Magnesium in PDB 1t8q: Structural Genomics, Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli
Enzymatic activity of Structural Genomics, Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli
All present enzymatic activity of Structural Genomics, Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli:
3.1.4.46;
Protein crystallography data
The structure of Structural Genomics, Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli, PDB code: 1t8q
was solved by
R.Zhang,
Y.Kim,
I.Dementieva,
N.Duke,
L.Stols,
M.Donnelly,
A.Joachimiak,
Midwest Center For Structural Genomics (Mcsg),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.56 /
2.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
62.759,
118.386,
242.048,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
23.3 /
26.5
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structural Genomics, Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli
(pdb code 1t8q). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Structural Genomics, Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli, PDB code: 1t8q:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 1t8q
Go back to
Magnesium Binding Sites List in 1t8q
Magnesium binding site 1 out
of 4 in the Structural Genomics, Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structural Genomics, Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1601
b:27.3
occ:1.00
|
OE1
|
A:GLU171
|
2.1
|
20.9
|
1.0
|
OE1
|
A:GLU63
|
2.2
|
32.0
|
1.0
|
O3
|
A:GOL1605
|
2.3
|
28.5
|
1.0
|
O1
|
A:GOL1605
|
2.3
|
29.8
|
1.0
|
OD1
|
A:ASP65
|
2.4
|
20.9
|
1.0
|
O
|
A:HOH1615
|
2.4
|
21.9
|
1.0
|
CD
|
A:GLU171
|
3.2
|
17.8
|
1.0
|
CD
|
A:GLU63
|
3.3
|
35.5
|
1.0
|
CG
|
A:ASP65
|
3.3
|
25.3
|
1.0
|
C3
|
A:GOL1605
|
3.3
|
33.2
|
1.0
|
C1
|
A:GOL1605
|
3.4
|
32.3
|
1.0
|
OD2
|
A:ASP65
|
3.4
|
19.1
|
1.0
|
OE2
|
A:GLU63
|
3.6
|
35.1
|
1.0
|
C2
|
A:GOL1605
|
3.7
|
32.5
|
1.0
|
OE2
|
A:GLU171
|
4.0
|
18.9
|
1.0
|
O2
|
A:GOL1605
|
4.0
|
33.2
|
1.0
|
CB
|
A:GLU171
|
4.0
|
24.1
|
1.0
|
O
|
A:HOH1657
|
4.1
|
31.2
|
1.0
|
NE2
|
A:HIS36
|
4.1
|
22.4
|
1.0
|
CG
|
A:GLU171
|
4.2
|
23.9
|
1.0
|
NE2
|
A:GLN208
|
4.3
|
33.2
|
1.0
|
CD2
|
A:HIS36
|
4.4
|
27.4
|
1.0
|
O
|
A:HOH1616
|
4.5
|
27.0
|
1.0
|
CG
|
A:GLU63
|
4.6
|
32.0
|
