Magnesium in PDB 5sk4: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-3-(2-Phenylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One
Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-3-(2-Phenylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One
All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-3-(2-Phenylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One:
3.1.4.17;
Protein crystallography data
The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-3-(2-Phenylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One, PDB code: 5sk4
was solved by
C.Joseph,
J.Benz,
A.Flohr,
M.Rogers-Evans,
M.G.Rudolph,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
35.02 /
2.00
|
Space group
|
H 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
135.407,
135.407,
235.581,
90,
90,
120
|
R / Rfree (%)
|
18.4 /
22.4
|
Other elements in 5sk4:
The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-3-(2-Phenylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One 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 6- Methyl-3-(2-Phenylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One
(pdb code 5sk4). 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 6- Methyl-3-(2-Phenylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One, PDB code: 5sk4:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 5sk4
Go back to
Magnesium Binding Sites List in 5sk4
Magnesium binding site 1 out
of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-3-(2-Phenylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One
 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 6- Methyl-3-(2-Phenylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg802
b:23.7
occ:1.00
|
O
|
A:HOH1032
|
2.0
|
25.2
|
1.0
|
OD1
|
A:ASP564
|
2.0
|
24.6
|
1.0
|
O
|
A:HOH934
|
2.0
|
22.5
|
1.0
|
O
|
A:HOH950
|
2.1
|
24.7
|
1.0
|
O
|
A:HOH969
|
2.1
|
21.2
|
1.0
|
O
|
A:HOH939
|
2.1
|
23.8
|
1.0
|
CG
|
A:ASP564
|
3.1
|
25.0
|
1.0
|
OD2
|
A:ASP564
|
3.5
|
25.3
|
1.0
|
ZN
|
A:ZN801
|
3.8
|
30.1
|
1.0
|
OE2
|
A:GLU592
|
4.0
|
31.1
|
1.0
|
NE2
|
A:HIS595
|
4.0
|
27.1
|
1.0
|
O
|
A:HOH1023
|
4.1
|
27.0
|
1.0
|
OG1
|
A:THR633
|
4.2
|
27.6
|
1.0
|
O
|
A:HOH990
|
4.2
|
33.7
|
1.0
|
CD2
|
A:HIS567
|
4.2
|
29.0
|
1.0
|
CD2
|
A:HIS563
|
4.3
|
24.4
|
1.0
|
O
|
A:HIS563
|
4.3
|
27.6
|
1.0
|
CD2
|
A:HIS595
|
4.3
|
27.1
|
1.0
|
CB
|
A:ASP564
|
4.4
|
24.6
|
1.0
|
NE2
|
A:HIS567
|
4.4
|
27.8
|
1.0
|
O
|
A:THR633
|
4.5
|
28.0
|
1.0
|
OD2
|
A:ASP674
|
4.5
|
29.8
|
1.0
|
NE2
|
A:HIS563
|
4.7
|
24.9
|
1.0
|
CB
|
A:THR633
|
4.7
|
26.9
|
1.0
|
CD2
|
A:HIS525
|
4.7
|
26.0
|
1.0
|
NE2
|
A:HIS525
|
4.7
|
26.2
|
1.0
|
CA
|
A:ASP564
|
4.8
|
25.3
|
1.0
|
CG
|
A:GLU592
|
4.8
|
28.2
|
1.0
|
CD
|
A:GLU592
|
4.8
|
29.5
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 5sk4
Go back to
Magnesium Binding Sites List in 5sk4
Magnesium binding site 2 out
of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-3-(2-Phenylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One
 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 6- Methyl-3-(2-Phenylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg802
b:21.5
occ:1.00
|
O
|
B:HOH943
|
1.9
|
22.9
|
1.0
|
O
|
B:HOH932
|
2.0
|
18.9
|
1.0
|
OD1
|
B:ASP564
|
2.1
|
23.4
|
1.0
|
O
|
B:HOH980
|
2.1
|
18.9
|
1.0
|
O
|
B:HOH918
|
2.1
|
19.7
|
1.0
|
O
|
B:HOH1009
|
2.1
|
24.6
|
1.0
|
CG
|
B:ASP564
|
3.1
|
24.3
|
1.0
|
OD2
|
B:ASP564
|
3.5
|
24.3
|
1.0
|
ZN
|
B:ZN801
|
3.8
|
28.6
|
1.0
|
NE2
|
B:HIS595
|
4.0
|
26.3
|
1.0
|
OE2
|
B:GLU592
|
4.1
|
30.6
|
1.0
|
O
|
B:HOH1000
