Magnesium in PDB 5sj3: Crystal Structure of Human Phosphodiesterase 10 in Complex with [1-(4- Chlorophenyl)-3-Methylthieno[2,3-C]Pyrazol-5-Yl]-Piperidin-1- Ylmethanone
Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with [1-(4- Chlorophenyl)-3-Methylthieno[2,3-C]Pyrazol-5-Yl]-Piperidin-1- Ylmethanone
All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with [1-(4- Chlorophenyl)-3-Methylthieno[2,3-C]Pyrazol-5-Yl]-Piperidin-1- Ylmethanone:
3.1.4.17;
Protein crystallography data
The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with [1-(4- Chlorophenyl)-3-Methylthieno[2,3-C]Pyrazol-5-Yl]-Piperidin-1- Ylmethanone, PDB code: 5sj3
was solved by
C.Joseph,
J.Benz,
A.Flohr,
M.Brunner,
M.G.Rudolph,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.60 /
2.10
|
Space group
|
H 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
135.56,
135.56,
235.55,
90,
90,
120
|
R / Rfree (%)
|
17.2 /
23.4
|
Other elements in 5sj3:
The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with [1-(4- Chlorophenyl)-3-Methylthieno[2,3-C]Pyrazol-5-Yl]-Piperidin-1- Ylmethanone also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with [1-(4- Chlorophenyl)-3-Methylthieno[2,3-C]Pyrazol-5-Yl]-Piperidin-1- Ylmethanone
(pdb code 5sj3). 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 Human Phosphodiesterase 10 in Complex with [1-(4- Chlorophenyl)-3-Methylthieno[2,3-C]Pyrazol-5-Yl]-Piperidin-1- Ylmethanone, PDB code: 5sj3:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 5sj3
Go back to
Magnesium Binding Sites List in 5sj3
Magnesium binding site 1 out
of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with [1-(4- Chlorophenyl)-3-Methylthieno[2,3-C]Pyrazol-5-Yl]-Piperidin-1- Ylmethanone
 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 Human Phosphodiesterase 10 in Complex with [1-(4- Chlorophenyl)-3-Methylthieno[2,3-C]Pyrazol-5-Yl]-Piperidin-1- Ylmethanone within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg802
b:28.6
occ:1.00
|
O
|
A:HOH928
|
1.9
|
22.4
|
1.0
|
O
|
A:HOH1002
|
2.0
|
22.6
|
1.0
|
O
|
A:HOH975
|
2.1
|
26.5
|
1.0
|
O
|
A:HOH949
|
2.1
|
26.5
|
1.0
|
OD1
|
A:ASP564
|
2.2
|
26.8
|
1.0
|
O
|
A:HOH932
|
2.3
|
26.3
|
1.0
|
CG
|
A:ASP564
|
3.1
|
30.9
|
1.0
|
OD2
|
A:ASP564
|
3.5
|
31.4
|
1.0
|
O
|
A:HOH956
|
3.8
|
30.8
|
1.0
|
ZN
|
A:ZN801
|
3.9
|
30.0
|
1.0
|
NE2
|
A:HIS595
|
4.0
|
25.9
|
1.0
|
OE2
|
A:GLU592
|
4.0
|
30.1
|
1.0
|
O
|
A:HOH1010
|
4.1
|
28.5
|
1.0
|
O
|
A:HOH1029
|
4.1
|
46.4
|
1.0
|
CD2
|
A:HIS567
|
4.4
|
26.9
|
1.0
|
OG1
|
A:THR633
|
4.4
|
26.1
|
1.0
|
O
|
A:HIS563
|
4.4
|
26.4
|
1.0
|
CD2
|
A:HIS595
|
4.4
|
23.9
|
1.0
|
CD2
|
A:HIS563
