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Magnesium in PDB 3uqd: Crystal Structure of the Phosphofructokinase-2 From Escherichia Coli in Complex with Substrates and Products

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

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

Protein crystallography data

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

Resolution Low / High (Å) 19.79 / 2.14
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 69.885, 155.189, 224.989, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 25.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Phosphofructokinase-2 From Escherichia Coli in Complex with Substrates and Products (pdb code 3uqd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of the Phosphofructokinase-2 From Escherichia Coli in Complex with Substrates and Products, PDB code: 3uqd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3uqd

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Magnesium binding site 1 out of 6 in the Crystal Structure of the Phosphofructokinase-2 From Escherichia Coli in Complex with Substrates and Products


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 Substrates and Products within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:39.9
occ:1.00
 O1B A:ATP401 1.8 25.2 1.0
O A:HOH644 2.4 20.6 1.0
O A:HOH539 2.5 31.0 1.0
O2G A:ATP401 2.5 25.8 1.0
O C:HOH537 2.6 28.9 1.0
O A:HOH643 2.7 0.7 1.0
PB A:ATP401 3.1 18.0 1.0
O3B A:ATP401 3.5 27.9 1.0
PG A:ATP401 3.5 28.2 1.0
O2B A:ATP401 3.9 15.8 1.0
NZ A:LYS185 3.9 19.4 1.0
CE A:LYS185 4.2 23.4 1.0
OE1 A:GLU190 4.2 36.1 1.0
O A:HOH677 4.2 44.1 1.0
O3G A:ATP401 4.2 33.9 1.0
OD2 A:ASP166 4.2 29.1 1.0
O3A A:ATP401 4.3 24.7 1.0
OD1 A:ASP166 4.3 34.0 1.0
CA A:GLY255 4.4 22.3 1.0
O1G C:ATP401 4.5 32.5 0.9
OE2 A:GLU190 4.5 36.2 1.0
O C:HOH576 4.5 39.1 1.0
MG A:MG404 4.7 69.1 1.0
O1G A:ATP401 4.7 24.6 1.0
CG A:ASP166 4.7 30.3 1.0
ND2 A:ASN187 4.8 24.9 1.0
CD A:GLU190 4.8 36.8 1.0

Magnesium binding site 2 out of 6 in 3uqd

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Magnesium binding site 2 out of 6 in the Crystal Structure of the Phosphofructokinase-2 From Escherichia Coli in Complex with Substrates and Products


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 Substrates and Products within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:69.1
occ:1.00
 O1G C:ATP401 1.6 32.5 0.9
O2B C:ATP401 1.6 49.9 0.9
O3G A:ATP401 1.8 33.9 1.0
O A:HOH645 2.3 0.4 1.0
O2B A:ATP401 2.4 15.8 1.0
O A:HOH699 2.8 26.7 1.0
PB C:ATP401 2.9 42.4 0.9
PG C:ATP401 2.9 36.0 0.9
PG A:ATP401 3.1 28.2 1.0
O3B C:ATP401 3.2 41.2 0.9
PB A:ATP401 3.5 18.0 1.0
O3B A:ATP401 3.5 27.9 1.0
O C:HOH537 3.5 28.9 1.0
O3G C:ATP401 3.8 39.3 0.9
O3A C:ATP401 3.8 0.4 0.9
ND2 A:ASN187 3.8 24.9 1.0
O2G A:ATP401 3.8 25.8 1.0
O C:HOH627 3.9 35.6 1.0
O C:HOH539 3.9 38.7 1.0
O2G C:ATP401 3.9 35.4 0.9
O A:HOH652 4.0 32.9 1.0
O1B C:ATP401 4.1 38.2 0.9
O1B A:ATP401 4.2 25.2 1.0
O1A A:ATP401 4.2 18.7 1.0
O1G A:ATP401 4.3 24.6 1.0
O C:HOH543 4.3 34.0 1.0
O A:HOH698 4.5 55.7 1.0
MG A:MG403 4.7 39.9 1.0
O3A A:ATP401 4.7 24.7 1.0
O A:HOH553 4.8 27.0 1.0
O2A C:ATP401 4.9 0.5 0.9
PA C:ATP401 4.9 0.6 0.9