1.0
|
CB
|
A:ASP65
|
4.6
|
22.2
|
1.0
|
NE
|
A:ARG37
|
4.8
|
24.6
|
1.0
|
CD
|
A:GLN208
|
4.9
|
31.8
|
1.0
|
NZ
|
A:LYS173
|
4.9
|
19.3
|
1.0
|
O
|
A:GLN64
|
5.0
|
24.6
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 1t8q
Go back to
Magnesium Binding Sites List in 1t8q
Magnesium binding site 2 out
of 4 in the Structural Genomics, Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structural Genomics, Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1602
b:22.8
occ:1.00
|
OE1
|
B:GLU171
|
2.2
|
21.4
|
1.0
|
O3
|
B:GOL1606
|
2.3
|
26.4
|
1.0
|
O1
|
B:GOL1606
|
2.3
|
23.2
|
1.0
|
OD1
|
B:ASP65
|
2.3
|
23.0
|
1.0
|
OE1
|
B:GLU63
|
2.3
|
22.3
|
1.0
|
O
|
B:HOH1612
|
2.3
|
19.9
|
1.0
|
CG
|
B:ASP65
|
3.2
|
22.3
|
1.0
|
CD
|
B:GLU63
|
3.2
|
23.2
|
1.0
|
CD
|
B:GLU171
|
3.2
|
21.4
|
1.0
|
C1
|
B:GOL1606
|
3.3
|
26.9
|
1.0
|
OD2
|
B:ASP65
|
3.3
|
20.3
|
1.0
|
C3
|
B:GOL1606
|
3.4
|
29.3
|
1.0
|
OE2
|
B:GLU63
|
3.5
|
22.5
|
1.0
|
C2
|
B:GOL1606
|
3.7
|
28.0
|
1.0
|
OE2
|
B:GLU171
|
3.9
|
20.8
|
1.0
|
CB
|
B:GLU171
|
4.0
|
22.1
|
1.0
|
O2
|
B:GOL1606
|
4.1
|
28.5
|
1.0
|
O
|
B:HOH1613
|
4.1
|
27.7
|
1.0
|
NE2
|
B:HIS36
|
4.2
|
22.3
|
1.0
|
CG
|
B:GLU171
|
4.2
|
21.8
|
1.0
|
NE2
|
B:GLN208
|
4.4
|
28.2
|
1.0
|
O
|
B:HOH1677
|
4.5
|
25.1
|
1.0
|
CG
|
B:GLU63
|
4.5
|
20.0
|
1.0
|
CB
|
B:ASP65
|
4.6
|
21.0
|
1.0
|
CD2
|
B:HIS36
|
4.6
|
20.5
|
1.0
|
NZ
|
B:LYS173
|
4.8
|
17.4
|
1.0
|
NE
|
B:ARG37
|
4.8
|
20.1
|
1.0
|
O
|
B:GLN64
|
4.9
|
25.6
|
1.0
|
CD
|
B:GLN208
|
4.9
|
28.9
|
1.0
|
CD
|
B:LYS173
|
5.0
|
18.4
|
1.0
|
CA
|
B:ASP65
|
5.0
|
21.8
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 1t8q
Go back to
Magnesium Binding Sites List in 1t8q
Magnesium binding site 3 out
of 4 in the Structural Genomics, Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structural Genomics, Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1603
b:29.4
occ:1.00
|
OE1
|
C:GLU171
|
2.3
|
30.1
|
1.0
|
OE1
|
C:GLU63
|
2.3
|
38.5
|
1.0
|
OD1
|
C:ASP65
|
2.3
|
26.1
|
1.0
|
O
|
C:HOH1614
|
2.3
|
35.1
|
1.0
|
O1
|
C:GOL1607
|
2.3
|
33.7
|
1.0
|
O3
|
C:GOL1607
|
2.4
|
38.5
|
1.0
|
CG
|
C:ASP65
|
3.1
|
27.4
|
1.0
|
CD
|
C:GLU63
|
3.2
|
36.3
|
1.0
|
OD2
|
C:ASP65
|
3.2
|
28.2
|
1.0
|
CD
|
C:GLU171
|
3.4
|
29.4
|
1.0
|
OE2
|
C:GLU63
