Magnesium in PDB 4zex: Crystal Structure of PFHAD1 in Complex with Glyceraldehyde-3-Phosphate

The structure of Crystal Structure of PFHAD1 in Complex with Glyceraldehyde-3-Phosphate, PDB code: 4zex 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)	19.93 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.600, 44.600, 84.100, 90.00, 101.30, 90.00
R / Rfree (%)	17.3 / 22.1

The binding sites of Magnesium atom in the Crystal Structure of PFHAD1 in Complex with Glyceraldehyde-3-Phosphate (pdb code 4zex). 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 Glyceraldehyde-3-Phosphate, PDB code: 4zex:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of PFHAD1 in Complex with Glyceraldehyde-3-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 Glyceraldehyde-3-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:32.8 occ:1.00 O A:HOH501 2.0 38.7 1.0 O3P A:G3H302 2.1 29.1 1.0 OD1 A:ASP238 2.2 24.6 1.0 O A:HOH411 2.3 33.9 1.0 O A:ASP29 2.3 18.6 1.0 CG A:ASP238 2.9 29.5 1.0 OD2 A:ASP238 3.0 37.7 1.0 HB1 A:ALA27 3.2 16.3 1.0 C A:ASP29 3.5 18.9 1.0 HA3 A:GLY30 3.6 22.6 1.0 P A:G3H302 3.6 24.9 1.0 HG1 A:THR31 3.6 18.8 1.0 H31 A:G3H302 3.7 0.7 1.0 H32 A:G3H302 3.8 0.7 1.0 HB2 A:ASP29 3.9 33.7 1.0 CB A:ALA27 4.0 13.6 1.0 HB3 A:ALA27 4.0 16.3 1.0 C3 A:G3H302 4.1 88.1 1.0 OD2 A:ASP242 4.2 21.4 1.0 HD1 A:PHE202 4.2 0.5 1.0 H A:ASP238 4.2 16.4 1.0 H A:GLY239 4.2 23.2 1.0 HA3 A:GLY239 4.3 19.5 1.0 CA A:GLY30 4.3 18.8 1.0 O1P A:G3H302 4.3 83.3 1.0 N A:GLY30 4.3 16.4 1.0 O A:THR201 4.4 31.8 1.0 OG1 A:THR31 4.4 15.7 1.0 HB2 A:ALA27 4.4 16.3 1.0 CB A:ASP238 4.4 17.3 1.0 O2P A:G3H302 4.4 24.4 1.0 CA A:ASP29 4.5 25.6 1.0 N A:GLY239 4.5 19.3 1.0 O4P A:G3H302 4.5 22.2 1.0 C A:GLY30 4.6 13.6 1.0 CB A:ASP29 4.6 28.1 1.0 N A:ASP29 4.6 24.3 1.0 H A:LEU28 4.7 14.4 1.0 HB3 A:ASP238 4.7 20.8 1.0 HB2 A:PHE202 4.7 78.2 1.0 H A:THR31 4.8 16.0 1.0 H A:ASP29 4.8 29.2 1.0 N A:ASP238 4.8 13.7 1.0 N A:THR31 4.8 13.3 1.0 CD1 A:PHE202 4.9 85.4 1.0 HB A:THR31 4.9 23.1 1.0 CA A:GLY239 4.9 16.2 1.0 HZ1 A:LYS215 4.9 19.2 1.0 C A:ASP238 5.0 18.4 1.0 CA A:ASP238 5.0 16.0 1.0 HB2 A:ASP238 5.0 20.8 1.0 N A:LEU28 5.0 12.0 1.0 OD1 A:ASN241 5.0 21.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of PFHAD1 in Complex with Glyceraldehyde-3-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 Glyceraldehyde-3-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:40.2 occ:1.00 OD1 B:ASP238 2.0 40.7 1.0 O B:HOH410 2.1 31.8 1.0 O4 B:PO4302 2.1 49.4 1.0 O B:ASP29 2.4 32.4 1.0 O B:HOH420 2.8 36.1 1.0 CG B:ASP238 2.9 37.7 1.0 HB1 B:ALA27 3.1 28.7 1.0 OD2 B:ASP238 3.2 35.5 1.0 C B:ASP29 3.5 31.0 1.0 P B:PO4302 3.6 39.2 1.0 HB3 B:ALA27 3.7 28.7 1.0 HG1 B:THR31 3.7 34.3 1.0 CB B:ALA27 3.8 23.9 1.0 HB2 B:ASP29 3.8 50.2 1.0 H B:GLY239 3.8 38.3 1.0 H B:ASP238 3.8 39.4 1.0 HA3 B:GLY30 3.8 36.6 1.0 HA3 B:GLY239 3.9 47.0 1.0 OD2 B:ASP242 4.0 33.2 1.0 HB2 B:ALA27 4.1 28.7 1.0 N B:GLY239 4.1 31.9 1.0 O1 B:PO4302 4.1 32.2 1.0 CB B:ASP238 4.3 33.0 1.0 O3 B:PO4302 4.4 39.7 1.0 CA B:ASP29 4.4 34.8 1.0 N B:GLY30 4.4 31.9 1.0 OG1 B:THR31 4.5 28.6 1.0 CA B:GLY30 4.5 30.5 1.0 O2 B:PO4302 4.5 39.3 1.0 N B:ASP238 4.5 32.8 1.0 CB B:ASP29 4.5 41.9 1.0 N B:ASP29 4.5 28.4 1.0 CA B:GLY239 4.5 39.1 1.0 H B:LEU28 4.6 30.6 1.0 H B:ASP29 4.6 34.0 1.0 HB3 B:ASP238 4.6 39.6 1.0 OD1 B:ASN241 4.6 35.3 1.0 C B:ASP238 4.7 32.1 1.0 HZ1 B:LYS215 4.7 35.4 1.0 CA B:ASP238 4.7 32.1 1.0 C B:GLY30 4.8 25.7 1.0 HD21 B:ASN241 4.8 53.4 1.0 HB3 B:ASP29 4.8 50.2 1.0 HB B:THR31 4.9 28.3 1.0 H B:THR31 4.9 30.7 1.0 HZ2 B:LYS215 4.9 35.4 1.0 N B:LEU28 4.9 25.5 1.0 HB2 B:ASP238 4.9 39.6 1.0 HA2 B:GLY239 4.9 47.0 1.0 N B:THR31 4.9 25.6 1.0 CG B:ASP242 5.0 35.8 1.0 C B:LEU28 5.0 23.8 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