Magnesium in PDB 2y4n: PAAK1 in Complex with Phenylacetyl Adenylate

All present enzymatic activity of PAAK1 in Complex with Phenylacetyl Adenylate:
6.2.1.30;

The structure of PAAK1 in Complex with Phenylacetyl Adenylate, PDB code: 2y4n was solved by A.Law, M.J.Boulanger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.01 / 1.92
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	57.260, 62.390, 76.590, 91.16, 108.33, 106.27
R / Rfree (%)	18.1 / 23.2

The binding sites of Magnesium atom in the PAAK1 in Complex with Phenylacetyl Adenylate (pdb code 2y4n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the PAAK1 in Complex with Phenylacetyl Adenylate, PDB code: 2y4n:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the PAAK1 in Complex with Phenylacetyl Adenylate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of PAAK1 in Complex with Phenylacetyl Adenylate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:29.9 occ:1.00 O A:LEU353 2.2 19.9 1.0 O A:HOH930 2.3 36.2 1.0 O A:HOH778 2.3 29.4 1.0 O A:HOH812 2.4 23.9 1.0 O A:GLN350 2.4 23.7 1.0 O A:HOH748 3.0 50.2 1.0 C A:LEU353 3.4 21.2 1.0 C A:GLN350 3.4 24.4 1.0 CA A:ARG351 3.7 25.3 1.0 N A:ARG351 4.0 24.4 1.0 C A:ARG351 4.0 25.2 1.0 O A:ARG351 4.1 22.3 1.0 N A:LEU353 4.1 23.0 1.0 CA A:LEU353 4.2 20.7 1.0 C A:ALA354 4.3 21.5 1.0 O A:ALA354 4.3 19.2 1.0 N A:ALA354 4.3 21.7 1.0 CA A:ALA354 4.5 21.5 1.0 O A:LEU348 4.5 24.4 1.0 O A:LEU347 4.5 21.4 1.0 CA A:GLN350 4.6 23.9 1.0 CB A:LEU353 4.7 20.4 1.0 N A:GLN350 4.7 24.0 1.0 N A:PRO355 4.7 21.4 1.0 N A:ALA352 4.8 24.9 1.0 C A:LEU348 4.9 24.1 1.0 CA A:LEU348 4.9 23.0 1.0 S2 A:BME504 4.9 43.8 1.0 SG A:CYS377 5.0 35.6 1.0

Magnesium binding site 2 out of 4 in the PAAK1 in Complex with Phenylacetyl Adenylate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of PAAK1 in Complex with Phenylacetyl Adenylate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:44.0 occ:1.00 O A:HOH616 2.3 30.7 1.0 O A:SER205 2.5 27.6 1.0 O A:VAL203 2.6 38.9 1.0 O A:HOH964 2.7 37.7 1.0 C A:VAL203 3.6 38.8 1.0 C A:SER205 3.7 28.7 1.0 O A:LEU207 3.8 24.9 1.0 N A:SER205 3.8 34.6 1.0 C A:GLN204 3.9 37.2 1.0 OG A:SER205 4.1 31.2 1.0 CA A:GLN204 4.1 38.4 1.0 O A:GLY230 4.2 28.1 1.0 N A:GLN204 4.2 37.3 1.0 CA A:SER205 4.3 30.4 1.0 O A:GLN204 4.3 37.4 1.0 O A:MET229 4.4 34.0 1.0 O A:HOH611 4.5 51.6 1.0 CA A:VAL203 4.6 40.6 1.0 N A:SER206 4.8 27.0 1.0 CB A:SER205 4.8 30.3 1.0 O A:PRO202 4.8 44.5 1.0 C A:SER206 4.8 26.1 1.0 C A:LEU207 4.9 26.3 1.0 N A:LEU207 4.9 25.9 1.0

Magnesium binding site 3 out of 4 in the PAAK1 in Complex with Phenylacetyl Adenylate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of PAAK1 in Complex with Phenylacetyl Adenylate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:34.1 occ:1.00 O B:LEU353 2.3 23.4 1.0 O B:HOH802 2.3 45.8 1.0 O B:HOH758 2.3 24.8 1.0 O B:HOH711 2.3 27.0 1.0 O B:GLN350 2.4 22.9 1.0 O B:HOH650 2.8 36.0 1.0 C B:GLN350 3.4 25.7 1.0 C B:LEU353 3.4 24.5 1.0 CA B:ARG351 3.6 26.2 1.0 C B:ARG351 3.9 26.1 1.0 N B:ARG351 3.9 24.2 1.0 N B:LEU353 3.9 23.1 1.0 O B:ARG351 4.0 26.4 1.0 CA B:LEU353 4.2 22.9 1.0 C B:ALA354 4.3 25.0 1.0 O B:ALA354 4.3 23.9 1.0 N B:ALA354 4.4 23.2 1.0 O B:LEU347 4.5 22.1 1.0 N B:ALA352 4.5 25.4 1.0 CA B:GLN350 4.5 25.0 1.0 CB B:LEU353 4.6 21.9 1.0 CA B:ALA354 4.6 25.5 1.0 O B:LEU348 4.6 23.8 1.0 N B:PRO355 4.7 27.5 1.0 N B:GLN350 4.7 26.7 1.0 CA B:LEU348 4.8 25.8 1.0 C B:ALA352 4.9 24.9 1.0 CB B:ARG351 4.9 27.3 1.0 SG B:CYS377 4.9 36.5 1.0 C B:LEU348 4.9 27.2 1.0 CD2 B:LEU348 5.0 36.2 1.0

Magnesium binding site 4 out of 4 in the PAAK1 in Complex with Phenylacetyl Adenylate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of PAAK1 in Complex with Phenylacetyl Adenylate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:45.8 occ:1.00 O B:HOH731 2.1 37.9 1.0 O B:HOH644 2.3 35.7 1.0 O B:HOH715 2.4 41.0 1.0 O B:VAL203 2.4 45.5 1.0 O B:SER205 2.5 35.8 1.0 O B:HOH846 2.9 49.7 1.0 C B:VAL203 3.4 45.0 1.0 C B:SER205 3.6 36.5 1.0 O B:LEU207 3.7 30.4 1.0 C B:GLN204 3.8 43.0 1.0 N B:SER205 3.9 41.8 1.0 CA B:GLN204 4.1 44.0 1.0 N B:GLN204 4.1 44.1 1.0 O B:GLY230 4.2 35.6 1.0 OG B:SER205 4.2 38.8 1.0 O B:GLN204 4.2 41.5 1.0 CA B:SER205 4.3 38.1 1.0 O B:MET229 4.3 40.1 1.0 O B:HOH678 4.5 43.9 1.0 CA B:VAL203 4.5 45.2 1.0 O B:PRO202 4.5 45.7 1.0 N B:SER206 4.6 33.5 1.0 C B:SER206 4.7 29.0 1.0 N B:LEU207 4.7 29.8 1.0 C B:LEU207 4.8 28.1 1.0 CA B:SER206 4.8 31.0 1.0 CB B:SER205 4.9 40.6 1.0 C B:GLY230 5.0 36.5 1.0

A.Law, M.J.Boulanger. Defining A Structural and Kinetic Rationale For Paralogous Copies of Phenylacetate-Coa Ligases From the Cystic Fibrosis Pathogen Burkholderia Cenocepacia J2315. J.Biol.Chem. V. 286 15577 2011.
ISSN: ISSN 0021-9258
PubMed: 21388965
DOI: 10.1074/JBC.M111.219683