|
3.5
|
36.0
|
1.0
|
C1
|
C:GOL1607
|
3.5
|
35.9
|
1.0
|
C3
|
C:GOL1607
|
3.5
|
37.1
|
1.0
|
C2
|
C:GOL1607
|
3.9
|
35.4
|
1.0
|
O2
|
C:GOL1607
|
4.0
|
36.3
|
1.0
|
OE2
|
C:GLU171
|
4.0
|
32.4
|
1.0
|
O
|
C:HOH1653
|
4.2
|
25.4
|
1.0
|
O
|
C:HOH1739
|
4.2
|
41.3
|
1.0
|
CB
|
C:GLU171
|
4.3
|
28.6
|
1.0
|
NE2
|
C:HIS36
|
4.3
|
30.1
|
1.0
|
CG
|
C:GLU171
|
4.4
|
31.1
|
1.0
|
NE2
|
C:GLN208
|
4.5
|
35.8
|
1.0
|
CB
|
C:ASP65
|
4.6
|
27.5
|
1.0
|
CG
|
C:GLU63
|
4.6
|
34.5
|
1.0
|
CD2
|
C:HIS36
|
4.6
|
31.6
|
1.0
|
NE
|
C:ARG37
|
4.7
|
29.0
|
1.0
|
NH2
|
C:ARG37
|
4.8
|
29.1
|
1.0
|
O
|
C:GLN64
|
4.9
|
28.9
|
1.0
|
NZ
|
C:LYS173
|
5.0
|
34.0
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 1t8q
Go back to
Magnesium Binding Sites List in 1t8q
Magnesium binding site 4 out
of 4 in the Structural Genomics, Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structural Genomics, Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1604
b:35.4
occ:1.00
|
OE1
|
D:GLU63
|
2.2
|
40.1
|
1.0
|
OD1
|
D:ASP65
|
2.2
|
33.5
|
1.0
|
O1
|
D:GOL1608
|
2.3
|
38.4
|
1.0
|
O
|
D:HOH1616
|
2.3
|
34.2
|
1.0
|
OE1
|
D:GLU171
|
2.3
|
38.0
|
1.0
|
O3
|
D:GOL1608
|
2.3
|
41.3
|
1.0
|
CD
|
D:GLU63
|
3.1
|
38.3
|
1.0
|
CG
|
D:ASP65
|
3.2
|
33.8
|
1.0
|
CD
|
D:GLU171
|
3.3
|
37.3
|
1.0
|
C3
|
D:GOL1608
|
3.3
|
42.9
|
1.0
|
C1
|
D:GOL1608
|
3.4
|
42.5
|
1.0
|
OD2
|
D:ASP65
|
3.4
|
34.3
|
1.0
|
OE2
|
D:GLU63
|
3.6
|
38.4
|
1.0
|
C2
|
D:GOL1608
|
3.8
|
41.8
|
1.0
|
CB
|
D:GLU171
|
4.0
|
35.1
|
1.0
|
OE2
|
D:GLU171
|
4.0
|
36.3
|
1.0
|
O2
|
D:GOL1608
|
4.0
|
42.3
|
1.0
|
O
|
D:HOH1746
|
4.2
|
53.3
|
1.0
|
NE2
|
D:HIS36
|
4.2
|
37.1
|
1.0
|
CG
|
D:GLU171
|
4.2
|
37.1
|
1.0
|
NE2
|
D:GLN208
|
4.3
|
44.8
|
1.0
|
CG
|
D:GLU63
|
4.3
|
38.0
|
1.0
|
O
|
D:HOH1639
|
4.5
|
45.3
|
1.0
|
CB
|
D:ASP65
|
4.5
|
32.7
|
1.0
|
CD2
|
D:HIS36
|
4.6
|
37.7
|
1.0
|
O
|
D:GLN64
|
4.7
|
34.9
|
1.0
|
CD
|
D:GLN208
|
4.8
|
45.2
|
1.0
|
NE
|
D:ARG37
|
4.9
|
40.2
|
1.0
|
CA
|
D:ASP65
|
4.9
|
31.9
|
1.0
|
CD
|
D:LYS173
|
5.0
|
31.6
|
1.0
|
|
Reference:
R.Zhang,
Y.Kim,
I.Dementieva,
N.Duke,
L.Stols,
M.Donnelly,
A.Joachimiak.
The Crystal Structure of Glycerophosphoryl Diester Phosphodiesterase From E. Coli To Be Published.
Page generated: Tue Aug 13 14:28:13 2024
|