Magnesium in PDB 7zeg: Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif-BN7GMP

All present enzymatic activity of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif-BN7GMP:
3.1.3.5; 3.1.3.91;

The structure of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif-BN7GMP, PDB code: 7zeg was solved by D.Kubacka, M.Kozarski, M.R.Baranowski, R.Wojcik, J.Jemielity, J.Kowalska, J.Basquin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.69 / 1.56
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.755, 79.135, 94.388, 90, 93.23, 90
R / Rfree (%)	24 / 27.3

The structure of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif-BN7GMP also contains other interesting chemical elements:

Fluorine

(F)

4 atoms

The binding sites of Magnesium atom in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif-BN7GMP (pdb code 7zeg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif-BN7GMP, PDB code: 7zeg:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif-BN7GMP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif-BN7GMP within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:20.3 occ:1.00 O A:HOH553 2.0 25.6 1.0 OD2 A:ASP41 2.0 18.3 1.0 O A:ASP43 2.1 22.7 1.0 OD1 A:ASP230 2.1 20.9 1.0 O A:HOH530 2.2 24.2 1.0 O A:HOH615 2.2 21.6 1.0 CG A:ASP41 2.9 21.9 1.0 CG A:ASP230 3.1 28.1 1.0 C A:ASP43 3.2 20.4 1.0 OD1 A:ASP41 3.3 20.9 1.0 OD2 A:ASP230 3.5 26.3 1.0 CA A:ASP43 3.9 21.7 1.0 CB A:ASP43 4.0 20.5 1.0 N A:ASP43 4.0 23.9 1.0 OD2 A:ASP234 4.0 18.0 1.0 OG1 A:THR45 4.1 20.1 1.0 O A:HOH612 4.1 28.9 1.0 CB A:ASP41 4.2 22.5 1.0 O A:HOH713 4.3 22.7 1.0 N A:MET44 4.3 21.0 1.0 OP2 A:IOO401 4.4 24.9 1.0 O A:HOH664 4.4 30.7 1.0 CB A:MET44 4.4 13.3 1.0 CB A:ASP230 4.5 18.9 1.0 N A:THR45 4.6 23.8 1.0 C A:PHE42 4.6 19.8 1.0 CA A:MET44 4.7 17.9 1.0 C A:MET44 4.7 21.1 1.0 CG A:MET44 4.8 21.7 1.0 N A:ASP230 4.8 18.4 1.0 NZ A:LYS205 4.8 24.3 1.0 CB A:THR45 4.9 16.6 1.0 CG A:ASP234 5.0 16.0 1.0

Magnesium binding site 2 out of 2 in the Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif-BN7GMP


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Cytosolic 5' Nucleotidase Iiib in Complex with 3,4-Dif-BN7GMP within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg405 b:35.9 occ:1.00 O B:HOH520 2.0 36.5 1.0 O B:HOH556 2.0 31.2 1.0 OD2 B:ASP41 2.0 38.3 1.0 O B:HOH552 2.0 36.5 1.0 O B:ASP43 2.1 33.9 1.0 OD1 B:ASP230 2.2 41.1 1.0 CG B:ASP41 3.0 38.7 1.0 CG B:ASP230 3.1 45.0 1.0 C B:ASP43 3.3 37.6 1.0 OD2 B:ASP230 3.3 43.3 1.0 OD1 B:ASP41 3.4 35.4 1.0 OG1 B:THR45 4.0 39.8 1.0 CA B:ASP43 4.0 36.4 1.0 OD2 B:ASP234 4.0 28.4 1.0 CB B:ASP43 4.1 35.9 1.0 N B:ASP43 4.1 28.5 1.0 CB B:ASP41 4.3 26.5 1.0 O B:HOH615 4.3 37.6 1.0 N B:MET44 4.3 38.3 1.0 OP2 B:IOO401 4.4 28.7 1.0 CB B:MET44 4.4 41.0 1.0 O B:HOH537 4.5 38.4 1.0 O B:HOH588 4.5 44.9 1.0 CB B:ASP230 4.5 33.5 1.0 N B:THR45 4.6 38.2 1.0 CA B:MET44 4.7 41.9 1.0 C B:MET44 4.7 45.1 1.0 C B:PHE42 4.7 25.5 1.0 CG B:MET44 4.8 42.4 1.0 NZ B:LYS205 4.8 30.5 1.0 N B:ASP230 4.9 35.4 1.0 CB B:THR45 5.0 32.0 1.0 CG B:ASP234 5.0 30.0 1.0

D.Kubacka, M.Kozarski, M.R.Baranowski, R.Wojcik, J.Panecka-Hofman, D.Strzelecka, J.Basquin, J.Jemielity, J.Kowalska. Substrate-Based Design of Cytosolic Nucleotidase Iiib Inhibitors and Structural Insights Into Inhibition Mechanism. Pharmaceuticals V. 15 2022.
ISSN: ESSN 1424-8247
PubMed: 35631380
DOI: 10.3390/PH15050554