Magnesium in PDB 5sjr: Crystal Structure of Human Phosphodiesterase 10 in Complex with (2R)- 2-[[3-Cyano-2-[4-(2-Ethoxyphenyl)Phenyl]-6-Fluoroquinolin-4- Yl]Amino]Propanoic Acid
Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with (2R)- 2-[[3-Cyano-2-[4-(2-Ethoxyphenyl)Phenyl]-6-Fluoroquinolin-4- Yl]Amino]Propanoic Acid
All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with (2R)- 2-[[3-Cyano-2-[4-(2-Ethoxyphenyl)Phenyl]-6-Fluoroquinolin-4- Yl]Amino]Propanoic Acid:
3.1.4.17;
Protein crystallography data
The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with (2R)- 2-[[3-Cyano-2-[4-(2-Ethoxyphenyl)Phenyl]-6-Fluoroquinolin-4- Yl]Amino]Propanoic Acid, PDB code: 5sjr
was solved by
C.Joseph,
J.Benz,
A.Flohr,
M.Koerner,
M.G.Rudolph,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.77 /
2.10
|
Space group
|
H 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
135.36,
135.36,
235.79,
90,
90,
120
|
R / Rfree (%)
|
20.9 /
26.3
|
Other elements in 5sjr:
The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with (2R)- 2-[[3-Cyano-2-[4-(2-Ethoxyphenyl)Phenyl]-6-Fluoroquinolin-4- Yl]Amino]Propanoic Acid 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 (2R)- 2-[[3-Cyano-2-[4-(2-Ethoxyphenyl)Phenyl]-6-Fluoroquinolin-4- Yl]Amino]Propanoic Acid
(pdb code 5sjr). 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 (2R)- 2-[[3-Cyano-2-[4-(2-Ethoxyphenyl)Phenyl]-6-Fluoroquinolin-4- Yl]Amino]Propanoic Acid, PDB code: 5sjr:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 5sjr
Go back to
Magnesium Binding Sites List in 5sjr
Magnesium binding site 1 out
of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with (2R)- 2-[[3-Cyano-2-[4-(2-Ethoxyphenyl)Phenyl]-6-Fluoroquinolin-4- Yl]Amino]Propanoic Acid
 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 (2R)- 2-[[3-Cyano-2-[4-(2-Ethoxyphenyl)Phenyl]-6-Fluoroquinolin-4- Yl]Amino]Propanoic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg803
b:30.4
occ:1.00
|
O
|
A:HOH973
|
1.8
|
47.8
|
1.0
|
OD1
|
A:ASP564
|
2.0
|
27.4
|
1.0
|
O
|
A:HOH932
|
2.1
|
24.6
|
1.0
|
O
|
A:HOH905
|
2.2
|
23.9
|
1.0
|
O
|
A:HOH935
|
2.2
|
35.4
|
1.0
|
O
|
A:HOH924
|
2.4
|
36.9
|
1.0
|
CG
|
A:ASP564
|
3.0
|
28.9
|
1.0
|
OD2
|
A:ASP564
|
3.3
|
37.3
|
1.0
|
O
|
A:HOH953
|
3.7
|
32.2
|
1.0
|
ZN
|
A:ZN802
|
3.7
|
38.3
|
1.0
|
NE2
|
A:HIS595
|
4.2
|
34.5
|
1.0
|
OE2
|
A:GLU592
|
4.2
|
32.8
|
1.0
|
O
|
A:HOH959
|
4.3
|
37.4
|
1.0
|
O
|
A:HIS563
|
4.3
|
30.1
|
1.0
|
CD2
|
A:HIS567
|
4.3
|
33.2
|
1.0
|
CB
|
A:ASP564
|
4.3
|
27.2
|
1.0
|
CD2
|
A:HIS563
|
4.4
|
