1 35.5 1.0 ND1 B:HIS217 4.1 37.0 1.0 CG B:HIS217 4.1 34.9 1.0 CB B:ARG202 4.5 33.9 1.0 CA B:CYS200 4.5 32.7 1.0 C B:ARG202 4.5 34.1 1.0 CB B:GLU221 4.7 31.5 1.0 C B:CYS203 4.7 38.1 1.0 N B:GLY204 4.7 36.9 1.0 N B:ARG202 4.8 33.9 1.0 CB B:GLU205 4.8 42.6 1.0 CA B:ARG202 4.8 33.7 1.0 N B:GLU205 4.9 39.5 1.0 C B:CYS200 5.0 32.8 1.0

M.Chauleau, A.Jacewicz, S.Shuman. DNA3'PP5'G De-Capping Activity of Aprataxin: Effect of Cap Nucleoside Analogs and Structural Basis For Guanosine Recognition. Nucleic Acids Res. V. 43 6075 2015.
ISSN: ESSN 1362-4962
PubMed: 26007660
DOI: 10.1093/NAR/GKV501