Magnesium in PDB 6fl4: A. Thaliana NUDT1 in Complex with 8-Oxo-Dgtp

All present enzymatic activity of A. Thaliana NUDT1 in Complex with 8-Oxo-Dgtp:
3.6.1.22; 3.6.1.55; 3.6.1.67;

The structure of A. Thaliana NUDT1 in Complex with 8-Oxo-Dgtp, PDB code: 6fl4 was solved by A.S.Jemth, E.Scaletti-Hutchinson, M.Carter, T.Helleday, P.Stenmark, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.00 / 1.60
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	64.898, 77.412, 122.420, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 21.4

The binding sites of Magnesium atom in the A. Thaliana NUDT1 in Complex with 8-Oxo-Dgtp (pdb code 6fl4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the A. Thaliana NUDT1 in Complex with 8-Oxo-Dgtp, PDB code: 6fl4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the A. Thaliana NUDT1 in Complex with 8-Oxo-Dgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A. Thaliana NUDT1 in Complex with 8-Oxo-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:21.9 occ:1.00 O1A A:8DG203 2.0 22.0 1.0 O A:HOH333 2.1 19.5 1.0 O1B A:8DG203 2.1 22.6 1.0 OE2 A:GLU60 2.2 14.2 1.0 O A:GLY40 2.2 12.5 1.0 O A:HOH387 2.2 20.6 1.0 CD A:GLU60 3.1 12.6 1.0 PA A:8DG203 3.3 23.0 1.0 MG A:MG202 3.3 23.8 1.0 PB A:8DG203 3.3 25.4 1.0 C A:GLY40 3.4 11.9 1.0 OE1 A:GLU60 3.5 13.1 1.0 O3A A:8DG203 3.6 23.9 1.0 N2 A:8DG203 3.7 19.7 1.0 O A:HOH305 3.7 19.7 1.0 O A:HOH402 3.9 27.3 1.0 CA A:GLY41 4.0 12.6 1.0 N A:GLY41 4.1 11.7 1.0 O2B A:8DG203 4.2 25.7 1.0 O A:HOH383 4.2 30.3 1.0 N A:GLY40 4.2 11.4 1.0 O5' A:8DG203 4.2 22.4 1.0 O A:HOH360 4.3 24.4 1.0 O2A A:8DG203 4.3 21.8 1.0 OE1 A:GLU56 4.3 17.1 1.0 CA A:GLY40 4.4 11.9 1.0 CG A:GLU60 4.4 11.6 1.0 O3B A:8DG203 4.5 28.4 1.0 O1G A:8DG203 4.6 38.0 1.0 NH1 A:ARG27 4.9 16.2 1.0 C2 A:8DG203 4.9 20.3 1.0

Magnesium binding site 2 out of 4 in the A. Thaliana NUDT1 in Complex with 8-Oxo-Dgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A. Thaliana NUDT1 in Complex with 8-Oxo-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:23.8 occ:1.00 O1G A:8DG203 2.0 38.0 1.0 O1B A:8DG203 2.2 22.6 1.0 O A:HOH304 2.4 28.8 1.0 OE1 A:GLU56 2.4 17.1 1.0 O A:HOH305 2.4 19.7 1.0 OE2 A:GLU60 2.4 14.2 1.0 MG A:MG201 3.3 21.9 1.0 PB A:8DG203 3.3 25.4 1.0 PG A:8DG203 3.3 39.6 0.8 CD A:GLU60 3.4 12.6 1.0 CD A:GLU56 3.4 14.7 1.0 O3B A:8DG203 3.7 28.4 1.0 CG A:GLU60 3.7 11.6 1.0 O A:GLY40 3.7 12.5 1.0 OE2 A:GLU56 3.8 16.5 1.0 O2B A:8DG203 3.9 25.7 1.0 O A:HOH387 3.9 20.6 1.0 OE1 A:GLU59 4.2 17.7 1.0 O2G A:8DG203 4.2 41.3 1.0 OE1 A:GLU107 4.3 19.5 1.0 O A:HOH327 4.3 20.2 1.0 O3G A:8DG203 4.3 42.0 1.0 CA A:GLY41 4.5 12.6 1.0 OE1 A:GLU60 4.5 13.1 1.0 NZ A:LYS110 4.5 24.9 1.0 C A:GLY40 4.6 11.9 1.0 OE2 A:GLU107 4.7 22.4 1.0 O3A A:8DG203 4.7 23.9 1.0 CG A:GLU56 4.8 12.9 1.0 O1A A:8DG203 4.8 22.0 1.0 N A:GLY41 4.9 11.7 1.0 CD A:GLU107 4.9 18.2 1.0

