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
Go back to
Magnesium Binding Sites List in 1pfk
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
Go back to
Magnesium Binding Sites List in 1pfk
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
Go back to
Magnesium Binding Sites List in 1pfk
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
Go back to
Magnesium Binding Sites List in 1pfk
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
|