Magnesium in PDB 7aom: Structure of NUDT15 in Complex with Ganciclovir Triphosphate

All present enzymatic activity of Structure of NUDT15 in Complex with Ganciclovir Triphosphate:
3.6.1.9;

The structure of Structure of NUDT15 in Complex with Ganciclovir Triphosphate, PDB code: 7aom was solved by D.Rehling, S.M.Zhang, T.Helleday, P.Stenmark, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.50 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.243, 49.532, 135.032, 90, 90, 90
R / Rfree (%)	20.4 / 22.3

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

Magnesium binding site 1 out of 2 in the Structure of NUDT15 in Complex with Ganciclovir Triphosphate


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 Ganciclovir Triphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:38.4 occ:1.00 O18 A:RQ2201 2.3 35.7 1.0 O A:HOH320 2.3 31.7 1.0 O A:HOH383 2.3 38.8 1.0 OE2 A:GLU67 2.4 34.6 1.0 O22 A:RQ2201 2.6 34.2 1.0 O A:GLY47 2.9 26.4 1.0 CD A:GLU67 3.3 31.1 1.0 P16 A:RQ2201 3.3 34.5 1.0 O A:HOH358 3.4 48.8 1.0 OE1 A:GLU67 3.4 30.5 1.0 N01 A:RQ2201 3.5 25.0 1.0 P20 A:RQ2201 3.8 43.3 1.0 O19 A:RQ2201 3.8 39.8 1.0 C A:GLY47 3.9 21.8 1.0 NH1 A:ARG34 3.9 26.3 1.0 OE1 A:GLN44 4.1 26.0 1.0 O17 A:RQ2201 4.1 40.2 1.0 CA A:GLY48 4.5 26.1 1.0 O23 A:RQ2201 4.5 64.3 1.0 N A:GLY48 4.6 22.9 1.0 N A:GLY47 4.6 22.5 1.0 O15 A:RQ2201 4.6 40.5 1.0 C02 A:RQ2201 4.7 26.7 1.0 CG A:GLU67 4.7 30.3 1.0 CA A:GLY47 4.8 23.9 1.0 OE1 A:GLU63 4.9 31.0 1.0 CD A:GLN44 4.9 25.8 1.0 O21 A:RQ2201 5.0 32.8 1.0 NE2 A:GLN44 5.0 26.7 1.0 CZ A:ARG34 5.0 38.3 1.0

Magnesium binding site 2 out of 2 in the Structure of NUDT15 in Complex with Ganciclovir Triphosphate


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 Ganciclovir Triphosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:32.8 occ:1.00 O21 B:RQ2201 2.0 33.5 1.0 OE2 B:GLU67 2.3 32.8 1.0 O B:GLY47 2.3 22.4 1.0 O B:HOH331 2.4 30.3 1.0 O B:HOH365 2.4 40.5 1.0 O18 B:RQ2201 2.5 35.5 1.0 O B:HOH306 3.2 44.0 1.0 P20 B:RQ2201 3.3 38.3 1.0 P16 B:RQ2201 3.3 34.2 1.0 CD B:GLU67 3.3 37.4 1.0 O19 B:RQ2201 3.4 35.9 1.0 C B:GLY47 3.4 26.4 1.0 O B:HOH302 3.5 42.4 1.0 OE1 B:GLU67 3.6 35.0 1.0 CA B:GLY48 3.8 27.9 1.0 N01 B:RQ2201 3.8 26.1 1.0 N B:GLY48 4.0 22.8 1.0 O B:HOH375 4.1 37.0 1.0 O23 B:RQ2201 4.1 46.8 1.0 OE1 B:GLU63 4.1 34.7 1.0 O17 B:RQ2201 4.2 35.0 1.0 O22 B:RQ2201 4.3 39.7 1.0 NH1 B:ARG34 4.6 30.0 1.0 N B:GLY47 4.6 26.8 1.0 O15 B:RQ2201 4.6 30.7 1.0 CA B:GLY47 4.6 24.0 1.0 CG B:GLU67 4.7 31.6 1.0 CD B:GLU63 4.8 30.9 1.0 OE1 B:GLN44 4.9 29.2 1.0 C14 B:RQ2201 4.9 33.2 1.0 C02 B:RQ2201 5.0 24.7 1.0 O26 B:RQ2201 5.0 51.0 1.0

S.M.Zhang, D.Rehling, A.-S.Jemth, A.Throup, N.Landazuri, I.Almlof, M.Goettmann, N.C.K.Valerie, S.R.Borhade, P.Wakchaure, B.D.G.Page, M.Desroses, E.J.Homan, M.Scobie, S.G.Rudd, U.Warpman Berglund, C.Soderberg-Naucler, P.Stenmark, T.Helleday. NUDT15-Mediated Hydrolysis Limits the Efficacy of Anti-Hcmv Drug Ganciclovir Cell Chem Biol 2021.
ISSN: ESSN 2451-9456