Magnesium binding site 3 out of 4 in the A. Thaliana NUDT1 in Complex with 8-Oxo-Dgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of A. Thaliana NUDT1 in Complex with 8-Oxo-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:32.1 occ:1.00 O B:HOH322 2.3 26.0 1.0 O2G B:8DG203 2.3 43.1 1.0 O1B B:8DG203 2.3 36.2 1.0 OE1 B:GLU56 2.4 18.1 1.0 O B:HOH325 2.4 27.9 1.0 OE2 B:GLU60 2.4 19.7 1.0 MG B:MG202 3.3 39.4 1.0 PB B:8DG203 3.4 44.6 0.9 CD B:GLU60 3.4 17.6 1.0 CD B:GLU56 3.5 17.4 1.0 PG B:8DG203 3.6 47.2 0.9 O B:GLY40 3.7 15.3 1.0 CG B:GLU60 3.7 15.0 1.0 O3B B:8DG203 3.8 42.6 1.0 O2B B:8DG203 3.9 44.9 1.0 OE2 B:GLU56 3.9 20.6 1.0 O B:HOH376 4.1 37.6 1.0 OE1 B:GLU107 4.2 21.2 1.0 O B:HOH314 4.2 25.3 1.0 OE1 B:GLU59 4.3 19.2 1.0 O3G B:8DG203 4.4 46.0 1.0 OE2 B:GLU107 4.4 23.6 1.0 CA B:GLY41 4.5 13.9 1.0 NZ B:LYS110 4.5 38.0 1.0 OE1 B:GLU60 4.5 17.9 1.0 C B:GLY40 4.6 13.9 1.0 O1G B:8DG203 4.7 52.8 1.0 CD B:GLU107 4.7 20.6 1.0 CG B:GLU56 4.8 16.2 1.0 O3A B:8DG203 4.9 39.5 1.0 O2A B:8DG203 4.9 37.3 1.0 N B:GLY41 5.0 13.0 1.0

Magnesium binding site 4 out of 4 in the A. Thaliana NUDT1 in Complex with 8-Oxo-Dgtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of A. Thaliana NUDT1 in Complex with 8-Oxo-Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:39.4 occ:1.00 O2A B:8DG203 2.1 37.3 1.0 O B:HOH357 2.1 35.3 1.0 O1B B:8DG203 2.1 36.2 1.0 O B:GLY40 2.2 15.3 1.0 OE2 B:GLU60 2.2 19.7 1.0 O B:HOH376 2.3 37.6 1.0 CD B:GLU60 3.2 17.6 1.0 PB B:8DG203 3.3 44.6 0.9 MG B:MG201 3.3 32.1 1.0 PA B:8DG203 3.3 35.6 0.8 C B:GLY40 3.4 13.9 1.0 O B:HOH325 3.5 27.9 1.0 OE1 B:GLU60 3.6 17.9 1.0 N2 B:8DG203 3.7 23.4 1.0 O3A B:8DG203 3.7 39.5 1.0 O B:HOH408 3.8 33.5 1.0 CA B:GLY41 4.0 13.9 1.0 O5' B:8DG203 4.1 36.4 1.0 N B:GLY41 4.1 13.0 1.0 O2B B:8DG203 4.1 44.9 1.0 N B:GLY40 4.2 12.9 1.0 O B:HOH395 4.3 30.9 1.0 OE1 B:GLU56 4.4 18.1 1.0 CA B:GLY40 4.4 14.0 1.0 CG B:GLU60 4.5 15.0 1.0 O B:HOH392 4.5 36.1 1.0 O3B B:8DG203 4.5 42.6 1.0 O1A B:8DG203 4.6 38.8 1.0 O2G B:8DG203 4.8 43.1 1.0 C2 B:8DG203 5.0 21.9 1.0

A.S.Jemth, E.Scaletti, M.Carter, T.Helleday, P.Stenmark. Crystal Structure and Substrate Specificity of the 8-Oxo-Dgtp Hydrolase NUDT1 From Arabidopsis Thaliana. Biochemistry V. 58 887 2019.
ISSN: ISSN 0006-2960
PubMed: 30614695
DOI: 10.1021/ACS.BIOCHEM.8B00950