|
4.4
|
23.4
|
1.0
|
CB
|
A:ASP564
|
4.5
|
27.5
|
1.0
|
O
|
A:THR633
|
4.6
|
27.3
|
1.0
|
NE2
|
A:HIS525
|
4.6
|
27.7
|
1.0
|
CD2
|
A:HIS525
|
4.6
|
26.7
|
1.0
|
NE2
|
A:HIS567
|
4.6
|
28.0
|
1.0
|
OD2
|
A:ASP674
|
4.6
|
35.1
|
1.0
|
CB
|
A:THR633
|
4.7
|
24.2
|
1.0
|
CA
|
A:ASP564
|
4.8
|
27.7
|
1.0
|
CD
|
A:GLU592
|
4.9
|
27.1
|
1.0
|
NE2
|
A:HIS563
|
4.9
|
23.1
|
1.0
|
CG
|
A:GLU592
|
4.9
|
25.4
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 5sj3
Go back to
Magnesium Binding Sites List in 5sj3
Magnesium binding site 2 out
of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with [1-(4- Chlorophenyl)-3-Methylthieno[2,3-C]Pyrazol-5-Yl]-Piperidin-1- Ylmethanone
 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 Human Phosphodiesterase 10 in Complex with [1-(4- Chlorophenyl)-3-Methylthieno[2,3-C]Pyrazol-5-Yl]-Piperidin-1- Ylmethanone within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg802
b:21.0
occ:1.00
|
O
|
B:HOH961
|
1.9
|
21.8
|
1.0
|
O
|
B:HOH919
|
2.0
|
16.5
|
1.0
|
O
|
B:HOH920
|
2.1
|
17.2
|
1.0
|
O
|
B:HOH1002
|
2.1
|
19.8
|
1.0
|
OD1
|
B:ASP564
|
2.1
|
26.2
|
1.0
|
O
|
B:HOH1012
|
2.1
|
21.4
|
1.0
|
CG
|
B:ASP564
|
3.0
|
25.3
|
1.0
|
OD2
|
B:ASP564
|
3.3
|
25.2
|
1.0
|
ZN
|
B:ZN801
|
3.8
|
28.1
|
1.0
|
O
|
B:HOH947
|
3.8
|
28.4
|
1.0
|
O
|
B:HOH1058
|
3.8
|
59.2
|
1.0
|
OE2
|
B:GLU592
|
4.1
|
26.2
|
1.0
|
NE2
|
B:HIS595
|
4.1
|
21.4
|
1.0
|
CD2
|
B:HIS563
|
4.2
|
21.2
|
1.0
|
OG1
|
B:THR633
|
4.2
|
26.4
|
1.0
|
O
|
B:HIS563
|
4.2
|
27.0
|
1.0
|
CD2
|
B:HIS567
|
4.3
|
26.3
|
1.0
|
O
|
B:HOH985
|
4.3
|
24.6
|
1.0
|
CD2
|
B:HIS595
|
4.4
|
22.6
|
1.0
|
OD2
|
B:ASP674
|
4.4
|
25.7
|
1.0
|
NE2
|
B:HIS567
|
4.4
|
24.4
|
1.0
|
CB
|
B:ASP564
|
4.4
|
23.0
|
1.0
|
NE2
|
B:HIS563
|
4.5
|
21.0
|
1.0
|
O
|
B:THR633
|
4.6
|
23.6
|
1.0
|
CD2
|
B:HIS525
|
4.6
|
20.3
|
1.0
|
CB
|
B:THR633
|
4.7
|
24.9
|
1.0
|
NE2
|
B:HIS525
|
4.7
|
25.4
|
1.0
|
CA
|
B:ASP564
|
4.7
|
24.5
|
1.0
|
CG
|
B:GLU592
|
4.8
|
26.0
|
1.0
|
CD
|
B:GLU592
|
4.9
|
26.4
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 5sj3
Go back to
Magnesium Binding Sites List in 5sj3
Magnesium binding site 3 out
of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with [1-(4- Chlorophenyl)-3-Methylthieno[2,3-C]Pyrazol-5-Yl]-Piperidin-1- Ylmethanone
 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 Human Phosphodiesterase 10 in Complex with [1-(4- Chlorophenyl)-3-Methylthieno[2,3-C]Pyrazol-5-Yl]-Piperidin-1- Ylmethanone within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg802
b:25.5
occ:1.00
|
O
|
C:HOH950
|
2.0
|
28.7
|
1.0
|
OD1
|
C:ASP564
|
2.0
|
23.4
|
1.0
|
O
|
C:HOH953
|
2.0
