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Magnesium in PDB 2q8m: T-Like Fructose-1,6-Bisphosphatase From Escherichia Coli with Amp, Glucose 6-Phosphate, and Fructose 1,6-Bisphosphate Bound

Enzymatic activity of T-Like Fructose-1,6-Bisphosphatase From Escherichia Coli with Amp, Glucose 6-Phosphate, and Fructose 1,6-Bisphosphate Bound

All present enzymatic activity of T-Like Fructose-1,6-Bisphosphatase From Escherichia Coli with Amp, Glucose 6-Phosphate, and Fructose 1,6-Bisphosphate Bound:
3.1.3.11;

Protein crystallography data

The structure of T-Like Fructose-1,6-Bisphosphatase From Escherichia Coli with Amp, Glucose 6-Phosphate, and Fructose 1,6-Bisphosphate Bound, PDB code: 2q8m was solved by J.K.Hines, C.E.Kruesel, H.J.Fromm, R.B.Honzatko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.77 / 2.05
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 124.640, 124.640, 132.280, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 23.5

Other elements in 2q8m:

The structure of T-Like Fructose-1,6-Bisphosphatase From Escherichia Coli with Amp, Glucose 6-Phosphate, and Fructose 1,6-Bisphosphate Bound also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the T-Like Fructose-1,6-Bisphosphatase From Escherichia Coli with Amp, Glucose 6-Phosphate, and Fructose 1,6-Bisphosphate Bound (pdb code 2q8m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the T-Like Fructose-1,6-Bisphosphatase From Escherichia Coli with Amp, Glucose 6-Phosphate, and Fructose 1,6-Bisphosphate Bound, PDB code: 2q8m:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2q8m

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Magnesium binding site 1 out of 4 in the T-Like Fructose-1,6-Bisphosphatase From Escherichia Coli with Amp, Glucose 6-Phosphate, and Fructose 1,6-Bisphosphate Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of T-Like Fructose-1,6-Bisphosphatase From Escherichia Coli with Amp, Glucose 6-Phosphate, and Fructose 1,6-Bisphosphate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg347

b:28.3
occ:0.50
 O1P A:FBP344 2.0 25.8 0.5
O A:HOH659 2.2 36.5 1.0
O A:HOH660 2.2 20.4 0.5
OD2 A:ASP110 2.2 28.3 1.0
OE1 A:GLU89 2.4 50.2 1.0
O A:LEU112 2.5 29.2 1.0
CG A:ASP110 3.3 28.8 1.0
C A:LEU112 3.3 29.4 1.0
P1 A:FBP344 3.4 29.0 0.5
CD A:GLU89 3.6 52.9 1.0
OD1 A:ASP110 3.8 27.5 1.0
O3P A:FBP344 3.9 26.9 0.5
MG A:MG348 4.0 26.0 0.5
N A:ASP113 4.0 28.4 1.0
OE2 A:GLU90 4.1 64.5 1.0
CA A:ASP113 4.1 30.1 1.0
O2P A:FBP344 4.1 26.3 0.5
N A:LEU112 4.2 26.4 1.0
CA A:LEU112 4.3 28.6 1.0
CG A:GLU89 4.3 50.8 1.0
O1 A:FBP344 4.5 25.7 0.5
OE2 A:GLU89 4.6 56.4 1.0
CB A:GLU89 4.6 48.5 1.0
CB A:ASP110 4.6 25.0 1.0
CA A:ASP110 4.7 25.2 1.0
CB A:LEU112 4.8 31.8 1.0
C A:ASP110 4.8 24.6 1.0
CD A:GLU90 4.9 64.6 1.0

Magnesium binding site 2 out of 4 in 2q8m

Go back to Magnesium Binding Sites List in 2q8m
Magnesium binding site 2 out of 4 in the T-Like Fructose-1,6-Bisphosphatase From Escherichia Coli with Amp, Glucose 6-Phosphate, and Fructose 1,6-Bisphosphate Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of T-Like Fructose-1,6-Bisphosphatase From Escherichia Coli with Amp, Glucose 6-Phosphate, and Fructose 1,6-Bisphosphate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg348

b:26.0
occ:0.50
 OD1 A:ASP110 1.9 27.5 1.0
O1 A:FBP344 2.1 25.7 0.5
OE1 A:GLU275 2.2 29.3 1.0
OD1 A:ASP113 2.3 31.7 1.0
O1P A:FBP344 2.5 25.8 0.5
P1 A:FBP344 2.9 29.0 0.5
CG A:ASP110 3.0 28.8 1.0
CD A:GLU275 3.2 26.3 1.0
C1 A:FBP344 3.2 24.1 1.0
CG A:ASP113 3.4 30.4 1.0
OD2 A:ASP110 3.5 28.3 1.0
CB A:ASP113 3.7 29.9 1.0
CG A:GLU275 3.7 22.7 1.0
CA A:ASP113 3.8 30.1 1.0
O3P A:FBP344 3.9 26.9 0.5
O2P A:FBP344 3.9 26.3 0.5
O3 A:FBP344 3.9 19.7 1.0
MG A:MG347 4.0 28.3 0.5
C2 A:FBP344 4.2 23.4 1.0
OE2 A:GLU275 4.2 23.0 1.0
CB A:ASP110 4.3 25.0 1.0
C3 A:FBP344 4.3 20.4 1.0
OD2 A:ASP113 4.5 29.2 1.0
N A:GLY114 4.5 33.0 1.0
O2 A:FBP344 4.6 23.9 1.0
OE1 A:GLU89 4.6 50.2 1.0
C A:ASP113 4.7 32.2 1.0
CD1 A:ILE127 4.7 16.4 1.0
N A:ASP113 4.8 28.4 1.0
CG A:GLU89 4.9 50.8 1.0
O A:LEU112 4.9 29.2 1.0
CD A:GLU89 5.0 52.9 1.0

