Magnesium in PDB 4hvy: A Thermostable Variant of Human NUDT18 Nudix Domain Obtained By Hot Colony Filtration

The structure of A Thermostable Variant of Human NUDT18 Nudix Domain Obtained By Hot Colony Filtration, PDB code: 4hvy was solved by I.Asial, Y.X.Cheng, H.Engman, B.Wu, M.Dollhopf, P.Nordlund, T.Cornvik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.52 / 1.46
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.200, 90.200, 75.030, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 21

The structure of A Thermostable Variant of Human NUDT18 Nudix Domain Obtained By Hot Colony Filtration also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

The binding sites of Magnesium atom in the A Thermostable Variant of Human NUDT18 Nudix Domain Obtained By Hot Colony Filtration (pdb code 4hvy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the A Thermostable Variant of Human NUDT18 Nudix Domain Obtained By Hot Colony Filtration, PDB code: 4hvy:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the A Thermostable Variant of Human NUDT18 Nudix Domain Obtained By Hot Colony Filtration


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A Thermostable Variant of Human NUDT18 Nudix Domain Obtained By Hot Colony Filtration within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:40.9 occ:1.00 O A:HOH433 2.9 54.6 1.0 NE1 A:TRP144 2.9 24.9 1.0 O A:HOH358 3.0 62.7 1.0 CD1 A:TRP144 3.9 25.6 1.0 CE2 A:TRP144 3.9 23.8 1.0 CB A:LEU129 3.9 26.4 1.0 O A:HOH315 4.0 52.3 1.0 O A:HOH446 4.0 70.3 1.0 CD2 A:LEU129 4.1 29.0 1.0 CD1 A:LEU98 4.1 27.9 1.0 CZ2 A:TRP144 4.2 24.9 1.0 CD2 A:LEU98 4.2 29.5 1.0 CD1 A:LEU129 4.3 26.9 1.0 CG A:LEU129 4.3 27.5 1.0 CG A:LEU98 4.8 27.0 1.0 O A:HOH332 4.9 43.2 1.0 O A:HOH348 4.9 71.7 1.0 CA A:LEU129 4.9 29.4 1.0

Magnesium binding site 2 out of 3 in the A Thermostable Variant of Human NUDT18 Nudix Domain Obtained By Hot Colony Filtration


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A Thermostable Variant of Human NUDT18 Nudix Domain Obtained By Hot Colony Filtration within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:29.9 occ:1.00 O A:LEU58 2.7 22.8 1.0 N A:PHE50 2.8 21.7 1.0 O A:ALA48 2.9 21.4 1.0 CD2 A:LEU73 3.0 36.8 1.0 CA A:VAL49 3.4 19.9 1.0 CD1 A:PHE50 3.5 21.5 1.0 C A:VAL49 3.5 19.8 1.0 CD A:PRO74 3.7 25.7 1.0 C A:LEU58 3.7 21.4 1.0 CB A:LEU58 3.7 21.1 0.1 C A:ALA48 3.8 20.3 1.0 N A:LEU58 3.8 22.1 1.0 CA A:PHE50 3.8 22.4 1.0 CB A:LEU58 3.8 22.7 0.9 CB A:PHE50 3.8 22.7 1.0 O A:PHE50 3.9 25.2 1.0 CG1 A:VAL57 3.9 21.6 0.6 CA A:LEU58 4.0 21.5 0.1 CA A:LEU58 4.0 21.2 0.9 N A:VAL49 4.0 20.6 1.0 CG A:PHE50 4.2 21.7 1.0 C A:PHE50 4.3 23.6 1.0 CG A:LEU73 4.3 33.1 1.0 CG A:PRO74 4.5 24.4 1.0 CE1 A:PHE50 4.5 22.2 1.0 CB A:VAL49 4.6 20.9 1.0 CB A:LEU73 4.6 29.2 1.0 CG1 A:VAL49 4.6 22.5 1.0 CG A:LEU58 4.7 23.4 0.9 O A:VAL49 4.7 21.2 1.0 C A:VAL57 4.8 23.4 1.0 CA A:LEU73 4.9 26.0 1.0 CG A:LEU58 4.9 20.6 0.1 N A:LEU59 4.9 21.2 1.0 N A:PRO74 4.9 25.0 1.0 CD2 A:LEU58 5.0 24.7 0.9

Magnesium binding site 3 out of 3 in the A Thermostable Variant of Human NUDT18 Nudix Domain Obtained By Hot Colony Filtration


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of A Thermostable Variant of Human NUDT18 Nudix Domain Obtained By Hot Colony Filtration within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg206 b:38.0 occ:1.00 OE1 A:GLN172 3.4 47.0 1.0 CB A:GLN172 3.8 40.1 1.0 CG A:GLN172 4.2 42.4 1.0 CD A:GLN172 4.3 45.2 1.0 O A:GLN172 4.7 42.6 1.0 CA A:GLN172 4.9 40.2 1.0 C A:GLN172 4.9 41.9 1.0

I.Asial, Y.X.Cheng, H.Engman, M.Dollhopf, B.Wu, P.Nordlund, T.Cornvik. Engineering Protein Thermostability Using A Generic Activity-Independent Biophysical Screen Inside the Cell. Nat Commun V. 4 2901 2013.
ISSN: ESSN 2041-1723
PubMed: 24352381
DOI: 10.1038/NCOMMS3901