Magnesium in PDB 7b7v: Structure of NUDT15 in Complex with Acyclovir Monophosphate

All present enzymatic activity of Structure of NUDT15 in Complex with Acyclovir Monophosphate:
3.6.1.9;

The structure of Structure of NUDT15 in Complex with Acyclovir Monophosphate, PDB code: 7b7v was solved by D.Rehling, P.Stenmark, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.09 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.643, 49.12, 135.22, 90, 90, 90
R / Rfree (%)	18.8 / 20.9

The structure of Structure of NUDT15 in Complex with Acyclovir Monophosphate also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Structure of NUDT15 in Complex with Acyclovir Monophosphate (pdb code 7b7v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of NUDT15 in Complex with Acyclovir Monophosphate, PDB code: 7b7v:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of NUDT15 in Complex with Acyclovir Monophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of NUDT15 in Complex with Acyclovir Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:25.2 occ:1.00 O A:GLY47 2.0 23.3 1.0 OE2 A:GLU67 2.1 22.6 1.0 O A:HOH362 2.1 24.1 1.0 O A:HOH367 2.1 22.8 1.0 O A:HOH354 2.2 25.6 1.0 O A:HOH329 2.2 25.5 1.0 CD A:GLU67 3.0 22.3 1.0 C A:GLY47 3.2 20.0 1.0 OE1 A:GLU67 3.4 23.6 1.0 O A:HOH314 3.9 28.6 1.0 N A:GLY48 4.0 21.8 1.0 CA A:GLY48 4.0 22.4 1.0 OP2 A:4DG201 4.1 45.1 1.0 O A:HOH392 4.1 30.8 1.0 N A:GLY47 4.2 21.9 1.0 O61 A:4DG201 4.2 48.5 1.0 CA A:GLY47 4.2 20.0 1.0 O A:HOH313 4.3 36.3 1.0 CG A:GLU67 4.4 20.7 1.0 OE1 A:GLN44 4.4 26.0 1.0 N2 A:4DG201 4.4 23.4 1.0 N3 A:4DG201 4.5 24.4 1.0 NH1 A:ARG34 4.5 28.9 1.0 O5' A:4DG201 4.5 47.0 1.0 P A:4DG201 4.6 42.9 1.0 NZ A:LYS116 4.6 44.5 1.0 OE1 A:GLU63 4.8 28.6 1.0 O4' A:4DG201 4.8 36.1 1.0 C2 A:4DG201 5.0 24.6 1.0

Magnesium binding site 2 out of 4 in the Structure of NUDT15 in Complex with Acyclovir Monophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of NUDT15 in Complex with Acyclovir Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:48.2 occ:1.00 O A:HOH335 2.1 40.6 1.0 O A:HOH415 2.1 48.5 1.0 O A:HOH313 2.2 36.3 1.0 O B:HOH397 2.2 42.9 1.0 O A:HOH307 2.2 36.2 1.0 O A:HOH342 2.2 35.5 1.0 O A:HOH311 3.9 33.2 1.0 O A:HOH354 4.0 25.6 1.0 OE2 A:GLU63 4.2 28.2 1.0 O A:HOH314 4.2 28.6 1.0 OE1 A:GLU63 4.3 28.6 1.0 OE1 A:GLU66 4.4 36.9 1.0 OP2 A:4DG201 4.6 45.1 1.0 CD A:GLU63 4.7 25.9 1.0 ND1 A:HIS49 4.7 40.5 1.0 NZ A:LYS116 4.8 44.5 1.0

Magnesium binding site 3 out of 4 in the Structure of NUDT15 in Complex with Acyclovir Monophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of NUDT15 in Complex with Acyclovir Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:30.0 occ:1.00 OE2 B:GLU67 2.1 28.6 1.0 O B:GLY47 2.1 26.1 1.0 O B:HOH367 2.2 31.5 1.0 O B:HOH310 2.2 28.0 1.0 O B:HOH349 2.2 32.5 1.0 O B:HOH359 2.2 29.2 1.0 CD B:GLU67 3.1 28.4 1.0 C B:GLY47 3.3 24.9 1.0 OE1 B:GLU67 3.4 25.5 1.0 O B:HOH340 3.9 33.0 1.0 O B:HOH347 4.0 32.9 1.0 O B:HOH306 4.1 43.9 1.0 OP1 B:4DG201 4.1 45.2 1.0 N B:GLY48 4.1 23.6 1.0 CA B:GLY48 4.1 24.8 1.0 N B:GLY47 4.2 24.4 1.0 NH1 B:ARG34 4.2 32.6 1.0 CA B:GLY47 4.3 22.8 1.0 O61 B:4DG201 4.3 46.0 1.0 OE1 B:GLN44 4.3 32.0 1.0 CG B:GLU67 4.4 22.5 1.0 N2 B:4DG201 4.4 29.8 1.0 N3 B:4DG201 4.5 28.6 1.0 P B:4DG201 4.6 59.0 1.0 NZ B:LYS116 4.6 43.1 1.0 OE1 B:GLU63 4.6 29.7 1.0 O5' B:4DG201 4.7 53.7 1.0 O4' B:4DG201 4.8 37.2 1.0 C2 B:4DG201 5.0 29.6 1.0 CE B:LYS116 5.0 43.6 1.0

Magnesium binding site 4 out of 4 in the Structure of NUDT15 in Complex with Acyclovir Monophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of NUDT15 in Complex with Acyclovir Monophosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:37.6 occ:1.00 O B:HOH307 2.1 35.3 1.0 O B:HOH324 2.1 37.0 1.0 O B:HOH383 2.2 47.4 1.0 O B:HOH331 2.2 39.7 1.0 O B:HOH306 2.2 43.9 1.0 O B:HOH340 2.3 33.0 1.0 OE1 B:GLU63 3.4 29.7 1.0 OE1 B:GLU66 3.5 33.9 1.0 O B:HOH367 3.8 31.5 1.0 O B:HOH377 3.8 41.9 1.0 OE2 B:GLU113 4.1 39.6 1.0 NZ B:LYS116 4.2 43.1 1.0 OE2 B:GLU67 4.2 28.6 1.0 CD B:GLU63 4.3 28.0 1.0 OE2 B:GLU63 4.4 33.7 1.0 OE1 B:GLU113 4.5 37.9 1.0 CD B:GLU66 4.7 33.1 1.0 CD B:GLU113 4.7 35.0 1.0 CG B:GLU67 4.8 22.5 1.0 CB B:GLU66 4.8 28.2 1.0 NH1 B:ARG62 5.0 28.3 1.0 CD B:GLU67 5.0 28.4 1.0

R.Nishii, T.Mizuno, D.Rehling, C.Smith, B.L.Clark, X.Zhao, B.Smart, T.Moriyama, Y.Yamada, L.Yang, P.G.Thomas, P.Stenmark, M.Kato, J.J.Yang. NUDT15 Polymorphism Influences the Metabolism and Therapeutic Effects of Acyclovir and Ganciclovir Nat Commun 2021.
ISSN: ESSN 2041-1723