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Magnesium in PDB 3umo: Crystal Structure of the Phosphofructokinase-2 From Escherichia Coli in Complex with Potassium

Enzymatic activity of Crystal Structure of the Phosphofructokinase-2 From Escherichia Coli in Complex with Potassium

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

Protein crystallography data

The structure of Crystal Structure of the Phosphofructokinase-2 From Escherichia Coli in Complex with Potassium, PDB code: 3umo 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) 48.97 / 1.70
Space group P 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 43.812, 88.770, 176.120, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 20.8

Other elements in 3umo:

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

Potassium (K) 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 Potassium (pdb code 3umo). 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 Potassium, PDB code: 3umo:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3umo

Go back to Magnesium Binding Sites List in 3umo
Magnesium binding site 1 out of 4 in the Crystal Structure of the Phosphofructokinase-2 From Escherichia Coli in Complex with Potassium


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 Potassium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg310

b:25.2
occ:1.00
 O2B A:ATP313 2.1 17.9 1.0
O1G A:ATP313 2.1 16.4 1.0
O A:HOH532 2.2 63.9 1.0
O A:HOH533 2.2 15.7 1.0
O A:HOH535 2.3 17.2 1.0
O B:HOH534 2.3 19.2 1.0
PB A:ATP313 3.2 18.7 1.0
PG A:ATP313 3.3 17.6 1.0
O3B A:ATP313 3.5 16.0 1.0
O1B A:ATP313 3.9 16.7 1.0
O A:HOH516 4.0 41.5 1.0
NZ A:LYS185 4.0 16.9 1.0
NZ B:LYS27 4.0 21.0 1.0
O3G A:ATP313 4.1 19.8 1.0
OD1 A:ASP166 4.1 22.1 1.0
OD2 A:ASP166 4.1 27.1 1.0
OE2 A:GLU190 4.1 20.9 1.0
O A:HOH435 4.1 28.2 1.0
O1G B:ATP312 4.3 14.2 0.6
O2G A:ATP313 4.4 15.9 1.0
O3G B:ATP312 4.4 21.8 0.4
O3A A:ATP313 4.4 14.6 1.0
CA A:GLY255 4.4 19.5 1.0
CE A:LYS185 4.4 17.1 1.0
OE1 A:GLU190 4.5 17.9 1.0
CG A:ASP166 4.5 22.5 1.0
O A:HOH447 4.7 35.9 1.0
CD A:GLU190 4.7 21.3 1.0
ND2 A:ASN187 4.7 15.9 1.0
MG A:MG311 4.8 23.3 1.0

Magnesium binding site 2 out of 4 in 3umo

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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 Potassium


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 Potassium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg311

b:23.3
occ:1.00
 O3G B:ATP312 2.1 21.8 0.4
O1B A:ATP313 2.1 16.7 1.0
O3G A:ATP313 2.1 19.8 1.0
O1G B:ATP312 2.2 14.2 0.6
O1B B:ATP312 2.2 15.1 0.4
O A:HOH686 2.2 30.0 1.0
O2B B:ATP312 2.3 22.1 0.6
O B:HOH531 2.3 18.2 1.0
PG A:ATP313 3.2 17.6 1.0
PB A:ATP313 3.2 18.7 1.0
PB B:ATP312 3.2 22.1 0.6
O3B A:ATP313 3.3 16.0 1.0
PG B:ATP312 3.3 20.9 0.4
PB B:ATP312 3.4 29.2 0.4
PG B:ATP312 3.4 19.7 0.6
O3B B:ATP312 3.6 24.4 0.6
O3A B:ATP312 3.6 28.1 0.6
O3B B:ATP312 3.7 24.5 0.4
O3A B:ATP312 3.7 31.3 0.4
ND2 A:ASN187 3.8 15.9 1.0
O B:HOH534 3.9 19.2 1.0
O1A A:ATP313 3.9 16.6 1.0
O1G A:ATP313 4.0 16.4 1.0
O A:HOH358 4.0 31.2 1.0
O A:HOH320 4.1 21.4 1.0
O A:HOH360 4.2 27.4 1.0
O2G B:ATP312 4.2 21.6 0.4
O2B A:ATP313 4.2 17.9 1.0
O B:HOH418 4.2 24.4 1.0
O3G B:ATP312 4.3 18.6 0.6
O3A A:ATP313 4.3 14.6 1.0
NZ B:LYS27 4.4 21.0 1.0
O1G B:ATP312 4.4 20.5 0.4
O2G B:ATP312 4.4 21.0 0.6
O2G A:ATP313 4.4 15.9 1.0
CE B:LYS27 4.4 20.4 1.0
N7 B:ATP312 4.5 32.6 0.4
O1B B:ATP312 4.7 23.5 0.6
O2B B:ATP312 4.7 26.5 0.4
MG A:MG310 4.8 25.2 1.0
PA A:ATP313 4.8 17.1 1.0
CG A:ASN187 5.0 16.4 1.0
O A:HOH473 5.0 39.5 1.0

