Magnesium in PDB 6t5j: Structure of NUDT15 in Complex with Inhibitor TH1760

All present enzymatic activity of Structure of NUDT15 in Complex with Inhibitor TH1760:
3.6.1.9;

The structure of Structure of NUDT15 in Complex with Inhibitor TH1760, PDB code: 6t5j was solved by M.Carter, D.Rehling, M.Desroses, S.M.Zhang, A.Hagenkort, N.C.K.Valerie, T.Helleday, P.Stenmark, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.31 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.790, 46.809, 137.596, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 19.5

The structure of Structure of NUDT15 in Complex with Inhibitor TH1760 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Structure of NUDT15 in Complex with Inhibitor TH1760 (pdb code 6t5j). 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 Inhibitor TH1760, PDB code: 6t5j:
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 Inhibitor TH1760


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 Inhibitor TH1760 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:17.2 occ:1.00 O A:HOH375 2.0 15.8 1.0 OE2 A:GLU67 2.0 16.3 1.0 O A:HOH354 2.0 22.8 1.0 OE1 A:GLU63 2.1 16.8 1.0 O A:HOH333 2.1 22.5 1.0 O A:HOH310 2.2 15.6 1.0 CD A:GLU67 3.0 18.0 1.0 CD A:GLU63 3.1 17.1 1.0 OE2 A:GLU63 3.4 18.6 1.0 CG A:GLU67 3.6 12.7 1.0 O A:GLY47 3.9 17.0 1.0 OE1 A:GLU67 4.0 17.6 1.0 OE1 A:GLU113 4.2 20.9 1.0 OE2 A:GLU113 4.2 21.8 1.0 O A:HOH509 4.2 37.8 1.0 OE1 A:GLU66 4.3 16.3 1.0 NZ A:LYS116 4.4 22.7 1.0 O A:HOH448 4.4 23.2 1.0 CG A:GLU63 4.5 12.6 1.0 O A:HOH366 4.5 28.6 1.0 C A:GLY47 4.5 10.0 1.0 CD A:GLU113 4.6 21.4 1.0 CA A:GLY48 4.7 13.2 1.0 CB A:GLU63 4.8 11.3 1.0 N A:GLY48 5.0 8.4 1.0

Magnesium binding site 2 out of 4 in the Structure of NUDT15 in Complex with Inhibitor TH1760


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 Inhibitor TH1760 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:29.9 occ:1.00 O A:HOH330 2.1 28.0 1.0 O A:HOH366 2.1 28.6 1.0 O B:HOH507 2.1 35.1 1.0 O A:HOH337 2.2 30.9 1.0 O B:HOH473 3.8 37.3 1.0 OE2 A:GLU51 4.0 20.7 0.6 O A:HOH509 4.1 37.8 1.0 O A:HOH315 4.1 23.8 1.0 O A:HOH481 4.2 39.5 1.0 NH1 A:ARG62 4.2 13.9 1.0 OE2 A:GLU66 4.3 15.5 1.0 O A:HOH352 4.4 17.8 1.0 OE1 A:GLU66 4.5 16.3 1.0 OE2 A:GLU51 4.7 22.7 0.4 CD A:GLU66 4.8 15.6 1.0 O A:HOH354 4.8 22.8 1.0 OE2 A:GLU63 5.0 18.6 1.0

Magnesium binding site 3 out of 4 in the Structure of NUDT15 in Complex with Inhibitor TH1760


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 Inhibitor TH1760 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:17.3 occ:1.00 OE2 B:GLU67 2.0 15.0 1.0 O B:HOH394 2.0 15.8 1.0 O B:HOH350 2.1 20.7 1.0 O B:HOH332 2.1 22.2 1.0 OE1 B:GLU63 2.2 16.5 1.0 O B:HOH313 2.2 14.2 1.0 CD B:GLU67 3.0 17.7 1.0 CD B:GLU63 3.2 16.9 1.0 CG B:GLU67 3.5 13.3 1.0 OE2 B:GLU63 3.5 17.7 1.0 O B:GLY47 3.9 16.4 1.0 OE1 B:GLU67 4.0 18.8 1.0 OE1 B:GLU113 4.2 21.2 1.0 OE2 B:GLU113 4.2 21.5 1.0 O B:HOH522 4.2 38.1 1.0 NZ B:LYS116 4.3 21.2 1.0 O B:HOH526 4.3 35.2 1.0 O B:HOH461 4.3 20.9 1.0 OE1 B:GLU66 4.3 16.7 1.0 CG B:GLU63 4.5 12.6 1.0 C B:GLY47 4.5 7.0 1.0 O B:HOH351 4.5 32.5 1.0 CD B:GLU113 4.6 21.4 1.0 CA B:GLY48 4.7 12.0 1.0 CB B:GLU63 4.8 10.8 1.0 O B:HOH446 4.9 40.0 1.0 N B:GLY48 4.9 9.5 1.0

Magnesium binding site 4 out of 4 in the Structure of NUDT15 in Complex with Inhibitor TH1760


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 Inhibitor TH1760 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:37.8 occ:1.00 O B:HOH327 2.0 39.3 1.0 O B:HOH318 2.2 24.5 1.0 O B:HOH351 2.3 32.5 1.0 O B:HOH512 2.3 45.1 1.0 OE2 B:GLU51 3.9 19.2 0.6 O B:HOH308 4.1 22.6 1.0 NH1 B:ARG62 4.1 12.4 1.0 OE2 B:GLU66 4.2 15.5 1.0 O B:HOH493 4.2 42.7 1.0 O B:HOH522 4.3 38.1 1.0 O B:HOH342 4.4 18.4 1.0 OE1 B:GLU66 4.5 16.7 1.0 CD B:GLU66 4.8 14.1 1.0 OE2 B:GLU51 4.8 21.8 0.4 CZ B:ARG62 5.0 14.9 1.0

S.M.Zhang, M.Desroses, A.Hagenkort, N.C.K.Valerie, D.Rehling, M.Carter, O.Wallner, T.Koolmeister, A.Throup, A.S.Jemth, I.Almlof, O.Loseva, T.Lundback, H.Axelsson, S.Regmi, A.Sarno, A.Kramer, L.Pudelko, L.Brautigam, A.Rasti, M.Gottmann, E.Wiita, J.Kutzner, T.Schaller, C.Kalderen, A.Cazares-Korner, B.D.G.Page, R.Krimpenfort, S.Eshtad, M.Altun, S.G.Rudd, S.Knapp, M.Scobie, E.J.Homan, U.W.Berglund, P.Stenmark, T.Helleday. Development of A Chemical Probe Against NUDT15. Nat.Chem.Biol. V. 16 1120 2020.
ISSN: ESSN 1552-4469
PubMed: 32690945
DOI: 10.1038/S41589-020-0592-Z