31.6
|
1.0
|
NE2
|
A:HIS525
|
4.4
|
32.5
|
1.0
|
OG1
|
A:THR633
|
4.5
|
38.7
|
1.0
|
CD2
|
A:HIS525
|
4.5
|
32.7
|
1.0
|
OD2
|
A:ASP674
|
4.5
|
35.5
|
1.0
|
O
|
A:THR633
|
4.6
|
34.7
|
1.0
|
CD2
|
A:HIS595
|
4.6
|
33.1
|
1.0
|
NE2
|
A:HIS567
|
4.6
|
32.2
|
1.0
|
CB
|
A:THR633
|
4.8
|
35.1
|
1.0
|
NE2
|
A:HIS563
|
4.8
|
30.7
|
1.0
|
CA
|
A:ASP564
|
4.8
|
29.0
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 5sjr
Go back to
Magnesium Binding Sites List in 5sjr
Magnesium binding site 2 out
of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with (2R)- 2-[[3-Cyano-2-[4-(2-Ethoxyphenyl)Phenyl]-6-Fluoroquinolin-4- Yl]Amino]Propanoic Acid
 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 (2R)- 2-[[3-Cyano-2-[4-(2-Ethoxyphenyl)Phenyl]-6-Fluoroquinolin-4- Yl]Amino]Propanoic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg803
b:21.6
occ:1.00
|
OD1
|
B:ASP564
|
2.0
|
32.3
|
1.0
|
O
|
B:HOH909
|
2.0
|
25.6
|
1.0
|
O
|
B:HOH951
|
2.0
|
27.4
|
1.0
|
O
|
B:HOH912
|
2.0
|
22.2
|
1.0
|
O
|
B:HOH932
|
2.1
|
22.3
|
1.0
|
O
|
B:HOH965
|
2.1
|
24.9
|
1.0
|
CG
|
B:ASP564
|
3.0
|
32.2
|
1.0
|
OD2
|
B:ASP564
|
3.3
|
24.8
|
1.0
|
ZN
|
B:ZN802
|
3.8
|
33.1
|
1.0
|
NE2
|
B:HIS595
|
3.9
|
35.4
|
1.0
|
O
|
B:HOH937
|
4.0
|
38.4
|
1.0
|
OE2
|
B:GLU592
|
4.1
|
38.4
|
1.0
|
O
|
B:HIS563
|
4.1
|
34.5
|
1.0
|
CD2
|
B:HIS595
|
4.2
|
32.5
|
1.0
|
CD2
|
B:HIS563
|
4.2
|
25.6
|
1.0
|
OG1
|
B:THR633
|
4.3
|
32.4
|
1.0
|
CD2
|
B:HIS567
|
4.3
|
30.0
|
1.0
|
CB
|
B:ASP564
|
4.3
|
29.8
|
1.0
|
OD2
|
B:ASP674
|
4.4
|
26.9
|
1.0
|
NE2
|
B:HIS567
|
4.5
|
30.6
|
1.0
|
O
|
B:HOH981
|
4.5
|
40.2
|
1.0
|
O
|
B:THR633
|
4.6
|
34.2
|
1.0
|
NE2
|
B:HIS563
|
4.6
|
25.7
|
1.0
|
CA
|
B:ASP564
|
4.6
|
31.6
|
1.0
|
CD2
|
B:HIS525
|
4.6
|
28.8
|
1.0
|
CB
|
B:THR633
|
4.6
|
32.5
|
1.0
|
NE2
|
B:HIS525
|
4.7
|
33.2
|
1.0
|
CG
|
B:GLU592
|
4.8
|
34.4
|
1.0
|
CD
|
B:GLU592
|
4.8
|
36.1
|
1.0
|
C
|
B:HIS563
|
4.9
|
31.4
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 5sjr
Go back to
Magnesium Binding Sites List in 5sjr
Magnesium binding site 3 out
of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with (2R)- 2-[[3-Cyano-2-[4-(2-Ethoxyphenyl)Phenyl]-6-Fluoroquinolin-4- Yl]Amino]Propanoic Acid
 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 (2R)- 2-[[3-Cyano-2-[4-(2-Ethoxyphenyl)Phenyl]-6-Fluoroquinolin-4- Yl]Amino]Propanoic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg803
b:25.5
occ:1.00
|
OD1
|
C:ASP564
|
1.9
|
28.2
|
1.0
|
O
|
C:HOH936
|
2.0
|
24.4
|
1.0
|
O
|
C:HOH967
|
2.1
|
30.1
|
1.0
|
O
|
C:HOH951
|
2.1
|