Magnesium binding site 3 out of 6 in 3uqd

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Magnesium binding site 3 out of 6 in the Crystal Structure of the Phosphofructokinase-2 From Escherichia Coli in Complex with Substrates and Products


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 Substrates and Products within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:50.1
occ:1.00
 O B:HOH541 2.7 22.1 1.0
O B:HOH607 2.8 29.5 1.0
O2B B:ADP402 2.8 31.4 1.0
O B:HOH547 2.8 37.9 1.0
O B:HOH608 2.9 63.9 1.0
O B:HOH661 3.0 1.0 1.0
O B:HOH641 3.1 42.2 1.0
O1P B:FBP401 3.8 36.5 0.9
O D:HOH648 3.8 30.9 1.0
PB B:ADP402 3.9 30.4 1.0
OE1 B:GLU190 4.0 47.8 1.0
O3B B:ADP402 4.0 25.8 1.0
OD1 B:ASP166 4.2 28.5 1.0
O B:HOH553 4.2 39.3 1.0
NZ B:LYS185 4.3 25.7 1.0
O B:HOH510 4.4 23.1 1.0
OD2 B:ASP166 4.4 31.4 1.0
OE2 B:GLU190 4.6 35.3 1.0
CD B:GLU190 4.7 41.9 1.0
CG B:ASP166 4.7 29.8 1.0
O1B B:ADP402 4.7 29.9 1.0
ND2 B:ASN187 4.8 22.3 1.0

Magnesium binding site 4 out of 6 in 3uqd

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Magnesium binding site 4 out of 6 in the Crystal Structure of the Phosphofructokinase-2 From Escherichia Coli in Complex with Substrates and Products


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 Substrates and Products within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg404

b:57.5
occ:1.00
 O C:HOH509 2.8 27.5 1.0
O C:HOH610 2.8 57.6 1.0
O1B C:ADP403 2.9 44.8 1.0
O C:HOH588 2.9 37.3 1.0
O C:HOH611 2.9 59.0 1.0
O C:HOH514 2.9 26.2 1.0
O3B C:ADP403 3.2 36.8 1.0
PB C:ADP403 3.5 36.6 1.0
O C:HOH548 3.7 40.0 1.0
O1P C:FBP402 4.1 39.7 0.9
O C:HOH535 4.3 31.4 1.0
O C:HOH639 4.3 40.0 1.0
O C:HOH530 4.4 29.9 1.0
OE1 C:GLU190 4.4 37.5 1.0
O2B C:ADP403 4.5 41.9 1.0
OD1 C:ASP166 4.5 32.0 1.0
NZ C:LYS185 4.5 13.2 1.0
OD2 C:ASP166 4.5 28.2 1.0
O C:HOH584 4.6 40.7 1.0
O C:HOH502 4.7 24.8 1.0
O3A C:ADP403 4.8 61.8 1.0
CE C:LYS185 4.8 29.0 1.0
O3P C:FBP402 4.9 27.2 0.9
CG C:ASP166 4.9 30.8 1.0
P1 C:FBP402 5.0 36.8 0.9

Magnesium binding site 5 out of 6 in 3uqd

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Magnesium binding site 5 out of 6 in the Crystal Structure of the Phosphofructokinase-2 From Escherichia Coli in Complex with Substrates and Products


