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

The structure of Paak Family Amp-Ligase with Amp and Substrate, PDB code: 6siy 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)	69.29 / 1.95
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	107.373, 138.584, 130.414, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.9

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

Magnesium

(Mg)

3 atoms

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

Zinc binding site 1 out of 2 in the Paak Family Amp-Ligase with Amp 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 Amp and Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:0.7 occ:1.00 SG A:CYS248 1.9 0.3 1.0 CB A:CYS248 2.8 78.2 1.0 NE2 A:HIS254 2.9 74.9 1.0 CB A:CYS310 3.0 0.7 1.0 SG A:CYS308 3.3 0.9 1.0 CD2 A:HIS254 3.6 80.0 1.0 CB A:CYS308 3.8 0.7 1.0 N A:CYS310 3.8 0.3 1.0 CE1 A:HIS254 3.9 81.3 1.0 CA A:CYS310 4.0 0.8 1.0 CB A:GLU250 4.2 98.1 1.0 CA A:CYS248 4.3 69.4 1.0 SG A:CYS310 4.3 0.3 1.0 O A:ARG252 4.6 77.3 1.0 N A:GLY309 4.7 0.0 1.0 C A:CYS248 4.7 66.3 1.0 CG A:GLU250 4.8 0.2 1.0 N A:GLU250 4.8 90.0 1.0 CG A:HIS254 4.8 76.4 1.0 N A:CYS248 4.8 62.2 1.0 C A:CYS308 4.8 0.6 1.0 CB A:ARG252 4.9 86.2 1.0 ND1 A:HIS254 4.9 79.8 1.0 CA A:CYS308 4.9 0.2 1.0 C A:GLY309 5.0 0.0 1.0 N A:ARG252 5.0 75.8 1.0

Zinc binding site 2 out of 2 in the Paak Family Amp-Ligase with Amp 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 Amp and Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn504 b:91.5 occ:1.00 NE2 B:HIS254 2.3 61.5 1.0 SG B:CYS248 2.3 71.7 1.0 SG B:CYS310 2.8 82.1 1.0 SG B:CYS308 3.0 89.8 1.0 CB B:CYS248 3.1 62.0 1.0 CB B:CYS308 3.1 92.7 1.0 CD2 B:HIS254 3.1 60.0 1.0 CB B:CYS310 3.2 91.5 1.0 CE1 B:HIS254 3.3 67.3 1.0 N B:CYS310 4.1 0.1 1.0 CA B:CYS310 4.2 95.7 1.0 CG B:HIS254 4.3 58.1 1.0 ND1 B:HIS254 4.3 66.0 1.0 O B:ARG252 4.5 54.2 1.0 CA B:CYS248 4.5 54.8 1.0 CB B:GLU250 4.5 82.4 1.0 CA B:CYS308 4.5 90.5 1.0 CB B:ARG252 4.7 72.4 1.0 C B:CYS308 4.8 90.2 1.0 N B:CYS248 5.0 50.9 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