Magnesium 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:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Paak Family Amp-Ligase with Amp (pdb code 6siw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Paak Family Amp-Ligase with Amp, PDB code: 6siw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Paak Family Amp-Ligase with Amp


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:50.8 occ:1.00 O1P A:AMP501 2.7 43.8 1.0 OE1 A:GLU240 2.8 36.0 1.0 O A:HOH691 3.0 46.8 1.0 OE2 A:GLU240 3.1 43.3 1.0 CD A:GLU240 3.3 45.3 1.0 OG A:SER87 3.4 41.2 1.0 CB A:SER87 3.5 38.8 1.0 O5' A:AMP501 3.7 40.2 1.0 P A:AMP501 3.8 42.6 1.0 C5' A:AMP501 3.8 36.0 1.0 CB A:SER238 3.9 36.2 1.0 N A:THR239 4.3 31.7 1.0 CE A:LYS62 4.5 65.3 1.0 CA A:SER238 4.6 34.0 1.0 O2P A:AMP501 4.6 45.7 1.0 OG A:SER238 4.6 36.4 1.0 CA A:SER87 4.6 40.0 1.0 C4' A:AMP501 4.7 36.0 1.0 CG A:GLU240 4.7 43.5 1.0 CD1 A:LEU297 4.8 49.0 1.0 O3' A:AMP501 4.8 34.9 1.0 NZ A:LYS62 4.9 66.1 1.0 CB A:THR239 4.9 32.8 1.0 N A:SER88 4.9 37.5 1.0 C A:SER238 4.9 33.9 1.0 O3P A:AMP501 4.9 45.7 1.0 O A:SER88 5.0 41.5 1.0

Magnesium binding site 2 out of 4 in the Paak Family Amp-Ligase with Amp


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:18.5 occ:1.00 O A:GLY147 2.6 30.9 1.0 O B:LEU81 2.6 33.2 1.0 O A:PRO120 2.7 34.5 1.0 OG1 A:THR149 2.8 26.1 1.0 O B:ARG78 2.8 32.5 1.0 O B:GLU79 2.8 37.0 1.0 N A:THR149 3.2 26.5 1.0 C B:GLU79 3.2 34.8 1.0 CA B:GLU79 3.6 38.9 1.0 C A:ALA148 3.6 25.3 1.0 C B:LEU81 3.7 29.6 1.0 N B:LEU81 3.7 31.6 1.0 C A:PRO120 3.7 32.5 1.0 C A:GLY147 3.8 28.6 1.0 C B:ARG78 3.8 35.7 1.0 CA A:THR149 3.8 25.6 1.0 CB A:THR149 3.9 25.1 1.0 CA A:ALA148 4.0 25.6 1.0 N B:HIS80 4.1 33.9 1.0 CA A:PRO120 4.1 32.5 1.0 N B:GLU79 4.1 37.2 1.0 CA B:LEU81 4.1 29.8 1.0 O A:ALA148 4.2 27.9 1.0 C B:HIS80 4.4 32.7 1.0 O A:ASP122 4.4 24.6 1.0 N A:ALA148 4.4 27.4 1.0 CB B:LEU81 4.4 29.4 1.0 O B:HOH719 4.6 41.5 1.0 CB A:PRO120 4.6 34.6 1.0 CA B:HIS80 4.7 33.7 1.0 N B:ALA82 4.9 27.3 1.0 CB B:GLU79 4.9 45.6 1.0 N A:SER121 4.9 32.4 1.0 CA A:GLY147 5.0 29.9 1.0

Magnesium binding site 3 out of 4 in the Paak Family Amp-Ligase with Amp


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg508 b:19.7 occ:1.00 O B:GLY147 2.6 30.7 1.0 O A:LEU81 2.6 31.7 1.0 OG1 B:THR149 2.7 26.3 1.0 O B:PRO120 2.7 40.9 1.0 O A:GLU79 2.8 35.7 1.0 O A:ARG78 3.0 35.9 1.0 N B:THR149 3.1 27.6 1.0 C A:GLU79 3.3 37.2 1.0 C B:ALA148 3.5 29.0 1.0 C A:LEU81 3.7 31.0 1.0 CA A:GLU79 3.7 37.1 1.0 C B:GLY147 3.7 32.6 1.0 C B:PRO120 3.8 41.0 1.0 CA B:THR149 3.8 27.6 1.0 N A:LEU81 3.8 34.3 1.0 CB B:THR149 3.8 28.0 1.0 CA B:ALA148 4.0 29.4 1.0 C A:ARG78 4.0 38.0 1.0 CA B:PRO120 4.1 40.3 1.0 O B:ALA148 4.2 29.4 1.0 N A:HIS80 4.2 37.3 1.0 CA A:LEU81 4.2 32.9 1.0 N B:ALA148 4.3 30.7 1.0 N A:GLU79 4.3 36.7 1.0 O B:ASP122 4.4 33.6 1.0 C A:HIS80 4.4 34.0 1.0 CB A:LEU81 4.4 31.5 1.0 CB B:PRO120 4.6 41.5 1.0 O B:HOH632 4.7 41.9 1.0 CA A:HIS80 4.8 37.2 1.0 N A:ALA82 4.8 32.0 1.0 CA B:GLY147 4.9 32.5 1.0 N B:SER121 5.0 41.8 1.0 CG2 B:THR149 5.0 28.6 1.0 CB A:GLU79 5.0 41.3 1.0

Magnesium binding site 4 out of 4 in the Paak Family Amp-Ligase with Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Paak Family Amp-Ligase with Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:60.7 occ:1.00 O2P B:AMP501 2.2 46.6 1.0 O B:HOH721 3.0 47.9 1.0 OE1 B:GLU240 3.0 42.7 1.0 O B:HOH631 3.2 50.2 1.0 OE2 B:GLU240 3.3 46.9 1.0 P B:AMP501 3.3 48.1 1.0 O5' B:AMP501 3.3 42.2 1.0 OG B:SER87 3.5 49.4 1.0 CD B:GLU240 3.5 40.8 1.0 CB B:SER87 3.6 36.9 1.0 C5' B:AMP501 3.7 37.1 1.0 CB B:SER238 3.9 30.9 1.0 O3P B:AMP501 4.1 52.4 1.0 N B:THR239 4.3 29.2 1.0 CE B:LYS62 4.5 55.9 1.0 CA B:SER238 4.5 31.9 1.0 C4' B:AMP501 4.5 33.4 1.0 O1P B:AMP501 4.5 41.8 1.0 OG B:SER238 4.7 33.0 1.0 O3' B:AMP501 4.7 29.4 1.0 CA B:SER87 4.8 32.5 1.0 C B:SER238 4.9 30.9 1.0 NZ B:LYS62 4.9 53.3 1.0 CB B:THR239 5.0 30.9 1.0 CG B:GLU240 5.0 42.0 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