|
4.1
|
29.3
|
1.0
|
CD2
|
B:HIS563
|
4.2
|
23.6
|
1.0
|
CD2
|
B:HIS595
|
4.2
|
25.6
|
1.0
|
OG1
|
B:THR633
|
4.2
|
23.7
|
1.0
|
O
|
B:HIS563
|
4.3
|
26.3
|
1.0
|
CD2
|
B:HIS567
|
4.3
|
25.1
|
1.0
|
OD2
|
B:ASP674
|
4.4
|
25.4
|
1.0
|
NE2
|
B:HIS567
|
4.4
|
25.1
|
1.0
|
O
|
B:HOH996
|
4.4
|
32.2
|
1.0
|
CB
|
B:ASP564
|
4.4
|
24.3
|
1.0
|
NE2
|
B:HIS563
|
4.5
|
24.0
|
1.0
|
O
|
B:THR633
|
4.5
|
24.9
|
1.0
|
CB
|
B:THR633
|
4.6
|
25.0
|
1.0
|
CD2
|
B:HIS525
|
4.7
|
26.7
|
1.0
|
NE2
|
B:HIS525
|
4.7
|
26.8
|
1.0
|
CG
|
B:GLU592
|
4.8
|
27.2
|
1.0
|
CA
|
B:ASP564
|
4.8
|
25.1
|
1.0
|
CD
|
B:GLU592
|
4.8
|
26.9
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 5sk4
Go back to
Magnesium Binding Sites List in 5sk4
Magnesium binding site 3 out
of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-3-(2-Phenylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One
 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 6- Methyl-3-(2-Phenylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg802
b:27.7
occ:1.00
|
O
|
C:HOH982
|
2.0
|
26.0
|
1.0
|
O
|
C:HOH934
|
2.0
|
28.4
|
1.0
|
O
|
C:HOH1026
|
2.1
|
26.0
|
1.0
|
O
|
C:HOH930
|
2.1
|
21.6
|
1.0
|
OD1
|
C:ASP564
|
2.1
|
26.1
|
1.0
|
O
|
C:HOH962
|
2.1
|
22.1
|
1.0
|
CG
|
C:ASP564
|
3.1
|
25.6
|
1.0
|
OD2
|
C:ASP564
|
3.5
|
25.6
|
1.0
|
ZN
|
C:ZN801
|
3.8
|
31.4
|
1.0
|
O
|
C:HOH997
|
4.1
|
33.2
|
1.0
|
NE2
|
C:HIS595
|
4.1
|
28.6
|
1.0
|
OE2
|
C:GLU592
|
4.1
|
31.2
|
1.0
|
CD2
|
C:HIS567
|
4.2
|
29.0
|
1.0
|
OG1
|
C:THR633
|
4.3
|
29.7
|
1.0
|
CD2
|
C:HIS563
|
4.3
|
26.1
|
1.0
|
OD2
|
C:ASP674
|
4.3
|
32.6
|
1.0
|
CD2
|
C:HIS595
|
4.4
|
26.9
|
1.0
|
O
|
C:HIS563
|
4.4
|
25.3
|
1.0
|
NE2
|
C:HIS567
|
4.4
|
28.0
|
1.0
|
O
|
C:HOH1000
|
4.5
|
36.6
|
1.0
|
CB
|
C:ASP564
|
4.5
|
24.1
|
1.0
|
O
|
C:THR633
|
4.5
|
27.9
|
1.0
|
NE2
|
C:HIS563
|
4.7
|
26.7
|
1.0
|
CD2
|
C:HIS525
|
4.7
|
30.2
|
1.0
|
CB
|
C:THR633
|
4.7
|
28.8
|
1.0
|
NE2
|
C:HIS525
|
4.7
|
32.2
|
1.0
|
CG
|
C:GLU592
|
4.8
|
28.8
|
1.0
|
CA
|
C:ASP564
|
4.8
|
24.1
|
1.0
|
CD
|
C:GLU592
|
4.9
|
29.4
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 5sk4
Go back to
Magnesium Binding Sites List in 5sk4
Magnesium binding site 4 out
of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-3-(2-Phenylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One
 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 6- Methyl-3-(2-Phenylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg802
b:33.4
occ:1.00
|
O
|
D:HOH978
|
2.0
|
29.3
|
1.0
|
O
|
D:HOH932
|
2.0
|
35.1
|
1.0
|
O
|
D:HOH911
|
2.1
|
29.5
|
1.0
|
O
|
D:HOH920
|
2.1
|
32.9
|
1.0
|
O
|
D:HOH979
|
2.2
|
34.7
|
1.0
|
OD1
|
D:ASP564
|
2.2
|
33.4
|
1.0
|
CG
|
D:ASP564
|
3.2
|
34.4
|
1.0
|
OD2
|
D:ASP564
|
3.6
|
37.1
|
1.0
|
ZN
|
D:ZN801
|
3.8
|
38.5
|
1.0
|
O
|
D:HOH985
|
3.9
|
32.0
|
1.0
|
OE2
|
D:GLU592
|
4.0
|
36.7
|
1.0
|
O
|
D:HOH989
|
4.1
|
39.2
|
1.0
|
OG1
|
D:THR633
|
4.2
|
36.2
|
1.0
|
NE2
|
D:HIS595
|
4.2
|
36.4
|
1.0
|
CD2
|
D:HIS567
|
4.3
|
43.7
|
1.0
|
CD2
|
D:HIS563
|
4.3
|
30.8
|
1.0
|
OD2
|
D:ASP674
|
4.3
|
35.7
|
1.0
|
NE2
|
D:HIS567
|
4.4
|
41.3
|
1.0
|
CD2
|
D:HIS595
|
4.4
|
36.1
|
1.0
|
O
|
D:HIS563
|
4.4
|
34.6
|
1.0
|
CB
|
D:ASP564
|
4.5
|
34.3
|
1.0
|
O
|
D:THR633
|
4.5
|
35.5
|
1.0
|
CB
|
D:THR633
|
4.6
|
36.2
|
1.0
|
NE2
|
D:HIS563
|
4.7
|
28.5
|
1.0
|
CD2
|
D:HIS525
|
4.8
|
40.9
|
1.0
|
NE2
|
D:HIS525
|
4.8
|
43.2
|
1.0
|
CA
|
D:ASP564
|
4.9
|
33.2
|
1.0
|
CD
|
D:GLU592
|
4.9
|
37.2
|
1.0
|
CG
|
D:GLU592
|
5.0
|
36.8
|
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 04:30:05 2024
|