30.6
|
1.0
|
O
|
C:HOH985
|
2.2
|
23.9
|
1.0
|
O
|
C:HOH910
|
2.2
|
19.0
|
1.0
|
CG
|
C:ASP564
|
2.9
|
25.1
|
1.0
|
OD2
|
C:ASP564
|
3.3
|
25.1
|
1.0
|
ZN
|
C:ZN802
|
3.8
|
33.2
|
1.0
|
O
|
C:HOH944
|
3.9
|
42.9
|
1.0
|
NE2
|
C:HIS595
|
3.9
|
29.1
|
1.0
|
CD2
|
C:HIS567
|
4.1
|
27.4
|
1.0
|
OE2
|
C:GLU592
|
4.1
|
38.6
|
1.0
|
O
|
C:HIS563
|
4.2
|
27.6
|
1.0
|
CD2
|
C:HIS595
|
4.2
|
29.2
|
1.0
|
CB
|
C:ASP564
|
4.3
|
22.9
|
1.0
|
O
|
C:HOH977
|
4.3
|
26.5
|
1.0
|
OG1
|
C:THR633
|
4.3
|
28.5
|
1.0
|
CD2
|
C:HIS563
|
4.3
|
22.6
|
1.0
|
OD2
|
C:ASP674
|
4.4
|
28.9
|
1.0
|
NE2
|
C:HIS567
|
4.4
|
28.0
|
1.0
|
CA
|
C:ASP564
|
4.6
|
25.4
|
1.0
|
CB
|
C:THR633
|
4.7
|
26.6
|
1.0
|
O
|
C:THR633
|
4.7
|
34.8
|
1.0
|
NE2
|
C:HIS563
|
4.8
|
27.1
|
1.0
|
CD2
|
C:HIS525
|
4.8
|
34.2
|
1.0
|
NE2
|
C:HIS525
|
4.9
|
33.4
|
1.0
|
CE1
|
C:HIS595
|
4.9
|
29.8
|
1.0
|
CD
|
C:GLU592
|
4.9
|
35.0
|
1.0
|
CG
|
C:GLU592
|
5.0
|
36.1
|
1.0
|
C
|
C:HIS563
|
5.0
|
25.1
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 5sjr
Go back to
Magnesium Binding Sites List in 5sjr
Magnesium binding site 4 out
of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with (2R)- 2-[[3-Cyano-2-[4-(2-Ethoxyphenyl)Phenyl]-6-Fluoroquinolin-4- Yl]Amino]Propanoic Acid
 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 (2R)- 2-[[3-Cyano-2-[4-(2-Ethoxyphenyl)Phenyl]-6-Fluoroquinolin-4- Yl]Amino]Propanoic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg803
b:52.8
occ:1.00
|
O
|
D:HOH932
|
1.5
|
55.5
|
1.0
|
O
|
D:HOH928
|
1.9
|
36.6
|
1.0
|
O
|
D:HOH922
|
2.1
|
42.7
|
1.0
|
OD1
|
D:ASP564
|
2.2
|
51.9
|
1.0
|
O
|
D:HOH906
|
2.4
|
46.7
|
1.0
|
O
|
D:HOH915
|
2.5
|
36.9
|
1.0
|
CG
|
D:ASP564
|
3.1
|
47.1
|
1.0
|
OD2
|
D:ASP564
|
3.4
|
57.0
|
1.0
|
O
|
D:HOH937
|
3.5
|
45.9
|
1.0
|
O
|
D:HOH936
|
3.6
|
53.7
|
1.0
|
ZN
|
D:ZN802
|
4.0
|
49.8
|
1.0
|
OE2
|
D:GLU592
|
4.1
|
50.7
|
1.0
|
NE2
|
D:HIS595
|
4.1
|
41.9
|
1.0
|
OG1
|
D:THR633
|
4.3
|
48.9
|
1.0
|
CD2
|
D:HIS567
|
4.4
|
47.9
|
1.0
|
NE2
|
D:HIS525
|
4.4
|
47.0
|
1.0
|
O
|
D:THR633
|
4.4
|
57.4
|
1.0
|
CD2
|
D:HIS595
|
4.5
|
47.4
|
1.0
|
CB
|
D:ASP564
|
4.5
|
46.7
|
1.0
|
CD2
|
D:HIS525
|
4.5
|
47.3
|
1.0
|
NE2
|
D:HIS567
|
4.6
|
47.4
|
1.0
|
CD2
|
D:HIS563
|
4.7
|
39.7
|
1.0
|
O
|
D:HIS563
|
4.7
|
49.7
|
1.0
|
OD2
|
D:ASP674
|
4.7
|
51.5
|
1.0
|
CB
|
D:THR633
|
4.8
|
56.2
|
1.0
|
CA
|
D:ASP564
|
4.9
|
44.9
|
1.0
|
CD
|
D:GLU592
|
4.9
|
44.3
|
1.0
|
CG
|
D:GLU592
|
5.0
|
46.6
|
1.0
|
NE2
|
D:HIS563
|
5.0
|
38.8
|
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 04:26:51 2024
|