Magnesium 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:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Paak Family Amp-Ligase with Amp and Substrate, PDB code: 6siy:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Paak Family Amp-Ligase with Amp and Substrate


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 Amp and Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg509 b:56.2 occ:1.00 O B:GLY147 2.7 53.7 1.0 O A:LEU81 2.8 58.1 1.0 OG1 B:THR149 2.9 49.1 1.0 O A:ARG78 2.9 53.0 1.0 O B:PRO120 3.0 57.7 1.0 O A:GLU79 3.0 58.2 1.0 N B:THR149 3.2 48.7 1.0 C A:GLU79 3.3 56.9 1.0 C B:ALA148 3.6 51.9 1.0 CA A:GLU79 3.6 60.0 1.0 CA B:THR149 3.8 49.6 1.0 N A:LEU81 3.8 62.3 1.0 C B:GLY147 3.9 52.5 1.0 C A:LEU81 3.9 56.3 1.0 CB B:THR149 3.9 48.7 1.0 C A:ARG78 3.9 58.4 1.0 C B:PRO120 3.9 56.9 1.0 CA B:ALA148 4.0 54.1 1.0 N A:HIS80 4.1 63.1 1.0 CA B:PRO120 4.2 56.1 1.0 N A:GLU79 4.2 57.8 1.0 O B:ASP122 4.2 49.1 1.0 CA A:LEU81 4.3 60.1 1.0 O B:ALA148 4.3 53.0 1.0 N B:ALA148 4.4 52.5 1.0 CB A:LEU81 4.4 58.1 1.0 C A:HIS80 4.5 62.4 1.0 CB B:PRO120 4.8 57.3 1.0 CA A:HIS80 4.8 65.8 1.0 CB A:GLU79 4.9 63.0 1.0

Magnesium binding site 2 out of 3 in the Paak Family Amp-Ligase with Amp and Substrate


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 Amp and Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg510 b:45.9 occ:1.00 O A:GLY147 2.7 51.4 1.0 O A:PRO120 2.8 53.6 1.0 O B:LEU81 2.9 45.8 1.0 OG1 A:THR149 2.9 40.1 1.0 O B:GLU79 2.9 48.9 1.0 O B:ARG78 3.0 44.0 1.0 N A:THR149 3.1 42.1 1.0 C B:GLU79 3.3 47.6 1.0 CA B:GLU79 3.5 49.2 1.0 C A:ALA148 3.6 42.6 1.0 CA A:THR149 3.8 42.4 1.0 C A:PRO120 3.8 51.5 1.0 C A:GLY147 3.8 45.4 1.0 N B:LEU81 3.9 46.5 1.0 CB A:THR149 3.9 41.1 1.0 O A:HOH659 3.9 59.0 1.0 C B:ARG78 3.9 50.1 1.0 CA A:ALA148 3.9 46.4 1.0 C B:LEU81 4.0 43.3 1.0 O A:ASP122 4.1 45.5 1.0 CA A:PRO120 4.1 50.7 1.0 N B:HIS80 4.2 46.0 1.0 N B:GLU79 4.2 46.5 1.0 O A:ALA148 4.3 48.4 1.0 CA B:LEU81 4.3 44.5 1.0 N A:ALA148 4.3 48.2 1.0 O A:HOH614 4.3 48.0 1.0 C B:HIS80 4.5 49.5 1.0 CB B:LEU81 4.5 42.8 1.0 CB A:PRO120 4.7 53.9 1.0 CA B:HIS80 4.8 46.4 1.0 CB B:GLU79 4.9 62.6 1.0

Magnesium binding site 3 out of 3 in the Paak Family Amp-Ligase with Amp and Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Paak Family Amp-Ligase with Amp and Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:70.0 occ:1.00 O1P B:AMP501 2.4 58.5 1.0 OE1 B:GLU240 2.5 66.8 1.0 O B:HOH631 2.8 52.5 1.0 OE2 B:GLU240 2.9 61.1 1.0 CD B:GLU240 3.1 52.9 1.0 P B:AMP501 3.2 57.3 1.0 O5' B:AMP501 3.4 50.3 1.0 O3P B:AMP501 3.4 52.9 1.0 OG B:SER87 3.5 60.9 1.0 CB B:SER87 4.0 46.9 1.0 CB B:SER238 4.0 42.5 1.0 C5' B:AMP501 4.0 45.3 1.0 N B:THR239 4.3 43.2 1.0 CG B:GLU240 4.5 62.5 1.0 NZ B:LYS62 4.6 65.7 1.0 O2P B:AMP501 4.7 50.8 1.0 OG B:SER238 4.7 42.1 1.0 CA B:SER238 4.7 45.9 1.0 OG1 B:THR239 4.7 49.2 1.0 OH B:TYR295 4.7 56.1 1.0 O3' B:AMP501 4.7 46.9 1.0 CE B:LYS62 4.7 66.9 1.0 C4' B:AMP501 4.9 46.7 1.0 CB B:THR239 4.9 43.8 1.0 C B:SER238 5.0 43.1 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