Magnesium in PDB 6oiw: Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol

All present enzymatic activity of Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol:
3.1.5.1;

The structure of Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol, PDB code: 6oiw was solved by C.O.Barnes, Y.Wu, G.Calero, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.48 / 3.35
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	191.240, 191.240, 298.610, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 21.2

The structure of Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol also contains other interesting chemical elements:

Manganese

(Mn)

6 atoms

The binding sites of Magnesium atom in the Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol (pdb code 6oiw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol, PDB code: 6oiw:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:0.5 occ:1.00 O2B A:T8T603 2.3 0.0 1.0 OD1 A:ASP269 2.7 0.9 1.0 O3B A:T8T603 3.3 0.2 1.0 PB A:T8T603 3.4 0.7 1.0 O A:HOH704 3.4 79.9 1.0 OD2 A:ASP268 3.5 0.0 1.0 NZ A:LYS211 3.6 0.8 1.0 CG A:ASP269 3.8 0.9 1.0 CE A:LYS211 3.8 0.5 1.0 O A:GLU265 4.1 96.1 1.0 O1B A:T8T603 4.1 0.7 1.0 O3G A:T8T603 4.2 0.2 1.0 CG A:ASP268 4.2 0.7 1.0 OD2 A:ASP269 4.2 0.7 1.0 CB A:ASP268 4.2 91.8 1.0 CG A:GLU265 4.4 0.9 1.0 PG A:T8T603 4.4 1.0 1.0 O3A A:T8T603 4.7 1.0 1.0 CE2 A:TYR272 4.8 0.8 1.0 N A:ASP269 4.8 94.1 1.0 C A:GLU265 4.9 97.2 1.0 OH A:TYR272 5.0 0.1 1.0 CA A:GLU265 5.0 92.8 1.0

Magnesium binding site 2 out of 3 in the Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg601 b:95.9 occ:1.00 OD1 E:ASP269 2.0 0.2 1.0 OD2 E:ASP268 3.1 0.7 1.0 CE2 E:TYR272 3.1 0.5 1.0 CG E:ASP269 3.2 0.6 1.0 O2A E:T8T603 3.3 0.3 1.0 OH E:TYR272 3.6 0.6 1.0 CZ E:TYR272 3.8 0.9 1.0 O3G E:T8T603 3.9 0.3 1.0 OD2 E:ASP269 3.9 0.8 1.0 CD2 E:TYR272 4.1 0.3 1.0 O E:HOH701 4.1 98.4 1.0 NZ E:LYS211 4.2 0.8 1.0 O3B E:T8T603 4.2 0.7 1.0 CG E:ASP268 4.2 0.6 1.0 CB E:ASP269 4.3 0.2 1.0 CA E:ASP269 4.3 0.9 1.0 O2G E:T8T603 4.3 0.8 1.0 PG E:T8T603 4.3 0.7 1.0 N E:ASP269 4.3 0.8 1.0 PA E:T8T603 4.6 0.1 1.0 C E:ASP268 4.8 0.8 1.0 CB E:ASP268 4.8 0.1 1.0 S1A E:T8T603 5.0 1.0 1.0

Magnesium binding site 3 out of 3 in the Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Escherichia Coli Dgtpase Bound to Dgtp-1-Thiol within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg601 b:0.9 occ:1.00 OD2 F:ASP268 2.5 0.6 1.0 O F:HOH702 3.2 99.6 1.0 O2A F:T8T603 3.6 0.3 0.9 OD1 F:ASP269 3.6 0.5 1.0 CG F:ASP268 3.7 0.8 1.0 OD2 F:ASP269 3.8 0.3 1.0 O3B F:T8T603 3.9 0.3 0.9 CG F:ASP269 3.9 0.4 1.0 O2G F:T8T603 4.0 0.5 0.9 NZ F:LYS211 4.2 0.2 1.0 PG F:T8T603 4.3 1.0 0.9 CE2 F:TYR272 4.4 0.4 1.0 O3G F:T8T603 4.4 0.3 0.9 CB F:ASP268 4.4 0.3 1.0 OD1 F:ASP268 4.5 0.4 1.0 O F:GLU265 4.5 0.6 1.0 CE F:LYS211 4.6 0.6 1.0 N F:ASP269 4.7 0.3 1.0 OH F:TYR272 4.8 0.9 1.0 O1B F:T8T603 4.8 0.8 0.9 PB F:T8T603 5.0 0.6 0.9

C.O.Barnes, Y.Wu, J.Song, G.Lin, E.L.Baxter, A.S.Brewster, V.Nagarajan, A.Holmes, S.M.Soltis, N.K.Sauter, J.Ahn, A.E.Cohen, G.Calero. The Crystal Structure of Dgtpase Reveals the Molecular Basis of Dgtp Selectivity. Proc.Natl.Acad.Sci.Usa V. 116 9333 2019.
ISSN: ESSN 1091-6490
PubMed: 31019074
DOI: 10.1073/PNAS.1814999116