Magnesium in PDB 4zew: Crystal Structure of PFHAD1 in Complex with Glucose-6-Phosphate

The structure of Crystal Structure of PFHAD1 in Complex with Glucose-6-Phosphate, PDB code: 4zew was solved by J.Park, N.H.Tolia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.62 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.700, 44.500, 84.800, 90.00, 101.40, 90.00
R / Rfree (%)	17.9 / 22

The binding sites of Magnesium atom in the Crystal Structure of PFHAD1 in Complex with Glucose-6-Phosphate (pdb code 4zew). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of PFHAD1 in Complex with Glucose-6-Phosphate, PDB code: 4zew:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of PFHAD1 in Complex with Glucose-6-Phosphate


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 PFHAD1 in Complex with Glucose-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:26.7 occ:1.00 O A:HOH418 2.0 26.8 1.0 O1P A:G6P302 2.1 23.2 1.0 OD1 A:ASP238 2.2 22.1 1.0 O A:HOH405 2.3 24.1 1.0 O A:ASP29 2.4 16.9 1.0 CG A:ASP238 2.9 21.7 1.0 OD2 A:ASP238 3.0 28.2 1.0 H62 A:G6P302 3.2 39.2 1.0 HB1 A:ALA27 3.3 16.3 1.0 H61 A:G6P302 3.5 39.2 1.0 C A:ASP29 3.5 21.0 1.0 HA3 A:GLY30 3.6 16.5 1.0 P A:G6P302 3.6 16.7 1.0 H A:GLY239 3.7 25.3 1.0 C6 A:G6P302 3.7 32.7 1.0 HG1 A:THR31 3.8 19.6 1.0 HB2 A:ASP29 3.8 19.8 1.0 O6 A:G6P302 4.1 39.7 1.0 CB A:ALA27 4.1 13.6 1.0 HB3 A:ALA27 4.1 16.3 1.0 OD2 A:ASP242 4.2 17.9 1.0 HA3 A:GLY239 4.3 24.4 1.0 N A:GLY239 4.3 21.1 1.0 CA A:GLY30 4.3 13.8 1.0 H A:ASP238 4.3 18.8 1.0 CB A:ASP238 4.4 17.0 1.0 N A:GLY30 4.4 15.9 1.0 O3P A:G6P302 4.4 16.2 1.0 O A:THR201 4.4 31.7 1.0 HB2 A:ALA27 4.5 16.3 1.0 CA A:ASP29 4.5 18.1 1.0 HB2 A:PHE202 4.5 51.4 1.0 OG1 A:THR31 4.5 16.4 1.0 CB A:ASP29 4.6 16.5 1.0 O2P A:G6P302 4.6 19.8 1.0 N A:ASP29 4.6 14.7 1.0 H A:ASP29 4.6 17.7 1.0 HB3 A:ASP238 4.7 20.4 1.0 C A:GLY30 4.7 13.7 1.0 H A:LEU28 4.8 15.9 1.0 H A:THR31 4.8 16.3 1.0 HZ1 A:LYS215 4.8 16.1 1.0 OD1 A:ASN241 4.8 21.0 1.0 CA A:GLY239 4.9 20.3 1.0 O A:HOH498 4.9 36.6 1.0 N A:THR31 4.9 13.6 1.0 HD21 A:ASN241 4.9 22.1 1.0 HB2 A:ASP238 4.9 20.4 1.0 N A:ASP238 4.9 15.7 1.0 CA A:ASP238 5.0 17.1 1.0 HB3 A:ASP29 5.0 19.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of PFHAD1 in Complex with Glucose-6-Phosphate


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 PFHAD1 in Complex with Glucose-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:27.4 occ:1.00 O4 B:PO4302 2.1 31.9 1.0 OD1 B:ASP238 2.2 35.0 1.0 O B:ASP29 2.3 26.2 1.0 O B:HOH409 2.3 35.4 1.0 O B:HOH407 2.3 30.0 1.0 OD2 B:ASP238 2.8 28.9 1.0 CG B:ASP238 2.8 36.5 1.0 HB1 B:ALA27 3.3 22.8 1.0 H B:GLY239 3.3 43.1 1.0 C B:ASP29 3.4 21.1 1.0 P B:PO4302 3.6 27.5 1.0 HB2 B:ASP29 3.6 33.9 1.0 HA3 B:GLY30 3.7 25.9 1.0 HG1 B:THR31 4.0 33.7 1.0 HA3 B:GLY239 4.0 31.6 1.0 N B:GLY239 4.0 35.9 1.0 HB3 B:ALA27 4.0 22.8 1.0 CB B:ALA27 4.1 19.0 1.0 O1 B:PO4302 4.2 21.9 1.0 H B:ASP238 4.2 35.6 1.0 CA B:ASP29 4.2 26.5 1.0 CB B:ASP238 4.3 29.0 1.0 N B:GLY30 4.3 21.2 1.0 OD2 B:ASP242 4.3 24.3 1.0 O3 B:PO4302 4.3 29.8 1.0 CB B:ASP29 4.3 28.2 1.0 CA B:GLY30 4.3 21.6 1.0 N B:ASP29 4.4 26.4 1.0 H B:ASP29 4.4 31.7 1.0 HB2 B:ALA27 4.4 22.8 1.0 O2 B:PO4302 4.5 38.5 1.0 HD21 B:ASN241 4.5 41.0 1.0 OD1 B:ASN241 4.6 30.4 1.0 CA B:GLY239 4.6 26.3 1.0 HB3 B:ASP238 4.6 34.8 1.0 H B:LEU28 4.7 22.7 1.0 OG1 B:THR31 4.7 28.1 1.0 HB3 B:ASP29 4.7 33.9 1.0 H B:THR31 4.8 25.8 1.0 HB2 B:ASP238 4.8 34.8 1.0 HZ1 B:LYS215 4.8 28.6 1.0 C B:GLY30 4.8 25.1 1.0 N B:ASP238 4.9 29.6 1.0 CA B:ASP238 4.9 31.1 1.0 C B:ASP238 4.9 34.2 1.0 N B:THR31 4.9 21.5 1.0 N B:LEU28 5.0 18.9 1.0

J.Park, A.M.Guggisberg, A.R.Odom, N.H.Tolia. Cap-Domain Closure Enables Diverse Substrate Recognition By the C2-Type Haloacid Dehalogenase-Like Sugar Phosphatase Plasmodium Falciparum HAD1. Acta Crystallogr. D Biol. V. 71 1824 2015CRYSTALLOGR..
ISSN: ESSN 1399-0047
PubMed: 26327372
DOI: 10.1107/S1399004715012067