Magnesium binding site 3 out of 4 in 2q8m

Go back to Magnesium Binding Sites List in 2q8m
Magnesium binding site 3 out of 4 in the T-Like Fructose-1,6-Bisphosphatase From Escherichia Coli with Amp, Glucose 6-Phosphate, and Fructose 1,6-Bisphosphate Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of T-Like Fructose-1,6-Bisphosphatase From Escherichia Coli with Amp, Glucose 6-Phosphate, and Fructose 1,6-Bisphosphate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg345

b:35.7
occ:0.50
 O1P B:FBP342 2.0 29.7 0.5
O B:LEU112 2.1 30.7 1.0
OE1 B:GLU89 2.1 55.8 1.0
O B:HOH490 2.3 36.2 1.0
OD2 B:ASP110 2.3 32.0 1.0
O B:HOH657 2.3 30.9 0.5
C B:LEU112 3.2 30.5 1.0
CD B:GLU89 3.3 55.4 1.0
P1 B:FBP342 3.3 30.7 0.5
CG B:ASP110 3.4 31.2 1.0
OD1 B:ASP110 3.8 29.8 1.0
OE2 B:GLU89 3.8 56.3 1.0
O2P B:FBP342 3.9 30.1 0.5
O B:GLU89 3.9 50.9 1.0
MG B:MG346 4.0 27.8 0.5
O3P B:FBP342 4.0 30.9 0.5
N B:ASP113 4.0 29.0 1.0
CA B:ASP113 4.0 31.4 1.0
N B:LEU112 4.2 29.0 1.0
CA B:LEU112 4.2 31.1 1.0
O B:HOH635 4.2 50.6 1.0
O1 B:FBP342 4.5 28.2 0.5
CG B:GLU89 4.5 53.6 1.0
CB B:LEU112 4.6 34.1 1.0
CB B:ASP110 4.7 29.8 1.0
C B:GLU89 4.7 51.1 1.0
CA B:ASP110 4.9 30.2 1.0
N B:GLY114 4.9 33.2 1.0
C B:ASP110 5.0 28.7 1.0
CB B:GLU89 5.0 51.2 1.0
N B:GLU91 5.0 60.9 1.0
C B:ASP113 5.0 32.8 1.0

Magnesium binding site 4 out of 4 in 2q8m

Go back to Magnesium Binding Sites List in 2q8m
Magnesium binding site 4 out of 4 in the T-Like Fructose-1,6-Bisphosphatase From Escherichia Coli with Amp, Glucose 6-Phosphate, and Fructose 1,6-Bisphosphate Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of T-Like Fructose-1,6-Bisphosphatase From Escherichia Coli with Amp, Glucose 6-Phosphate, and Fructose 1,6-Bisphosphate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg346

b:27.8
occ:0.50
 OD1 B:ASP110 2.0 29.8 1.0
O1 B:FBP342 2.1 28.2 0.5
OD1 B:ASP113 2.3 35.1 1.0
O1P B:FBP342 2.4 29.7 0.5
OE1 B:GLU275 2.7 36.7 1.0
P1 B:FBP342 2.8 30.7 0.5
CG B:ASP110 3.0 31.2 1.0
CG B:ASP113 3.3 30.7 1.0
CD B:GLU275 3.3 30.4 1.0
C1 B:FBP342 3.3 24.3 1.0
OD2 B:ASP110 3.5 32.0 1.0
CB B:ASP113 3.5 31.6 1.0
CA B:ASP113 3.7 31.4 1.0
O2P B:FBP342 3.8 30.1 0.5
CG B:GLU275 3.8 28.7 1.0
O3 B:FBP342 3.8 22.6 1.0
MG B:MG345 4.0 35.7 0.5
O3P B:FBP342 4.0 30.9 0.5
OE2 B:GLU275 4.1 29.5 1.0
C2 B:FBP342 4.2 25.0 1.0
C3 B:FBP342 4.3 22.2 1.0
CB B:ASP110 4.3 29.8 1.0
OE1 B:GLU89 4.4 55.8 1.0
OD2 B:ASP113 4.4 31.5 1.0
O2 B:FBP342 4.5 23.5 1.0
N B:GLY114 4.6 33.2 1.0
C B:ASP113 4.6 32.8 1.0
O B:LEU112 4.6 30.7 1.0
N B:ASP113 4.8 29.0 1.0
CD1 B:ILE127 4.8 22.2 1.0

Reference:

J.K.Hines, C.E.Kruesel, H.J.Fromm, R.B.Honzatko. Structure of Inhibited Fructose-1,6-Bisphosphatase From Escherichia Coli: Distinct Allosteric Inhibition Sites For Amp and Glucose 6-Phosphate and the Characterization of A Gluconeogenic Switch. J.Biol.Chem. V. 282 24697 2007.
ISSN: ISSN 0021-9258
PubMed: 17567577
DOI: 10.1074/JBC.M703580200
Page generated: Mon Dec 14 07:36:07 2020

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