Zinc in PDB 6six: Paak Family Amp-Ligase with Anp

The structure of Paak Family Amp-Ligase with Anp, PDB code: 6six 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)	84.92 / 1.88
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	107.380, 138.139, 130.524, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 21.1

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

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Paak Family Amp-Ligase with Anp (pdb code 6six). 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, PDB code: 6six:
Jump to Zinc binding site number: 1; 2;

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:42.8 occ:0.80 NE2 A:HIS254 2.0 42.6 1.0 SG A:CYS310 2.3 55.3 1.0 SG A:CYS248 2.3 43.7 1.0 SG A:CYS308 2.4 60.4 1.0 CD2 A:HIS254 3.0 41.7 1.0 CE1 A:HIS254 3.0 44.5 1.0 CB A:CYS248 3.0 41.9 1.0 CB A:CYS308 3.0 61.4 1.0 CB A:CYS310 3.2 58.7 1.0 ND1 A:HIS254 4.1 44.6 1.0 CG A:HIS254 4.1 42.2 1.0 N A:CYS310 4.2 61.8 1.0 CA A:CYS310 4.3 60.4 1.0 CA A:CYS308 4.4 60.8 1.0 CB A:ARG252 4.5 54.6 1.0 CA A:CYS248 4.5 38.6 1.0 CB A:GLU250 4.5 58.9 1.0 O A:ARG252 4.6 40.6 1.0 CG A:GLU250 4.7 62.6 1.0 C A:CYS308 4.8 60.0 1.0 NH1 A:ARG252 4.8 82.2 1.0 CG2 A:THR316 4.9 47.5 1.0 N A:CYS248 5.0 35.9 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:42.1 occ:1.00 NE2 B:HIS254 2.1 41.1 1.0 SG B:CYS248 2.2 41.4 1.0 SG B:CYS310 2.3 43.0 1.0 SG B:CYS308 2.4 45.2 1.0 CB B:CYS248 3.0 40.1 1.0 CD2 B:HIS254 3.0 39.8 1.0 CE1 B:HIS254 3.1 42.7 1.0 CB B:CYS308 3.1 45.2 1.0 CB B:CYS310 3.2 45.7 1.0 CG B:HIS254 4.1 38.1 1.0 ND1 B:HIS254 4.1 40.6 1.0 N B:CYS310 4.2 47.5 1.0 CA B:CYS310 4.3 47.1 1.0 CB B:ARG252 4.4 42.6 1.0 CB B:GLU250 4.4 52.6 1.0 CA B:CYS248 4.4 38.0 1.0 O B:ARG252 4.5 38.9 1.0 CA B:CYS308 4.5 45.4 1.0 CG B:GLU250 4.6 56.4 1.0 C B:CYS308 4.8 46.5 1.0 N B:CYS248 4.9 34.8 1.0 CG2 B:THR316 4.9 43.0 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