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Magnesium in PDB 3ump: Crystal Structure of the Phosphofructokinase-2 From Escherichia Coli in Complex with Cesium and Atp

Enzymatic activity of Crystal Structure of the Phosphofructokinase-2 From Escherichia Coli in Complex with Cesium and Atp

All present enzymatic activity of Crystal Structure of the Phosphofructokinase-2 From Escherichia Coli in Complex with Cesium and Atp:
2.7.1.11;

Protein crystallography data

The structure of Crystal Structure of the Phosphofructokinase-2 From Escherichia Coli in Complex with Cesium and Atp, PDB code: 3ump was solved by H.M.Pereira, A.Caniuguir, M.Baez, R.Cabrera, R.C.Garratt, J.Babul, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.05 / 1.85
Space group P 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 43.856, 88.914, 176.405, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 20.9

Other elements in 3ump:

The structure of Crystal Structure of the Phosphofructokinase-2 From Escherichia Coli in Complex with Cesium and Atp also contains other interesting chemical elements:

Caesium (Cs) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Phosphofructokinase-2 From Escherichia Coli in Complex with Cesium and Atp (pdb code 3ump). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Phosphofructokinase-2 From Escherichia Coli in Complex with Cesium and Atp, PDB code: 3ump:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3ump

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Magnesium binding site 1 out of 4 in the Crystal Structure of the Phosphofructokinase-2 From Escherichia Coli in Complex with Cesium and Atp


Mono view


Stereo pair view

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

b:32.6
occ:1.00
 O2B A:ATP313 2.0 25.4 1.0
O1G A:ATP313 2.1 19.8 1.0
O A:HOH535 2.2 23.5 1.0
O A:HOH536 2.2 75.5 1.0
O A:HOH534 2.3 21.9 1.0
O B:HOH533 2.4 21.3 1.0
PB A:ATP313 3.1 20.7 1.0
PG A:ATP313 3.2 21.5 1.0
O3B A:ATP313 3.4 22.7 1.0
O A:HOH510 3.8 59.7 1.0
O1B A:ATP313 3.9 21.9 1.0
NZ A:LYS185 3.9 21.3 1.0
OD1 A:ASP166 4.0 38.0 1.0
NZ B:LYS27 4.1 30.4 1.0
O3G A:ATP313 4.1 23.0 1.0
O A:HOH428 4.2 45.1 1.0
OD2 A:ASP166 4.2 37.6 1.0
OE2 A:GLU190 4.3 26.6 1.0
O1G B:ATP312 4.3 20.8 0.6
O2G A:ATP313 4.3 20.3 1.0
O3G B:ATP312 4.4 28.3 0.4
CA A:GLY255 4.4 20.0 1.0
O3A A:ATP313 4.4 18.3 1.0
CE A:LYS185 4.4 21.3 1.0
OE1 A:GLU190 4.5 21.3 1.0
CG A:ASP166 4.5 33.6 1.0
MG A:MG311 4.8 33.9 1.0
O A:HOH442 4.8 42.5 1.0
CD A:GLU190 4.8 28.2 1.0
ND2 A:ASN187 4.9 21.9 1.0

Magnesium binding site 2 out of 4 in 3ump

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Magnesium binding site 2 out of 4 in the Crystal Structure of the Phosphofructokinase-2 From Escherichia Coli in Complex with Cesium and Atp


Mono view


Stereo pair view

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

b:33.9
occ:1.00
 O1B A:ATP313 2.0 21.9 1.0
O3G B:ATP312 2.0 28.3 0.4
O A:HOH532 2.1 73.5 1.0
O3G A:ATP313 2.1 23.0 1.0
O1G B:ATP312 2.2 20.8 0.6
O1B B:ATP312 2.2 21.4 0.4
O2B B:ATP312 2.3 24.2 0.6
O A:HOH530 2.3 18.5 1.0
PG A:ATP313 3.2 21.5 1.0
PB A:ATP313 3.2 20.7 1.0
PB B:ATP312 3.2 24.1 0.6
PG B:ATP312 3.3 24.5 0.4
O3B A:ATP313 3.3 22.7 1.0
PG B:ATP312 3.3 24.6 0.6
PB B:ATP312 3.3 30.8 0.4
O3B B:ATP312 3.6 29.3 0.6
O3B B:ATP312 3.6 30.1 0.4
O3A B:ATP312 3.6 37.1 0.6
O3A B:ATP312 3.7 40.8 0.4
ND2 A:ASN187 3.8 21.9 1.0
O B:HOH358 3.8 33.9 1.0
O1A A:ATP313 3.9 20.2 1.0
O B:HOH533 3.9 21.3 1.0
O A:HOH354 4.0 36.0 1.0
O1G A:ATP313 4.0 19.8 1.0
O2G B:ATP312 4.1 25.0 0.4
O3G B:ATP312 4.2 22.3 0.6
O2B A:ATP313 4.2 25.4 1.0
NZ B:LYS27 4.2 30.4 1.0
O A:HOH320 4.3 22.2 1.0
O3A A:ATP313 4.3 18.3 1.0
O1G B:ATP312 4.3 26.7 0.4
CE B:LYS27 4.4 26.3 1.0
N7 B:ATP312 4.4 30.8 0.4
O2G A:ATP313 4.4 20.3 1.0
O2G B:ATP312 4.4 27.8 0.6
O B:HOH412 4.4 32.4 1.0
O1B B:ATP312 4.7 28.2 0.6
O2B B:ATP312 4.7 28.9 0.4
PA A:ATP313 4.7 20.5 1.0
MG A:MG310 4.8 32.6 1.0
O A:HOH461 4.9 36.9 1.0
CG A:ASN187 5.0 22.4 1.0

