Magnesium in PDB 4zev: Crystal Structure of PFHAD1 in Complex with Mannose-6-Phosphate

The structure of Crystal Structure of PFHAD1 in Complex with Mannose-6-Phosphate, PDB code: 4zev 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)	19.60 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.600, 44.500, 84.500, 90.00, 101.30, 90.00
R / Rfree (%)	18.8 / 21.9

The binding sites of Magnesium atom in the Crystal Structure of PFHAD1 in Complex with Mannose-6-Phosphate (pdb code 4zev). 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 Mannose-6-Phosphate, PDB code: 4zev:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of PFHAD1 in Complex with Mannose-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 Mannose-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:26.5 occ:1.00 O A:HOH431 2.1 35.2 1.0 OD1 A:ASP238 2.2 25.4 1.0 O2P A:M6P302 2.2 29.9 1.0 O A:HOH412 2.3 24.6 1.0 O A:ASP29 2.4 18.6 1.0 CG A:ASP238 2.9 26.5 1.0 OD2 A:ASP238 2.9 35.9 1.0 HB1 A:ALA27 3.3 17.9 1.0 H62 A:M6P302 3.3 0.4 1.0 C A:ASP29 3.5 20.1 1.0 P A:M6P302 3.6 24.7 1.0 HA3 A:GLY30 3.6 21.0 1.0 H A:GLY239 3.7 23.4 1.0 HG1 A:THR31 3.7 20.8 1.0 O6 A:M6P302 3.8 87.5 1.0 HB2 A:ASP29 3.8 23.2 1.0 C6 A:M6P302 4.1 87.9 1.0 CB A:ALA27 4.1 14.9 1.0 HB3 A:ALA27 4.1 17.9 1.0 OD2 A:ASP242 4.2 18.2 1.0 N A:GLY239 4.3 19.5 1.0 HA3 A:GLY239 4.3 22.2 1.0 CB A:ASP238 4.3 17.7 1.0 O1P A:M6P302 4.3 21.3 1.0 CA A:GLY30 4.3 17.5 1.0 H A:ASP238 4.3 17.8 1.0 N A:GLY30 4.4 18.7 1.0 CA A:ASP29 4.4 20.0 1.0 O A:THR201 4.4 32.0 1.0 HB2 A:ALA27 4.5 17.9 1.0 H5 A:M6P302 4.5 0.0 1.0 OG1 A:THR31 4.5 17.3 1.0 CB A:ASP29 4.6 19.3 1.0 N A:ASP29 4.6 17.1 1.0 O A:HOH548 4.6 35.6 1.0 H A:ASP29 4.6 20.5 1.0 HB3 A:ASP238 4.6 21.2 1.0 HD1 A:PHE202 4.6 0.2 1.0 HB2 A:PHE202 4.6 90.1 1.0 O3P A:M6P302 4.7 23.5 1.0 H A:LEU28 4.7 14.2 1.0 C A:GLY30 4.7 15.3 1.0 H A:THR31 4.8 19.0 1.0 HZ1 A:LYS215 4.8 17.3 1.0 OD1 A:ASN241 4.8 17.4 1.0 HB2 A:ASP238 4.8 21.2 1.0 CA A:GLY239 4.9 18.5 1.0 HD21 A:ASN241 4.9 19.8 1.0 N A:THR31 4.9 15.8 1.0 H61 A:M6P302 4.9 0.4 1.0 HB3 A:ASP29 4.9 23.2 1.0 N A:ASP238 4.9 14.8 1.0 C5 A:M6P302 4.9 88.4 1.0 CA A:ASP238 4.9 16.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of PFHAD1 in Complex with Mannose-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 Mannose-6-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:27.5 occ:1.00 O4 B:PO4302 2.1 33.1 1.0 O B:ASP29 2.2 26.7 1.0 OD1 B:ASP238 2.3 36.6 1.0 O B:HOH411 2.3 31.4 1.0 O B:HOH453 2.6 35.6 1.0 CG B:ASP238 2.9 30.6 1.0 OD2 B:ASP238 2.9 28.5 1.0 HB1 B:ALA27 3.3 23.6 1.0 C B:ASP29 3.3 25.0 1.0 HB2 B:ASP29 3.5 34.9 1.0 HA3 B:GLY30 3.6 27.0 1.0 P B:PO4302 3.6 30.4 1.0 HA3 B:GLY239 3.8 33.3 1.0 HG1 B:THR31 3.9 34.2 1.0 H B:ASP238 3.9 33.1 1.0 HB3 B:ALA27 4.0 23.6 1.0 CB B:ALA27 4.1 19.7 1.0 H B:GLY239 4.2 36.5 1.0 CA B:ASP29 4.2 26.8 1.0 OD2 B:ASP242 4.2 33.2 1.0 N B:GLY30 4.3 22.5 1.0 O1 B:PO4302 4.3 26.1 1.0 CB B:ASP29 4.3 29.1 1.0 N B:GLY239 4.3 30.4 1.0 CA B:GLY30 4.3 22.5 1.0 O3 B:PO4302 4.3 33.3 1.0 H B:ASP29 4.4 29.4 1.0 CB B:ASP238 4.4 27.8 1.0 N B:ASP29 4.4 24.5 1.0 HB2 B:ALA27 4.5 23.6 1.0 CA B:GLY239 4.5 27.8 1.0 O2 B:PO4302 4.6 29.6 1.0 HB3 B:ASP29 4.6 34.9 1.0 OG1 B:THR31 4.7 28.5 1.0 N B:ASP238 4.7 27.6 1.0 H B:LEU28 4.7 22.5 1.0 OD1 B:ASN241 4.7 31.8 1.0 HA2 B:GLY239 4.7 33.3 1.0 C B:GLY30 4.8 22.0 1.0 HD21 B:ASN241 4.8 40.6 1.0 HB3 B:ASP238 4.8 33.4 1.0 HZ1 B:LYS215 4.8 24.6 1.0 C B:ASP238 4.8 33.1 1.0 H B:THR31 4.8 22.5 1.0 CA B:ASP238 4.9 30.7 1.0 HB2 B:ASP238 4.9 33.4 1.0 N B:THR31 5.0 18.8 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