Magnesium in PDB 6siz: Paak Family Amp-Ligase with Anp and Substrate

The structure of Paak Family Amp-Ligase with Anp and Substrate, PDB code: 6siz 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)	51.80 / 1.77
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	107.450, 138.810, 130.700, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 22.8

The structure of Paak Family Amp-Ligase with Anp 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 Anp and Substrate (pdb code 6siz). 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 Anp and Substrate, PDB code: 6siz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Paak Family Amp-Ligase with Anp 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 Anp and Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg508 b:48.0 occ:1.00 O B:GLY147 2.7 45.9 1.0 O A:LEU81 2.8 44.4 1.0 OG1 B:THR149 2.8 40.6 1.0 O B:PRO120 2.9 48.6 1.0 O A:ARG78 3.0 48.7 1.0 O A:GLU79 3.0 49.5 1.0 N B:THR149 3.2 40.0 1.0 C A:GLU79 3.4 48.6 1.0 C B:ALA148 3.6 40.9 1.0 CA A:GLU79 3.7 50.5 1.0 CA B:THR149 3.8 40.0 1.0 N A:LEU81 3.8 51.4 1.0 CB B:THR149 3.9 40.0 1.0 C A:LEU81 3.9 47.7 1.0 C B:GLY147 3.9 44.1 1.0 C B:PRO120 3.9 47.7 1.0 C A:ARG78 4.0 50.0 1.0 CA B:ALA148 4.0 41.7 1.0 CA B:PRO120 4.2 47.4 1.0 N A:HIS80 4.2 50.1 1.0 O B:ASP122 4.2 42.4 1.0 CA A:LEU81 4.3 48.1 1.0 O B:ALA148 4.3 43.6 1.0 N A:GLU79 4.3 51.3 1.0 N B:ALA148 4.4 42.2 1.0 CB A:LEU81 4.5 48.5 1.0 C A:HIS80 4.5 49.9 1.0 O B:HOH636 4.6 46.9 1.0 CB B:PRO120 4.7 49.8 1.0 CA A:HIS80 4.8 50.5 1.0 CB A:GLU79 5.0 54.7 1.0

Magnesium binding site 2 out of 4 in the Paak Family Amp-Ligase with Anp 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 Anp and Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg509 b:40.6 occ:1.00 OG1 A:THR149 2.8 33.0 1.0 O A:GLY147 2.8 42.7 1.0 O B:LEU81 2.9 40.3 1.0 O A:PRO120 2.9 40.5 1.0 O B:GLU79 2.9 45.4 1.0 O B:ARG78 3.0 38.8 1.0 N A:THR149 3.1 33.7 1.0 C B:GLU79 3.3 42.5 1.0 O A:HOH649 3.6 46.2 1.0 CA B:GLU79 3.6 45.2 1.0 C A:ALA148 3.7 34.8 1.0 N B:LEU81 3.8 38.0 1.0 CA A:THR149 3.8 32.0 1.0 CB A:THR149 3.8 32.1 1.0 C A:PRO120 3.9 42.2 1.0 C B:ARG78 3.9 40.1 1.0 C A:GLY147 4.0 38.4 1.0 C B:LEU81 4.0 36.1 1.0 CA A:ALA148 4.0 35.8 1.0 O A:ASP122 4.1 36.7 1.0 N B:HIS80 4.2 40.7 1.0 CA A:PRO120 4.2 42.3 1.0 O A:HOH612 4.2 37.6 1.0 N B:GLU79 4.2 42.0 1.0 CA B:LEU81 4.3 37.1 1.0 O A:ALA148 4.4 41.4 1.0 O B:HOH712 4.4 45.6 1.0 N A:ALA148 4.5 36.7 1.0 CB B:LEU81 4.5 35.4 1.0 C B:HIS80 4.5 39.9 1.0 CB A:PRO120 4.7 45.4 1.0 CA B:HIS80 4.8 41.7 1.0 CB B:GLU79 4.9 50.4 1.0

Magnesium binding site 3 out of 4 in the Paak Family Amp-Ligase with Anp 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 Anp and Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg510 b:73.3 occ:1.00 O3A A:ANP503 2.3 57.1 1.0 O1G A:ANP503 2.5 70.5 1.0 OE2 A:GLU240 2.8 65.4 1.0 OE1 A:GLU240 2.8 75.3 1.0 O1A A:ANP503 2.9 55.9 1.0 OG A:SER87 3.0 54.0 1.0 CD A:GLU240 3.1 67.8 1.0 PA A:ANP503 3.2 55.4 1.0 PB A:ANP503 3.3 66.4 1.0 N3B A:ANP503 3.3 68.5 1.0 CB A:SER87 3.5 48.5 1.0 PG A:ANP503 3.5 73.0 1.0 O1B A:ANP503 3.7 61.7 1.0 NZ A:LYS62 3.8 78.9 1.0 O2A A:ANP503 4.1 56.9 1.0 O5' A:ANP503 4.4 50.4 1.0 OH A:TYR295 4.4 58.8 1.0 O2G A:ANP503 4.4 72.9 1.0 CG A:GLU240 4.6 68.8 1.0 O3G A:ANP503 4.6 71.3 1.0 O2B A:ANP503 4.6 55.0 1.0 CA A:SER87 4.7 49.1 1.0 C5' A:ANP503 4.8 46.9 1.0 CB A:SER238 4.8 48.3 1.0 OG1 A:THR239 4.8 48.8 1.0 N A:THR239 4.9 50.5 1.0 CE A:LYS62 5.0 75.3 1.0

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


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 Anp and Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg508 b:61.9 occ:1.00 OE2 B:GLU263 2.7 46.1 1.0 OG1 B:THR283 2.8 43.8 1.0 O B:ILE261 3.0 46.4 1.0 N B:THR283 3.3 41.6 1.0 CB B:THR283 3.6 44.5 1.0 CG1 B:VAL281 3.6 48.3 1.0 C B:VAL282 3.6 43.9 1.0 CD B:GLU263 3.7 51.2 1.0 C B:ILE261 3.8 46.3 1.0 CG B:ARG294 3.9 58.2 1.0 O B:VAL281 3.9 46.7 1.0 CA B:ARG294 3.9 46.6 1.0 N B:VAL282 3.9 41.9 1.0 CA B:VAL282 3.9 42.9 1.0 CD B:ARG294 4.0 70.6 1.0 CZ B:PHE54 4.0 55.2 1.0 CG2 B:ILE261 4.0 48.1 1.0 C B:VAL281 4.0 45.7 1.0 CG B:GLU263 4.0 47.8 1.0 CA B:THR283 4.0 43.3 1.0 CB B:ILE261 4.2 49.1 1.0 O B:VAL282 4.3 40.5 1.0 CB B:ARG294 4.3 53.9 1.0 CB B:GLU263 4.3 48.2 1.0 N B:ARG294 4.4 46.2 1.0 N B:GLU263 4.4 43.8 1.0 N B:PHE262 4.5 45.5 1.0 CB B:VAL281 4.6 44.8 1.0 CA B:ILE261 4.6 47.4 1.0 CA B:PHE262 4.7 44.3 1.0 CE2 B:PHE54 4.7 57.2 1.0 C B:PHE262 4.7 45.9 1.0 OE1 B:GLU263 4.8 52.5 1.0 CE1 B:PHE54 4.9 55.8 1.0 CA B:VAL281 4.9 44.0 1.0 CG2 B:THR283 5.0 47.7 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