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Magnesium in PDB 3cqd: Structure of the Tetrameric Inhibited Form of Phosphofructokinase-2 From Escherichia Coli

Enzymatic activity of Structure of the Tetrameric Inhibited Form of Phosphofructokinase-2 From Escherichia Coli

All present enzymatic activity of Structure of the Tetrameric Inhibited Form of Phosphofructokinase-2 From Escherichia Coli:
2.7.1.11;

Protein crystallography data

The structure of Structure of the Tetrameric Inhibited Form of Phosphofructokinase-2 From Escherichia Coli, PDB code: 3cqd was solved by A.L.Ambrosio, R.Cabrera, A.Caniuguir, R.C.Garratt, J.Babul, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.94 / 1.98
Space group P 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 42.822, 86.834, 171.308, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 23.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the Tetrameric Inhibited Form of Phosphofructokinase-2 From Escherichia Coli (pdb code 3cqd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of the Tetrameric Inhibited Form of Phosphofructokinase-2 From Escherichia Coli, PDB code: 3cqd:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3cqd

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Magnesium binding site 1 out of 4 in the Structure of the Tetrameric Inhibited Form of Phosphofructokinase-2 From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Tetrameric Inhibited Form of Phosphofructokinase-2 From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg310

b:11.8
occ:1.00
 O3G A:ATP314 2.0 15.6 1.0
O1B A:ATP314 2.0 15.4 1.0
O A:HOH319 2.0 9.6 1.0
O B:HOH321 2.1 10.6 1.0
O1B B:ATP311 2.1 10.1 1.0
O3G B:ATP311 2.2 12.5 1.0
PB A:ATP314 3.1 20.1 1.0
PB B:ATP311 3.3 10.3 1.0
PG A:ATP314 3.3 17.1 1.0
PG B:ATP311 3.3 12.3 1.0
O3B B:ATP311 3.3 11.4 1.0
O3B A:ATP314 3.5 20.7 1.0
O3A A:ATP314 3.6 25.0 1.0
O B:HOH327 3.7 15.7 1.0
ND2 B:ASN187 3.7 12.6 1.0
O1A B:ATP311 3.8 10.1 1.0
O B:HOH315 3.9 10.6 1.0
O1G B:ATP311 4.0 11.0 1.0
O2G A:ATP314 4.1 17.7 1.0
O B:HOH324 4.1 12.3 1.0
N7 A:ATP314 4.1 22.6 0.6
CE A:LYS27 4.2 16.5 1.0
NZ A:LYS27 4.3 20.1 1.0
O2B B:ATP311 4.3 14.2 1.0
O A:HOH321 4.3 18.7 1.0
O3A B:ATP311 4.4 12.0 1.0
O1G A:ATP314 4.4 20.5 1.0
O B:HOH341 4.4 20.1 1.0
O2B A:ATP314 4.5 21.0 1.0
O2G B:ATP311 4.5 13.5 1.0
PA B:ATP311 4.7 10.8 1.0
MG B:MG310 4.8 13.6 1.0
C8 A:ATP314 4.9 23.3 0.6
CG B:ASN187 4.9 13.8 1.0

Magnesium binding site 2 out of 4 in 3cqd

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Magnesium binding site 2 out of 4 in the Structure of the Tetrameric Inhibited Form of Phosphofructokinase-2 From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Tetrameric Inhibited Form of Phosphofructokinase-2 From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg311

b:12.5
occ:1.00
 O2B A:ATP313 2.0 13.5 1.0
O A:HOH318 2.0 12.2 1.0
O B:HOH320 2.1 9.9 1.0
O1G A:ATP313 2.1 13.2 1.0
O A:HOH316 2.1 11.1 1.0
O A:HOH317 2.1 11.4 1.0
PB A:ATP313 3.1 12.1 1.0
PG A:ATP313 3.3 13.6 1.0
O3B A:ATP313 3.4 12.8 1.0
O1B A:ATP313 3.8 11.8 1.0
NZ B:LYS27 3.9 16.3 1.0
OD1 A:ASP166 3.9 18.1 1.0
NZ A:LYS185 4.0 12.6 1.0
O A:HOH350 4.0 21.1 1.0
OD2 A:ASP166 4.0 18.7 1.0
OE2 A:GLU190 4.0 16.4 1.0
O3G A:ATP313 4.1 14.1 1.0
O3G B:ATP312 4.2 14.6 1.0
OE1 A:GLU190 4.2 16.8 1.0
CA A:GLY255 4.3 13.2 1.0
O2G A:ATP313 4.3 13.6 1.0
CE A:LYS185 4.4 12.3 1.0
CG A:ASP166 4.4 18.1 1.0
O3A A:ATP313 4.4 12.8 1.0
CD A:GLU190 4.5 16.3 1.0
ND2 A:ASN187 4.6 11.9 1.0
O A:HOH349 4.7 18.7 1.0
MG A:MG312 4.8 11.7 1.0

