Atomistry » Magnesium » PDB 3u8u-3umo » 3umo
Atomistry »
  Magnesium »
    PDB 3u8u-3umo »
      3umo »

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

Go back to Magnesium Binding Sites List in 3umo
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

Go back to Magnesium Binding Sites List in 3umo
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy