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Magnesium in PDB 1pfk: Crystal Structure of the Complex of Phosphofructokinase From Escherichia Coli with Its Reaction Products

Enzymatic activity of Crystal Structure of the Complex of Phosphofructokinase From Escherichia Coli with Its Reaction Products

All present enzymatic activity of Crystal Structure of the Complex of Phosphofructokinase From Escherichia Coli with Its Reaction Products:
2.7.1.11;

Protein crystallography data

The structure of Crystal Structure of the Complex of Phosphofructokinase From Escherichia Coli with Its Reaction Products, PDB code: 1pfk was solved by Y.Shirakihara, P.R.Evans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.00 / 2.40
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 112.300, 85.400, 77.100, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Complex of Phosphofructokinase From Escherichia Coli with Its Reaction Products (pdb code 1pfk). 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 Complex of Phosphofructokinase From Escherichia Coli with Its Reaction Products, PDB code: 1pfk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1pfk

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Magnesium binding site 1 out of 4 in the Crystal Structure of the Complex of Phosphofructokinase From Escherichia Coli with Its Reaction 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 Complex of Phosphofructokinase From Escherichia Coli with Its Reaction Products within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg325

b:61.5
occ:1.00
 OD2 A:ASP103 1.9 47.6 1.0
O2P A:FBP323 2.0 45.4 0.5
O2B A:ADP324 2.2 49.4 1.0
O A:HOH386 2.3 44.1 1.0
O A:HOH417 2.4 43.3 1.0
O A:HOH402 2.4 49.0 1.0
CG A:ASP103 3.1 46.3 1.0
PB A:ADP324 3.5 46.2 1.0
P1 A:FBP323 3.5 45.7 0.5
OD1 A:ASP103 3.5 46.5 1.0
O3A A:ADP324 3.9 47.5 1.0
OD2 A:ASP129 4.0 40.4 1.0
O3P A:FBP323 4.1 45.7 0.5
O3B A:ADP324 4.1 46.1 1.0
N A:ASP103 4.1 41.7 1.0
O1A A:ADP324 4.1 46.4 1.0
O1P A:FBP323 4.2 45.6 0.5
CB A:ASP103 4.3 44.7 1.0
NH1 A:ARG171 4.3 62.0 1.0
O A:HOH435 4.4 28.4 1.0
O1 A:FBP323 4.4 41.5 1.0
N A:GLY104 4.4 43.0 1.0
OD2 A:ASP127 4.5 32.7 1.0
OD1 A:ASP129 4.5 42.5 1.0
O1B A:ADP324 4.6 46.3 1.0
PA A:ADP324 4.6 46.5 1.0
CG A:ASP129 4.7 41.1 1.0
CA A:ASP103 4.7 43.1 1.0
CA A:GLY102 4.7 35.6 1.0
CD A:ARG171 4.8 57.1 1.0
C A:GLY102 4.9 40.1 1.0
OG1 A:THR125 4.9 13.3 1.0

Magnesium binding site 2 out of 4 in 1pfk

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Magnesium binding site 2 out of 4 in the Crystal Structure of the Complex of Phosphofructokinase From Escherichia Coli with Its Reaction 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 Complex of Phosphofructokinase From Escherichia Coli with Its Reaction Products within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg327

b:27.5
occ:1.00
 O A:HOH369 1.9 22.7 1.0
O A:HOH368 2.0 20.9 1.0
OE1 A:GLU187 2.1 31.3 1.0
O2B A:ADP326 2.2 36.1 1.0
O A:GLY185 2.3 24.0 1.0
O1A A:ADP326 2.4 41.0 1.0
CD A:GLU187 3.1 33.5 1.0
PB A:ADP326 3.3 34.0 1.0
C A:GLY185 3.4 25.5 1.0
OE2 A:GLU187 3.5 33.0 1.0
PA A:ADP326 3.5 38.3 1.0
O3A A:ADP326 3.6 37.4 1.0
O3B A:ADP326 3.9 31.4 1.0
CA A:GLY185 4.3 26.4 1.0
O A:TYR319 4.3 48.2 1.0
O A:HOH381 4.3 15.3 1.0
C5' A:ADP326 4.3 45.8 1.0
NZ A:LYS213 4.3 32.1 1.0
NH1 A:ARG154 4.3 25.6 1.0
C A:CYS186 4.4 31.9 1.0
O5' A:ADP326 4.4 41.6 1.0
NH2 B:ARG21 4.4 19.5 1.0
N A:CYS186 4.4 25.7 1.0
CG A:GLU187 4.5 34.0 1.0
O1B A:ADP326 4.5 36.3 1.0
N A:GLU187 4.5 33.1 1.0
O2A A:ADP326 4.6 41.4 1.0
O A:CYS186 4.6 33.4 1.0
CA A:CYS186 4.6 27.9 1.0
NE2 A:HIS215 4.8 32.5 1.0
CE A:LYS213 4.8 30.9 1.0
CA A:GLU187 5.0 32.2 1.0