Magnesium binding site 3 out of 4 in 3cqd

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Magnesium binding site 3 out of 4 in the Structure of the Tetrameric Inhibited Form of Phosphofructokinase-2 From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Tetrameric Inhibited Form of Phosphofructokinase-2 From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg312

b:11.7
occ:1.00
 O3G B:ATP312 2.0 14.6 1.0
O A:HOH357 2.1 15.6 1.0
O3G A:ATP313 2.1 14.1 1.0
O1B B:ATP312 2.1 19.3 1.0
O1B A:ATP313 2.1 11.8 1.0
O A:HOH358 2.1 12.4 1.0
PB A:ATP313 3.2 12.1 1.0
PG A:ATP313 3.2 13.6 1.0
PB B:ATP312 3.2 18.8 1.0
O3B A:ATP313 3.2 12.8 1.0
PG B:ATP312 3.3 15.8 1.0
O3B B:ATP312 3.6 18.3 1.0
O3A B:ATP312 3.6 24.8 1.0
O A:HOH343 3.7 19.8 1.0
ND2 A:ASN187 3.7 11.9 1.0
O1A A:ATP313 3.8 11.3 1.0
O A:HOH359 3.9 12.3 1.0
O1G A:ATP313 4.0 13.2 1.0
O B:HOH320 4.0 9.9 1.0
O2G B:ATP312 4.1 15.2 1.0
N7 B:ATP312 4.2 22.4 0.6
O2B A:ATP313 4.2 13.5 1.0
O B:HOH359 4.2 26.2 1.0
NZ B:LYS27 4.3 16.3 1.0
O3A A:ATP313 4.3 12.8 1.0
O A:HOH512 4.4 22.3 1.0
O1G B:ATP312 4.4 17.3 1.0
CE B:LYS27 4.4 13.6 1.0
O2G A:ATP313 4.4 13.6 1.0
O2B B:ATP312 4.6 19.6 1.0
PA A:ATP313 4.7 11.6 1.0
MG A:MG311 4.8 12.5 1.0
CG A:ASN187 4.9 13.5 1.0
C8 B:ATP312 4.9 23.3 0.6

Magnesium binding site 4 out of 4 in 3cqd

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Magnesium binding site 4 out of 4 in the Structure of the Tetrameric Inhibited Form of Phosphofructokinase-2 From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Tetrameric Inhibited Form of Phosphofructokinase-2 From Escherichia Coli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg310

b:13.6
occ:1.00
 O2B B:ATP311 2.0 14.2 1.0
O B:HOH316 2.0 11.2 1.0
O1G B:ATP311 2.0 11.0 1.0
O B:HOH318 2.0 9.9 1.0
O B:HOH315 2.1 10.6 1.0
O B:HOH317 2.2 11.9 1.0
PB B:ATP311 3.1 10.3 1.0
PG B:ATP311 3.3 12.3 1.0
O3B B:ATP311 3.4 11.4 1.0
O B:HOH441 3.6 41.0 1.0
O1B B:ATP311 3.8 10.1 1.0
NZ A:LYS27 3.9 20.1 1.0
NZ B:LYS185 3.9 10.0 1.0
O B:HOH328 3.9 21.8 1.0
OD2 B:ASP166 4.0 12.6 1.0
OD1 B:ASP166 4.1 16.5 1.0
O3G B:ATP311 4.1 12.5 1.0
OE2 B:GLU190 4.1 13.0 1.0
O3G A:ATP314 4.2 15.6 1.0
CE B:LYS185 4.3 10.5 1.0
OE1 B:GLU190 4.3 13.1 1.0
O2G B:ATP311 4.3 13.5 1.0
CA B:GLY255 4.4 12.3 1.0
O3A B:ATP311 4.4 12.0 1.0
CG B:ASP166 4.5 13.8 1.0
CD B:GLU190 4.6 13.2 1.0
ND2 B:ASN187 4.6 12.6 1.0
MG A:MG310 4.8 11.8 1.0
O B:HOH329 4.9 19.8 1.0
O A:HOH381 4.9 38.9 1.0

Reference:

R.Cabrera, A.L.Ambrosio, R.C.Garratt, V.Guixe, J.Babul. Crystallographic Structure of Phosphofructokinase-2 From Escherichia Coli in Complex with Two Atp Molecules. Implications For Substrate Inhibition. J.Mol.Biol. V. 383 588 2008.
ISSN: ISSN 0022-2836
PubMed: 18762190
DOI: 10.1016/J.JMB.2008.08.029
Page generated: Mon Dec 14 08:02:08 2020

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