Zinc in PDB 6siw: Paak Family Amp-Ligase with Amp

The structure of Paak Family Amp-Ligase with Amp, PDB code: 6siw 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)	84.65 / 1.96
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	107.131, 138.094, 130.426, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 23.6

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

Magnesium

(Mg)

4 atoms

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

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:52.3 occ:1.00 SG A:CYS308 2.0 55.4 1.0 SG A:CYS310 2.0 57.8 1.0 NE2 A:HIS254 2.2 38.1 1.0 CB A:CYS308 2.5 51.7 1.0 CE1 A:HIS254 3.0 36.2 1.0 SG A:CYS248 3.1 42.4 1.0 CB A:CYS310 3.2 52.2 1.0 CD2 A:HIS254 3.2 36.3 1.0 CB A:CYS248 3.6 35.9 1.0 N A:CYS310 3.9 56.4 1.0 CA A:CYS308 4.0 56.7 1.0 CA A:CYS310 4.1 53.1 1.0 ND1 A:HIS254 4.2 36.7 1.0 CG A:HIS254 4.3 36.9 1.0 C A:CYS308 4.4 56.2 1.0 CB A:GLU250 4.6 52.4 1.0 N A:GLY309 4.7 57.0 1.0 CG2 A:THR316 4.7 39.7 1.0 CB A:ARG252 4.7 47.2 1.0 N A:CYS308 4.9 61.0 1.0 C A:CYS310 4.9 50.5 1.0 N A:GLY311 5.0 53.0 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:45.3 occ:1.00 SG B:CYS310 1.8 50.3 1.0 SG B:CYS308 2.3 53.3 1.0 NE2 B:HIS254 2.4 39.8 1.0 CB B:CYS308 2.8 51.9 1.0 SG B:CYS248 2.8 42.8 1.0 CB B:CYS310 3.0 47.3 1.0 CD2 B:HIS254 3.2 34.8 1.0 CB B:CYS248 3.2 40.0 1.0 CE1 B:HIS254 3.3 37.4 1.0 N B:CYS310 3.8 49.2 1.0 CA B:CYS310 3.9 48.8 1.0 CA B:CYS308 4.2 52.3 1.0 ND1 B:HIS254 4.3 36.3 1.0 CG B:HIS254 4.3 37.0 1.0 C B:CYS308 4.5 56.1 1.0 CB B:GLU250 4.6 56.9 1.0 CA B:CYS248 4.7 39.7 1.0 CB B:ARG252 4.8 49.5 1.0 N B:GLY309 4.8 54.9 1.0 C B:CYS310 4.8 49.5 1.0 N B:GLY311 5.0 49.8 1.0 CG B:GLU250 5.0 62.1 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