Magnesium binding site 3 out of 4 in 1pfk

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Magnesium binding site 3 out of 4 in the Crystal Structure of the Complex of Phosphofructokinase From Escherichia Coli with Its Reaction 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 Complex of Phosphofructokinase From Escherichia Coli with Its Reaction Products within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg325

b:64.8
occ:1.00
 O1A B:ADP324 2.3 51.8 1.0
O B:HOH419 2.4 41.0 1.0
O2B B:ADP324 2.7 58.5 1.0
PA B:ADP324 3.4 52.7 1.0
OD2 B:ASP103 3.6 60.1 1.0
O3A B:ADP324 3.7 56.9 1.0
PB B:ADP324 3.8 57.8 1.0
O B:HOH387 3.9 45.7 1.0
N B:GLY104 4.1 44.1 1.0
CA B:GLY104 4.2 42.9 1.0
O2A B:ADP324 4.4 53.1 1.0
O B:HOH416 4.4 45.0 1.0
O5' B:ADP324 4.6 53.3 1.0
O3B B:ADP324 4.6 58.2 1.0
CG B:ASP103 4.8 59.0 1.0
O1B B:ADP324 4.9 59.0 1.0

Magnesium binding site 4 out of 4 in 1pfk

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Magnesium binding site 4 out of 4 in the Crystal Structure of the Complex of Phosphofructokinase From Escherichia Coli with Its Reaction 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 Complex of Phosphofructokinase From Escherichia Coli with Its Reaction Products within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg327

b:14.3
occ:1.00
 O B:HOH370 2.1 25.9 1.0
O1A B:ADP326 2.2 29.8 1.0
O B:HOH369 2.2 28.2 1.0
OE1 B:GLU187 2.2 21.0 1.0
O2B B:ADP326 2.2 29.2 1.0
O B:GLY185 2.3 19.2 1.0
CD B:GLU187 3.0 19.7 1.0
OE2 B:GLU187 3.1 20.6 1.0
PB B:ADP326 3.3 29.6 1.0
PA B:ADP326 3.3 29.2 1.0
O3A B:ADP326 3.5 30.6 1.0
C B:GLY185 3.5 18.8 1.0
O3B B:ADP326 3.6 30.8 1.0
NH1 B:ARG154 4.3 16.1 1.0
C5' B:ADP326 4.3 33.7 1.0
CA B:GLY185 4.3 19.5 1.0
O5' B:ADP326 4.3 31.8 1.0
O2A B:ADP326 4.4 29.1 1.0
CG B:GLU187 4.4 17.8 1.0
C B:CYS186 4.5 18.9 1.0
CE B:LYS213 4.5 18.4 1.0
N B:CYS186 4.5 17.0 1.0
NZ B:LYS213 4.5 19.4 1.0
NH2 A:ARG21 4.6 13.9 1.0
O1B B:ADP326 4.6 28.1 1.0
O B:HOH382 4.6 18.5 1.0
O B:CYS186 4.6 18.1 1.0
O B:TYR319 4.6 38.7 1.0
CA B:CYS186 4.7 18.7 1.0
N B:GLU187 4.8 18.3 1.0
NE2 B:HIS215 4.9 28.1 1.0

Reference:

Y.Shirakihara, P.R.Evans. Crystal Structure of the Complex of Phosphofructokinase From Escherichia Coli with Its Reaction Products. J.Mol.Biol. V. 204 973 1988.
ISSN: ISSN 0022-2836
PubMed: 2975709
DOI: 10.1016/0022-2836(88)90056-3
Page generated: Tue Aug 13 10:51:17 2024

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