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

All present enzymatic activity of Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 2,5-Di-O-Bn-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 2,5-Di-O-Bn-INSP4, PDB code: 4nzo 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)	35.53 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.110, 111.133, 41.299, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 21.5

The binding sites of Magnesium atom in the Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 2,5-Di-O-Bn-INSP4 (pdb code 4nzo). 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 2,5-Di-O-Bn-INSP4, PDB code: 4nzo:
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 2,5-Di-O-Bn-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 2,5-Di-O-Bn-INSP4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:12.4 occ:1.00 O A:HOH721 1.7 31.4 1.0 O3G A:ANP401 1.8 33.4 1.0 OD1 A:ASN323 2.1 23.0 1.0 O1B A:ANP401 2.2 26.0 1.0 OD2 A:ASP321 2.3 21.7 1.0 OD1 A:ASP321 2.4 20.3 1.0 CG A:ASP321 2.7 18.0 1.0 PG A:ANP401 3.0 36.0 1.0 CG A:ASN323 3.1 20.5 1.0 PB A:ANP401 3.5 26.9 1.0 ND2 A:ASN323 3.5 23.9 1.0 O A:HOH720 3.5 32.5 1.0 N3B A:ANP401 3.6 28.2 1.0 O1G A:ANP401 3.6 27.8 1.0 MG A:MG404 3.9 18.6 1.0 CB A:ASP321 4.1 16.1 1.0 O A:ALA191 4.2 18.4 1.0 CE1 A:HIS194 4.2 21.7 1.0 O2G A:ANP401 4.2 33.7 1.0 O A:HOH836 4.3 44.7 1.0 NH1 A:ARG134 4.4 16.6 0.7 CB A:ASN323 4.5 18.1 1.0 O2B A:ANP401 4.5 24.7 1.0 O3A A:ANP401 4.5 24.5 1.0 ND1 A:HIS194 4.6 21.2 1.0 O A:HOH564 4.7 26.8 1.0 O A:HOH577 4.8 18.1 1.0 NH2 A:ARG134 4.8 14.4 0.3 O A:HOH834 4.8 37.0 1.0 CA A:ASN323 4.8 16.0 1.0 O A:VAL322 4.9 14.9 1.0 OD2 A:ASP309 4.9 22.4 1.0 O2A A:ANP401 4.9 23.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 2,5-Di-O-Bn-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 2,5-Di-O-Bn-INSP4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:18.6 occ:1.00 OD2 A:ASP309 1.8 22.4 1.0 O A:HOH665 2.0 24.7 1.0 O2A A:ANP401 2.0 23.0 1.0 O1G A:ANP401 2.0 27.8 1.0 OD2 A:ASP321 2.3 21.7 1.0 N3B A:ANP401 2.3 28.2 1.0 PG A:ANP401 2.8 36.0 1.0 CG A:ASP309 3.1 19.1 1.0 PA A:ANP401 3.3 22.4 1.0 CG A:ASP321 3.3 18.0 1.0 PB A:ANP401 3.4 26.9 1.0 O3G A:ANP401 3.6 33.4 1.0 CB A:ASP321 3.6 16.1 1.0 O3A A:ANP401 3.7 24.5 1.0 O1B A:ANP401 3.7 26.0 1.0 OD1 A:ASP309 3.7 24.3 1.0 MG A:MG403 3.9 12.4 1.0 O2G A:ANP401 4.0 33.7 1.0 ND2 A:ASN323 4.1 23.9 1.0 NZ A:LYS248 4.1 36.3 1.0 CB A:ASP309 4.2 17.0 1.0 O3' A:ANP401 4.2 20.7 1.0 O1A A:ANP401 4.3 21.9 1.0 O5' A:ANP401 4.3 22.0 1.0 OD1 A:ASP321 4.4 20.3 1.0 C5' A:ANP401 4.4 21.3 1.0 O A:HOH791 4.6 55.3 1.0 O2B A:ANP401 4.7 24.7 1.0 C3' A:ANP401 4.7 21.1 1.0 OD1 A:ASN323 4.9 23.0 1.0 CG A:ASN323 5.0 20.5 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 2,5-Di-O-Bn-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 2,5-Di-O-Bn-INSP4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:40.0 occ:1.00 O A:HOH645 2.3 41.0 1.0 O A:ILE73 2.3 22.2 1.0 O A:SER68 2.4 27.4 1.0 O A:PHE70 2.5 27.0 1.0 O A:HOH756 2.7 47.5 1.0 C A:SER68 3.3 25.5 1.0 C A:ILE73 3.5 21.4 1.0 C A:PHE70 3.6 27.8 1.0 CA A:SER68 3.8 23.9 1.0 O A:LYS71 4.1 31.6 1.0 N A:ILE73 4.1 24.6 1.0 N A:PHE70 4.2 25.3 1.0 O A:HOH769 4.3 46.1 1.0 CA A:ILE73 4.3 21.7 1.0 N A:LEU69 4.3 27.4 1.0 C A:LYS71 4.4 30.3 1.0 NE2 A:GLN43 4.4 41.1 1.0 C A:LEU69 4.4 29.4 1.0 CA A:PHE70 4.5 25.3 1.0 CB A:SER68 4.5 22.3 1.0 N A:THR74 4.5 20.5 1.0 N A:LYS71 4.5 29.2 1.0 O A:HOH724 4.6 24.4 1.0 CA A:LYS71 4.6 33.1 1.0 O A:ILE67 4.6 20.7 1.0 CA A:LEU69 4.7 30.4 1.0 CB A:ILE73 4.7 21.3 1.0 CA A:THR74 4.8 21.8 1.0 O A:LEU69 4.9 29.4 1.0 N A:TYR72 5.0 28.7 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