Magnesium binding site 3 out of 4 in 3ump

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Magnesium binding site 3 out of 4 in the Crystal Structure of the Phosphofructokinase-2 From Escherichia Coli in Complex with Cesium and Atp


Mono view


Stereo pair view

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

b:33.6
occ:1.00
 O3G A:ATP314 1.9 23.8 0.4
O1B B:ATP313 2.1 23.5 1.0
O1G A:ATP314 2.1 18.4 0.6
O3G B:ATP313 2.2 21.2 1.0
O1B A:ATP314 2.2 21.6 0.4
O2B A:ATP314 2.2 25.2 0.6
O A:HOH545 2.2 30.0 1.0
O B:HOH527 2.3 18.5 1.0
PB A:ATP314 3.2 23.1 0.6
PG A:ATP314 3.2 23.6 0.4
PG B:ATP313 3.3 21.9 1.0
PB B:ATP313 3.3 20.0 1.0
PB A:ATP314 3.3 29.6 0.4
PG A:ATP314 3.3 23.9 0.6
O3B B:ATP313 3.4 18.6 1.0
O3A A:ATP314 3.6 35.8 0.6
O3B A:ATP314 3.6 29.0 0.6
O3B A:ATP314 3.6 29.8 0.4
O3A A:ATP314 3.7 38.6 0.4
O A:HOH411 3.7 37.8 1.0
ND2 B:ASN187 3.8 19.9 1.0
O1A B:ATP313 3.9 21.0 1.0
O A:HOH543 3.9 21.4 1.0
O B:HOH433 4.0 43.0 1.0
O1G B:ATP313 4.1 20.3 1.0
O2G A:ATP314 4.2 25.0 0.4
O3G A:ATP314 4.2 23.4 0.6
O B:HOH321 4.3 23.1 1.0
O1G A:ATP314 4.3 22.9 0.4
O2B B:ATP313 4.3 20.5 1.0
O3A B:ATP313 4.3 17.9 1.0
O2G A:ATP314 4.4 22.8 0.6
O A:HOH529 4.4 30.6 1.0
NZ A:LYS27 4.4 27.9 1.0
CE A:LYS27 4.4 27.4 1.0
O2G B:ATP313 4.5 19.0 1.0
N7 A:ATP314 4.5 33.2 0.4
O1B A:ATP314 4.6 26.4 0.6
O B:HOH500 4.7 42.8 1.0
O2B A:ATP314 4.7 27.7 0.4
PA B:ATP313 4.8 19.5 1.0
MG B:MG311 5.0 33.8 1.0
CG B:ASN187 5.0 20.9 1.0

Magnesium binding site 4 out of 4 in 3ump

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Magnesium binding site 4 out of 4 in the Crystal Structure of the Phosphofructokinase-2 From Escherichia Coli in Complex with Cesium and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Phosphofructokinase-2 From Escherichia Coli in Complex with Cesium and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg311

b:33.8
occ:1.00
 O2B B:ATP313 1.9 20.5 1.0
O B:HOH542 2.0 18.6 1.0
O B:HOH317 2.1 23.2 1.0
O1G B:ATP313 2.3 20.3 1.0
O B:HOH448 2.3 77.6 1.0
O A:HOH543 2.4 21.4 1.0
PB B:ATP313 3.1 20.0 1.0
PG B:ATP313 3.4 21.9 1.0
O3B B:ATP313 3.4 18.6 1.0
NZ B:LYS185 3.7 22.5 1.0
O1B B:ATP313 3.9 23.5 1.0
OD1 B:ASP166 4.0 37.8 1.0
OD2 B:ASP166 4.0 38.5 1.0
O B:HOH374 4.1 39.4 1.0
CE B:LYS185 4.2 24.7 1.0
OE2 B:GLU190 4.2 26.9 1.0
O3G B:ATP313 4.2 21.2 1.0
NZ A:LYS27 4.3 27.9 1.0
O3A B:ATP313 4.3 17.9 1.0
CA B:GLY255 4.4 20.8 1.0
OE1 B:GLU190 4.4 22.7 1.0
CG B:ASP166 4.5 31.3 1.0
O2G B:ATP313 4.5 19.0 1.0
O1G A:ATP314 4.5 18.4 0.6
O3G A:ATP314 4.6 23.8 0.4
CD B:GLU190 4.8 27.2 1.0
ND2 B:ASN187 4.8 19.9 1.0
O B:HOH378 5.0 39.3 1.0
MG A:MG312 5.0 33.6 1.0

Reference:

M.Baez, R.Cabrera, H.M.Pereira, A.Blanco, P.Villalobos, C.A.Ramirez-Sarmiento, A.Caniuguir, V.Guixe, R.C.Garratt, J.Babul. A Ribokinase Family Conserved Monovalent Cation Binding Site Enhances the Mgatp-Induced Inhibition in E. Coli Phosphofructokinase-2 Biophys.J. V. 105 185 2013.
ISSN: ISSN 0006-3495
PubMed: 23823238
DOI: 10.1016/J.BPJ.2013.05.028
Page generated: Mon Aug 11 04:17:31 2025

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