Magnesium 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:

Zinc

(Zn)

2 atoms

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

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Paak Family Amp-Ligase with Anp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:28.9 occ:1.00 OG1 A:THR149 2.8 29.0 1.0 O A:GLY147 2.8 33.4 1.0 O B:ARG78 2.9 30.4 1.0 O B:LEU81 2.9 32.1 1.0 O A:PRO120 2.9 33.3 1.0 O B:GLU79 3.0 32.1 1.0 N A:THR149 3.1 29.5 1.0 C B:GLU79 3.3 32.4 1.0 CA B:GLU79 3.6 35.0 1.0 C A:ALA148 3.7 30.0 1.0 O A:HOH693 3.7 36.0 1.0 CA A:THR149 3.8 28.0 1.0 N B:LEU81 3.8 31.4 1.0 CB A:THR149 3.8 28.6 1.0 C B:ARG78 3.8 33.2 1.0 C A:PRO120 3.9 33.3 1.0 C B:LEU81 3.9 29.8 1.0 C A:GLY147 4.0 32.5 1.0 O A:ASP122 4.1 28.4 1.0 CA A:ALA148 4.1 31.9 1.0 CA A:PRO120 4.1 33.4 1.0 N B:GLU79 4.2 33.0 1.0 N B:HIS80 4.2 31.8 1.0 CA B:LEU81 4.3 30.0 1.0 O A:HOH646 4.4 29.1 1.0 CB B:LEU81 4.4 29.2 1.0 O A:ALA148 4.4 32.3 1.0 N A:ALA148 4.5 31.2 1.0 C B:HIS80 4.5 32.8 1.0 O B:HOH768 4.7 43.2 1.0 CB A:PRO120 4.8 34.5 1.0 CA B:HIS80 4.8 33.1 1.0 CB B:GLU79 4.9 40.6 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Paak Family Amp-Ligase with Anp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg508 b:34.3 occ:1.00 OG1 B:THR149 2.7 36.2 1.0 O B:GLY147 2.8 37.2 1.0 O A:LEU81 2.8 38.6 1.0 O A:ARG78 2.8 40.3 1.0 O B:PRO120 2.9 42.6 1.0 O A:GLU79 3.0 39.3 1.0 N B:THR149 3.2 33.6 1.0 C A:GLU79 3.4 40.4 1.0 CA A:GLU79 3.7 41.5 1.0 C B:ALA148 3.7 35.7 1.0 N A:LEU81 3.8 40.6 1.0 CA B:THR149 3.8 33.7 1.0 C A:LEU81 3.8 38.9 1.0 CB B:THR149 3.8 35.1 1.0 C A:ARG78 3.9 40.6 1.0 O B:HOH734 3.9 45.6 1.0 C B:PRO120 3.9 41.2 1.0 C B:GLY147 4.0 36.3 1.0 CA B:PRO120 4.1 40.4 1.0 CA B:ALA148 4.1 35.9 1.0 CA A:LEU81 4.2 38.8 1.0 N A:HIS80 4.2 41.2 1.0 O B:ASP122 4.2 36.1 1.0 N A:GLU79 4.2 40.9 1.0 CB A:LEU81 4.3 37.8 1.0 O B:HOH655 4.4 40.9 1.0 O B:ALA148 4.4 39.2 1.0 C A:HIS80 4.5 41.2 1.0 N B:ALA148 4.5 34.2 1.0 CB B:PRO120 4.7 41.2 1.0 O A:HOH766 4.7 52.3 1.0 CA A:HIS80 4.8 42.3 1.0 CB A:GLU79 5.0 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