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Phosphofructokinase-2 From Escherichia Coli in Complex with Substrates and Products within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg403

b:57.8
occ:1.00
 O2B D:ATP401 2.0 25.6 1.0
O2G D:ATP401 2.1 23.7 1.0
O D:HOH616 2.5 0.0 1.0
O D:HOH557 2.6 52.1 1.0
O D:HOH504 2.9 21.9 1.0
O D:HOH617 2.9 43.4 1.0
PB D:ATP401 3.2 20.3 1.0
PG D:ATP401 3.3 20.0 1.0
O3B D:ATP401 3.5 22.4 1.0
NZ D:LYS185 3.8 22.2 1.0
OD2 D:ASP166 3.9 40.8 1.0
O D:HOH595 4.0 41.8 1.0
O3G D:ATP401 4.1 30.6 1.0
O1B D:ATP401 4.1 20.6 1.0
CA D:GLY255 4.2 25.3 1.0
CE D:LYS185 4.2 24.6 1.0
OD1 D:ASP166 4.2 38.8 1.0
O D:HOH655 4.2 32.1 1.0
O1G D:ATP401 4.4 22.1 1.0
O3A D:ATP401 4.4 32.2 1.0
OE1 D:GLU190 4.4 31.3 1.0
CG D:ASP166 4.5 40.5 1.0
C D:GLY255 4.7 28.0 1.0
O1G B:ATP404 4.8 41.2 0.9
OE2 D:GLU190 4.8 23.6 1.0
O D:HOH551 5.0 32.4 1.0

Magnesium binding site 6 out of 6 in 3uqd

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Magnesium binding site 6 out of 6 in the Crystal Structure of the Phosphofructokinase-2 From Escherichia Coli in Complex with Substrates and Products


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Phosphofructokinase-2 From Escherichia Coli in Complex with Substrates and Products within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg404

b:55.9
occ:1.00
 O1G B:ATP404 1.5 41.2 0.9
O1B B:ATP404 2.1 51.2 0.9
O1B D:ATP401 2.4 20.6 1.0
O3G D:ATP401 2.5 30.6 1.0
PG B:ATP404 2.8 44.7 0.9
O D:HOH544 3.1 33.3 1.0
O B:HOH662 3.1 53.3 1.0
PB B:ATP404 3.1 42.6 0.9
O3B B:ATP404 3.2 56.9 0.9
PB D:ATP401 3.5 20.3 1.0
ND2 D:ASN187 3.6 26.7 1.0
O3G B:ATP404 3.6 46.9 0.9
PG D:ATP401 3.7 20.0 1.0
O3B D:ATP401 3.7 22.4 1.0
O D:HOH504 3.9 21.9 1.0
O2G B:ATP404 3.9 48.5 0.9
O D:HOH518 3.9 25.9 1.0
O B:HOH560 4.0 34.0 1.0
O2A B:ATP404 4.1 1.0 0.9
O1A D:ATP401 4.1 32.4 1.0
O2B B:ATP404 4.1 78.5 0.9
O D:HOH631 4.3 43.3 1.0
O3A B:ATP404 4.4 0.5 0.9
O2B D:ATP401 4.4 25.6 1.0
O2G D:ATP401 4.5 23.7 1.0
PA B:ATP404 4.7 0.5 0.9
O3A D:ATP401 4.7 32.2 1.0
CG D:ASN187 4.8 31.6 1.0
O5' B:ATP404 4.9 70.0 0.9
O1G D:ATP401 4.9 22.1 1.0

Reference:

J.Murillo-Lopez, K.Zinovjev, H.Pereira, A.Caniuguir, R.Garratt, J.Babul, R.Recabarren, J.Alzate-Morales, J.Caballero, I.Tunon, R.Cabrera. Studying the Phosphoryl Transfer Mechanism of Thee. Coliphosphofructokinase-2: From X-Ray Structure to Quantum Mechanics/Molecular Mechanics Simulations. Chem Sci V. 10 2882 2019.
ISSN: ISSN 2041-6520
PubMed: 30996866
DOI: 10.1039/C9SC00094A
Page generated: Thu Aug 15 12:37:38 2024

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