Sodium 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:

Magnesium

(Mg)

3 atoms

The binding sites of Sodium 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 Sodium atom.
In total 4 binding sites of Sodium where determined in the A Thermostable Variant of Human NUDT18 Nudix Domain Obtained By Hot Colony Filtration, PDB code: 4hvy:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 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 Sodium with other atoms in the Na 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:Na205 b:62.9 occ:1.00 O A:HOH444 2.5 65.8 1.0 OE1 A:GLN89 2.8 32.8 1.0 O A:HOH324 3.1 78.3 1.0 CD A:GLN89 3.6 31.5 1.0 CG1 A:VAL85 3.7 30.2 1.0 NE2 A:GLN89 3.9 32.4 1.0 CG A:GLU86 3.9 33.6 1.0 N A:GLU86 4.3 28.0 1.0 CB A:VAL85 4.4 29.6 1.0 C A:VAL85 4.5 27.2 1.0 CA A:GLU86 4.5 28.6 1.0 O A:VAL85 4.8 25.7 1.0 OE2 A:GLU86 4.8 43.5 1.0 CB A:GLU86 4.9 31.4 1.0 CD A:GLU86 4.9 39.7 1.0 CG A:GLN89 5.0 29.7 1.0 OG1 A:THR83 5.0 35.7 1.0

Sodium binding site 2 out of 4 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 Sodium with other atoms in the Na 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:Na207 b:65.4 occ:1.00 ND1 A:HIS99 2.9 34.2 1.0 O A:HOH401 3.4 68.4 1.0 O A:THR125 3.4 36.8 1.0 CB A:HIS99 3.5 28.4 1.0 CG A:HIS99 3.6 31.6 1.0 OG1 A:THR125 3.6 32.5 1.0 O A:HOH326 3.7 62.0 1.0 CE1 A:HIS99 3.9 34.7 1.0 C A:THR125 4.0 33.9 1.0 CB A:THR125 4.1 31.7 1.0 N A:GLY126 4.5 33.1 1.0 CA A:GLY126 4.5 33.4 1.0 O A:HOH374 4.6 80.5 1.0 CA A:THR125 4.7 31.7 1.0 CD2 A:HIS99 4.8 33.6 1.0 O A:HOH413 5.0 48.9 1.0 NE2 A:HIS99 5.0 33.7 1.0

Sodium binding site 3 out of 4 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 Sodium with other atoms in the Na 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:Na208 b:65.7 occ:1.00 ND1 A:HIS157 3.2 45.7 1.0 N A:HIS157 3.3 35.1 1.0 O A:HOH435 3.6 50.7 1.0 CA A:ALA156 3.7 32.9 1.0 C A:ALA156 4.0 34.2 1.0 CG A:HIS157 4.1 44.1 1.0 CB A:HIS157 4.1 41.3 1.0 CE1 A:HIS157 4.1 46.8 1.0 CB A:ALA156 4.2 33.8 1.0 CA A:HIS157 4.3 39.0 1.0 N A:ALA156 4.9 31.2 1.0 O A:ARG155 4.9 34.5 1.0 O A:HOH415 5.0 65.7 1.0

Sodium binding site 4 out of 4 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 Sodium with other atoms in the Na binding site number 4 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:Na209 b:72.9 occ:1.00 NE A:ARG155 3.8 38.9 1.0 CB A:ALA156 4.1 33.8 1.0 CZ A:ARG155 4.2 42.0 1.0 NH2 A:ARG155 4.2 43.8 1.0 OH A:TYR72 4.4 37.5 1.0 O A:HOH354 4.5 59.6 1.0 CD A:ARG155 4.5 36.4 1.0 CG A:ARG155 4.5 34.8 1.0 CZ A:TYR72 4.7 35.1 1.0 O A:HOH415 4.7 65.7 1.0 O A:HOH390 4.7 57.8 1.0 NH2 A:ARG117 5.0 28.5 0.3

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