|
19.3
|
1.0
|
O
|
C:HOH971
|
2.0
|
25.5
|
1.0
|
O
|
C:HOH1008
|
2.1
|
25.7
|
1.0
|
O
|
C:HOH932
|
2.1
|
22.8
|
1.0
|
CG
|
C:ASP564
|
3.0
|
24.0
|
1.0
|
OD2
|
C:ASP564
|
3.3
|
22.7
|
1.0
|
ZN
|
C:ZN801
|
3.8
|
29.4
|
1.0
|
O
|
C:HOH965
|
3.8
|
39.1
|
1.0
|
OE2
|
C:GLU592
|
4.0
|
31.6
|
1.0
|
NE2
|
C:HIS595
|
4.0
|
28.1
|
1.0
|
O
|
C:HOH956
|
4.2
|
28.3
|
1.0
|
OG1
|
C:THR633
|
4.2
|
27.3
|
1.0
|
CD2
|
C:HIS567
|
4.3
|
22.5
|
1.0
|
O
|
C:HIS563
|
4.3
|
22.4
|
1.0
|
CD2
|
C:HIS563
|
4.3
|
21.1
|
1.0
|
CD2
|
C:HIS595
|
4.3
|
28.6
|
1.0
|
CB
|
C:ASP564
|
4.4
|
22.2
|
1.0
|
OD2
|
C:ASP674
|
4.4
|
27.1
|
1.0
|
O
|
C:THR633
|
4.4
|
28.8
|
1.0
|
NE2
|
C:HIS567
|
4.5
|
23.8
|
1.0
|
CD2
|
C:HIS525
|
4.6
|
28.5
|
1.0
|
NE2
|
C:HIS525
|
4.7
|
29.9
|
1.0
|
CB
|
C:THR633
|
4.7
|
25.8
|
1.0
|
NE2
|
C:HIS563
|
4.7
|
22.5
|
1.0
|
CA
|
C:ASP564
|
4.8
|
22.7
|
1.0
|
CG
|
C:GLU592
|
4.9
|
27.8
|
1.0
|
CD
|
C:GLU592
|
4.9
|
30.3
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 5sj3
Go back to
Magnesium Binding Sites List in 5sj3
Magnesium binding site 4 out
of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with [1-(4- Chlorophenyl)-3-Methylthieno[2,3-C]Pyrazol-5-Yl]-Piperidin-1- Ylmethanone
 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 Human Phosphodiesterase 10 in Complex with [1-(4- Chlorophenyl)-3-Methylthieno[2,3-C]Pyrazol-5-Yl]-Piperidin-1- Ylmethanone within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg802
b:32.4
occ:1.00
|
O
|
D:HOH941
|
2.1
|
31.2
|
1.0
|
O
|
D:HOH953
|
2.1
|
26.7
|
1.0
|
O
|
D:HOH938
|
2.1
|
24.9
|
1.0
|
O
|
D:HOH952
|
2.1
|
27.8
|
1.0
|
O
|
D:HOH977
|
2.1
|
24.7
|
1.0
|
OD1
|
D:ASP564
|
2.1
|
29.6
|
1.0
|
CG
|
D:ASP564
|
3.1
|
28.1
|
1.0
|
OD2
|
D:ASP564
|
3.5
|
34.7
|
1.0
|
O
|
D:HOH919
|
3.7
|
38.0
|
1.0
|
ZN
|
D:ZN801
|
3.8
|
35.9
|
1.0
|
OE2
|
D:GLU592
|
4.0
|
35.1
|
1.0
|
NE2
|
D:HIS595
|
4.0
|
29.7
|
1.0
|
O
|
D:HOH988
|
4.1
|
33.6
|
1.0
|
CD2
|
D:HIS567
|
4.2
|
37.6
|
1.0
|
CD2
|
D:HIS595
|
4.3
|
30.8
|
1.0
|
CD2
|
D:HIS563
|
4.3
|
24.9
|
1.0
|
OG1
|
D:THR633
|
4.4
|
30.9
|
1.0
|
NE2
|
D:HIS567
|
4.4
|
33.7
|
1.0
|
O
|
D:HIS563
|
4.4
|
29.7
|
1.0
|
CB
|
D:ASP564
|
4.5
|
28.0
|
1.0
|
CD2
|
D:HIS525
|
4.5
|
35.1
|
1.0
|
OD2
|
D:ASP674
|
4.5
|
31.0
|
1.0
|
NE2
|
D:HIS525
|
4.6
|
43.3
|
1.0
|
O
|
D:THR633
|
4.6
|
38.1
|
1.0
|
NE2
|
D:HIS563
|
4.7
|
23.4
|
1.0
|
CA
|
D:ASP564
|
4.8
|
26.2
|
1.0
|
CB
|
D:THR633
|
4.9
|
33.8
|
1.0
|
CD
|
D:GLU592
|
4.9
|
35.8
|
1.0
|
|
Reference:
A.Flohr,
D.Schlatter,
B.Kuhn,
M.G.Rudolph.
Crystal Structure of A Human Phosphodiesterase 10 Complex To Be Published.
Page generated: Mon Sep 30 04:17:36 2024
|