Magnesium in PDB 4nzn: Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 2-O-Bn-5-Pa-INSP4

All present enzymatic activity of Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 2-O-Bn-5-Pa-INSP4:
2.7.4.21; 2.7.4.24;

The structure of Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 2-O-Bn-5-Pa-INSP4, PDB code: 4nzn was solved by H.Wang, S.B.Shears, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.12 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.316, 110.690, 41.301, 90.00, 90.00, 90.00
R / Rfree (%)	14.1 / 18

The binding sites of Magnesium atom in the Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 2-O-Bn-5-Pa-INSP4 (pdb code 4nzn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 2-O-Bn-5-Pa-INSP4, PDB code: 4nzn:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 2-O-Bn-5-Pa-INSP4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 2-O-Bn-5-Pa-INSP4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:12.9 occ:1.00 O A:HOH734 1.8 21.2 1.0 O3G A:ANP401 1.9 20.6 1.0 OD1 A:ASN323 2.0 17.6 1.0 O1B A:ANP401 2.1 17.5 1.0 OD2 A:ASP321 2.3 16.1 1.0 OD1 A:ASP321 2.4 15.1 1.0 CG A:ASP321 2.7 14.6 1.0 PG A:ANP401 3.1 25.0 1.0 CG A:ASN323 3.1 16.5 1.0 PB A:ANP401 3.3 16.4 1.0 ND2 A:ASN323 3.6 18.2 1.0 N3B A:ANP401 3.6 20.8 1.0 O1G A:ANP401 3.6 20.6 1.0 O A:HOH733 3.8 41.3 1.0 MG A:MG404 3.9 15.9 1.0 CB A:ASP321 4.2 13.2 1.0 O2B A:ANP401 4.3 19.3 1.0 O A:ALA191 4.3 17.3 1.0 O A:HOH639 4.4 52.4 1.0 NH1 A:ARG134 4.4 12.8 0.7 O2G A:ANP401 4.4 25.0 1.0 CB A:ASN323 4.4 14.3 1.0 O3A A:ANP401 4.5 14.8 1.0 CE1 A:HIS194 4.5 17.5 1.0 O2A A:ANP401 4.6 14.0 1.0 O A:HOH566 4.6 28.1 1.0 O A:HOH580 4.7 19.5 1.0 ND1 A:HIS194 4.7 17.5 1.0 CA A:ASN323 4.8 14.6 1.0 O A:VAL322 4.9 12.9 1.0 NH2 A:ARG134 4.9 15.5 0.3 PA A:ANP401 5.0 13.7 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 2-O-Bn-5-Pa-INSP4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 2-O-Bn-5-Pa-INSP4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:15.9 occ:1.00 O1G A:ANP401 2.0 20.6 1.0 OD2 A:ASP309 2.0 22.8 1.0 O2A A:ANP401 2.0 14.0 1.0 O A:HOH673 2.1 23.6 1.0 OD2 A:ASP321 2.1 16.1 1.0 N3B A:ANP401 2.8 20.8 1.0 PG A:ANP401 2.9 25.0 1.0 CG A:ASP321 3.2 14.6 1.0 CG A:ASP309 3.2 19.4 1.0 PA A:ANP401 3.3 13.7 1.0 CB A:ASP321 3.5 13.2 1.0 PB A:ANP401 3.7 16.4 1.0 O1B A:ANP401 3.7 17.5 1.0 O3G A:ANP401 3.8 20.6 1.0 O3A A:ANP401 3.8 14.8 1.0 MG A:MG403 3.9 12.9 1.0 OD1 A:ASP309 3.9 25.0 1.0 O A:HOH779 4.0 44.4 1.0 ND2 A:ASN323 4.0 18.2 1.0 NZ A:LYS248 4.1 35.1 1.0 O3' A:ANP401 4.1 16.8 1.0 O2G A:ANP401 4.1 25.0 1.0 O A:HOH856 4.2 41.0 1.0 CB A:ASP309 4.2 14.6 1.0 OD1 A:ASP321 4.2 15.1 1.0 O A:HOH839 4.3 43.5 1.0 O1A A:ANP401 4.3 15.5 1.0 O5' A:ANP401 4.4 12.9 1.0 C5' A:ANP401 4.5 13.7 1.0 OD1 A:ASN323 4.7 17.6 1.0 C3' A:ANP401 4.7 15.0 1.0 CG A:ASN323 4.8 16.5 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 2-O-Bn-5-Pa-INSP4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 2-O-Bn-5-Pa-INSP4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:23.6 occ:1.00 O A:ILE73 2.3 18.0 1.0 O A:HOH694 2.3 43.5 1.0 O A:PHE70 2.3 19.2 1.0 O A:HOH653 2.4 27.1 1.0 O A:SER68 2.4 19.4 1.0 O A:HOH778 2.6 40.3 1.0 C A:SER68 3.4 19.3 1.0 C A:ILE73 3.4 17.9 1.0 C A:PHE70 3.5 22.3 1.0 CA A:SER68 3.9 17.8 1.0 N A:ILE73 4.0 19.3 1.0 O A:LYS71 4.1 25.0 1.0 CA A:ILE73 4.2 18.1 1.0 C A:LYS71 4.2 23.1 1.0 NE2 A:GLN43 4.2 35.7 1.0 N A:PHE70 4.2 21.4 1.0 O A:HOH797 4.3 50.2 1.0 C A:LEU69 4.4 22.6 1.0 N A:LYS71 4.4 23.1 1.0 CA A:LYS71 4.4 26.0 1.0 N A:LEU69 4.4 21.6 1.0 CA A:PHE70 4.4 20.8 1.0 N A:THR74 4.5 17.8 1.0 O A:HOH737 4.6 21.4 1.0 CB A:ILE73 4.6 18.3 1.0 CB A:SER68 4.6 19.0 1.0 O A:ILE67 4.7 17.1 1.0 CA A:LEU69 4.7 23.2 1.0 CA A:THR74 4.8 18.2 1.0 O A:HOH729 4.8 49.6 1.0 N A:TYR72 4.8 20.8 1.0 O A:LEU69 4.8 25.1 1.0 C A:TYR72 5.0 20.1 1.0

H.Wang, H.Y.Godage, A.M.Riley, J.D.Weaver, S.B.Shears, B.V.Potter. Synthetic Inositol Phosphate Analogs Reveal That PPIP5K2 Has A Surface-Mounted Substrate Capture Site That Is A Target For Drug Discovery. Chem.Biol. V. 21 689 2014.
ISSN: ISSN 1074-5521
PubMed: 24768307
DOI: 10.1016/J.CHEMBIOL.2014.03.009