Magnesium binding site 3 out of 4 in 3umo

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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 Potassium


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 Potassium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg312

b:22.0
occ:1.00
 O3G A:ATP315 2.0 21.2 0.4
O1B A:ATP315 2.1 18.4 0.4
O1G A:ATP315 2.1 15.9 0.6
O1B B:ATP313 2.1 15.2 1.0
O2B A:ATP315 2.2 14.7 0.6
O3G B:ATP313 2.2 16.7 1.0
O B:HOH669 2.2 71.8 1.0
O A:HOH536 2.3 18.4 1.0
PB A:ATP315 3.2 22.5 0.6
PG B:ATP313 3.3 17.4 1.0
PB A:ATP315 3.3 29.5 0.4
PG A:ATP315 3.3 21.2 0.4
PB B:ATP313 3.3 17.2 1.0
PG A:ATP315 3.3 21.0 0.6
O3B B:ATP313 3.4 15.3 1.0
O3B A:ATP315 3.5 27.8 0.6
O3A A:ATP315 3.6 31.1 0.6
O3A A:ATP315 3.6 32.5 0.4
O3B A:ATP315 3.7 26.9 0.4
O B:HOH452 3.8 31.5 1.0
ND2 B:ASN187 3.9 16.4 1.0
O A:HOH339 4.0 16.1 1.0
O1A B:ATP313 4.0 15.9 1.0
O B:HOH441 4.1 28.2 1.0
O1G B:ATP313 4.1 14.4 1.0
O2G A:ATP315 4.2 22.6 0.4
O3G A:ATP315 4.2 20.7 0.6
O B:HOH325 4.2 17.9 1.0
O A:HOH529 4.3 23.6 1.0
O2B B:ATP313 4.3 17.8 1.0
NZ A:LYS27 4.4 19.7 1.0
CE A:LYS27 4.4 19.5 1.0
O1G A:ATP315 4.4 19.6 0.4
O2G A:ATP315 4.4 18.4 0.6
O3A B:ATP313 4.4 14.0 1.0
N7 A:ATP315 4.4 34.0 0.4
O2G B:ATP313 4.5 16.5 1.0
O1B A:ATP315 4.6 26.0 0.6
O2B A:ATP315 4.6 28.5 0.4
MG B:MG311 4.8 23.8 1.0
PA B:ATP313 4.8 14.8 1.0
O B:HOH516 4.9 33.1 1.0

Magnesium binding site 4 out of 4 in 3umo

Go back to Magnesium Binding Sites List in 3umo
Magnesium binding site 4 out of 4 in the Crystal Structure of the Phosphofructokinase-2 From Escherichia Coli in Complex with Potassium


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 Potassium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg311

b:23.8
occ:1.00
 O2B B:ATP313 2.0 17.8 1.0
O A:HOH339 2.2 16.1 1.0
O1G B:ATP313 2.2 14.4 1.0
O B:HOH342 2.2 62.2 1.0
O B:HOH310 2.2 15.3 1.0
O B:HOH318 2.3 16.5 1.0
PB B:ATP313 3.1 17.2 1.0
PG B:ATP313 3.3 17.4 1.0
O3B B:ATP313 3.4 15.3 1.0
O B:HOH448 3.7 44.3 1.0
O1B B:ATP313 3.9 15.2 1.0
NZ B:LYS185 4.0 14.9 1.0
O3G B:ATP313 4.1 16.7 1.0
O B:HOH375 4.1 28.4 1.0
NZ A:LYS27 4.1 19.7 1.0
OE2 B:GLU190 4.1 19.9 1.0
OD2 B:ASP166 4.2 27.4 1.0
OD1 B:ASP166 4.2 25.1 1.0
O B:HOH557 4.3 39.9 1.0
O1G A:ATP315 4.3 15.9 0.6
O3G A:ATP315 4.3 21.2 0.4
O A:HOH344 4.3 63.9 1.0
OE1 B:GLU190 4.4 15.9 1.0
O3A B:ATP313 4.4 14.0 1.0
CE B:LYS185 4.4 17.4 1.0
O2G B:ATP313 4.4 16.5 1.0
CA B:GLY255 4.5 15.0 1.0
CG B:ASP166 4.6 21.6 1.0
ND2 B:ASN187 4.7 16.4 1.0
CD B:GLU190 4.7 20.3 1.0
MG A:MG312 4.8 22.0 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: Thu Aug 15 12:35:37 2024

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