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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 6oiw:

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

Manganese (Mn) 6 atoms

Magnesium Binding Sites:

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 6oiw

Go back to Magnesium Binding Sites List in 6oiw
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 6oiw

Go back to Magnesium Binding Sites List in 6oiw
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 6oiw

Go back to Magnesium Binding Sites List in 6oiw
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

Reference:

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
Page generated: Mon Dec 14 23:43:10 2020

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