Zinc in PDB 6siz: Paak Family Amp-Ligase with Anp and Substrate

The structure of Paak Family Amp-Ligase with Anp and Substrate, PDB code: 6siz was solved by J.H.Naismith, H.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.80 / 1.77
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	107.450, 138.810, 130.700, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 22.8

The structure of Paak Family Amp-Ligase with Anp and Substrate also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the Paak Family Amp-Ligase with Anp and Substrate (pdb code 6siz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Paak Family Amp-Ligase with Anp and Substrate, PDB code: 6siz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Paak Family Amp-Ligase with Anp and Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Paak Family Amp-Ligase with Anp and Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:59.5 occ:1.00 NE2 A:HIS254 2.1 49.6 1.0 SG A:CYS248 2.2 53.5 1.0 SG A:CYS310 2.4 66.3 1.0 SG A:CYS308 2.5 68.0 1.0 CB A:CYS248 3.0 49.3 1.0 CD2 A:HIS254 3.0 49.5 1.0 CB A:CYS310 3.1 65.2 1.0 CE1 A:HIS254 3.1 53.2 1.0 CB A:CYS308 3.2 72.0 1.0 CG A:HIS254 4.1 50.4 1.0 ND1 A:HIS254 4.2 51.8 1.0 N A:CYS310 4.2 71.8 1.0 CA A:CYS310 4.3 69.6 1.0 CB A:GLU250 4.4 67.7 1.0 CA A:CYS248 4.4 48.4 1.0 CB A:ARG252 4.5 61.1 1.0 O A:ARG252 4.6 49.1 1.0 CA A:CYS308 4.6 72.6 1.0 CG A:GLU250 4.6 73.1 1.0 C A:CYS308 4.9 71.8 1.0 N A:CYS248 4.9 45.5 1.0 CG2 A:THR316 5.0 58.9 1.0

Zinc binding site 2 out of 2 in the Paak Family Amp-Ligase with Anp and Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Paak Family Amp-Ligase with Anp and Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:49.2 occ:1.00 NE2 B:HIS254 2.0 44.1 1.0 SG B:CYS248 2.3 48.8 1.0 SG B:CYS310 2.4 51.5 1.0 SG B:CYS308 2.5 54.2 1.0 CD2 B:HIS254 3.0 43.0 1.0 CE1 B:HIS254 3.1 47.1 1.0 CB B:CYS248 3.1 45.6 1.0 CB B:CYS308 3.2 54.6 1.0 CB B:CYS310 3.2 52.3 1.0 CG B:HIS254 4.1 42.4 1.0 ND1 B:HIS254 4.1 43.7 1.0 N B:CYS310 4.3 54.9 1.0 CA B:CYS310 4.3 54.5 1.0 CB B:ARG252 4.4 50.0 1.0 CB B:GLU250 4.5 57.8 1.0 O B:ARG252 4.5 41.4 1.0 CA B:CYS248 4.5 43.0 1.0 CA B:CYS308 4.6 55.1 1.0 CG B:GLU250 4.8 62.4 1.0 CG2 B:THR316 4.8 50.4 1.0 C B:CYS308 4.9 55.3 1.0 N B:CYS248 4.9 41.2 1.0

H.Song, C.Rao, Z.Deng, Y.Yi, J.H.Naismith. The Biosynthetic Pathway of the Benzoxazole in Nataxazole Proceeds Via An Unstable Ester and Has Synthetic Utility. Angew.Chem.Int.Ed.Engl. 2020.
ISSN: ESSN 1521-3773
PubMed: 31903677
DOI: 10.1002/ANIE.201915685