Magnesium in PDB 5sj9: Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-3-Propan-2-Yl-[1,2, 4]Triazolo[4,3-A]Pyridine-8-Carboxamide
Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-3-Propan-2-Yl-[1,2, 4]Triazolo[4,3-A]Pyridine-8-Carboxamide
All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-3-Propan-2-Yl-[1,2, 4]Triazolo[4,3-A]Pyridine-8-Carboxamide:
3.1.4.17;
Protein crystallography data
The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-3-Propan-2-Yl-[1,2, 4]Triazolo[4,3-A]Pyridine-8-Carboxamide, PDB code: 5sj9
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)
|
43.60 /
2.39
|
Space group
|
H 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
135.419,
135.419,
235.128,
90,
90,
120
|
R / Rfree (%)
|
17.6 /
23.3
|
Other elements in 5sj9:
The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-3-Propan-2-Yl-[1,2, 4]Triazolo[4,3-A]Pyridine-8-Carboxamide 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 N-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-3-Propan-2-Yl-[1,2, 4]Triazolo[4,3-A]Pyridine-8-Carboxamide
(pdb code 5sj9). 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 N-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-3-Propan-2-Yl-[1,2, 4]Triazolo[4,3-A]Pyridine-8-Carboxamide, PDB code: 5sj9:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 5sj9
Go back to
Magnesium Binding Sites List in 5sj9
Magnesium binding site 1 out
of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-3-Propan-2-Yl-[1,2, 4]Triazolo[4,3-A]Pyridine-8-Carboxamide
 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 N-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-3-Propan-2-Yl-[1,2, 4]Triazolo[4,3-A]Pyridine-8-Carboxamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg802
b:46.7
occ:1.00
|
O
|
A:HOH938
|
1.9
|
38.8
|
1.0
|
O
|
A:HOH904
|
1.9
|
33.2
|
1.0
|
O
|
A:HOH937
|
2.0
|
37.9
|
1.0
|
O
|
A:HOH950
|
2.0
|
35.6
|
1.0
|
OD1
|
A:ASP564
|
2.0
|
40.8
|
1.0
|
O
|
A:HOH906
|
2.2
|
40.1
|
1.0
|
CG
|
A:ASP564
|
3.0
|
37.4
|
1.0
|
OD2
|
A:ASP564
|
3.4
|
42.4
|
1.0
|
ZN
|
A:ZN801
|
3.8
|
46.2
|
1.0
|
NE2
|
A:HIS595
|
3.9
|
40.9
|
1.0
|
OE2
|
A:GLU592
|
4.1
|
47.4
|
1.0
|
CD2
|
A:HIS567
|
4.2
|
40.5
|
1.0
|
CD2
|
A:HIS595
|
4.3
|
41.5
|
1.0
|
CD2
|
A:HIS563
|
4.3
|
42.0
|
1.0
|
O
|
A:HIS563
|
4.3
|
45.3
|
1.0
|
OG1
|
A:THR633
|
4.3
|
44.4
|
1.0
|
CB
|
A:ASP564
|
4.4
|
37.5
|
1.0
|
O
|
A:THR633
|
4.5
|
38.7
|
1.0
|
NE2
|
A:HIS567
|
4.5
|
39.4
|
1.0
|
NE2
|
A:HIS563
|
4.5
|
38.9
|
1.0
|
CD2
|
A:HIS525
|
4.6
|
46.7
|
1.0
|
CG
|
A:GLU592
|
4.6
|
40.9
|
1.0
|
NE2
|
A:HIS525
|
4.6
|
44.1
|
1.0
|
OD2
|
A:ASP674
|
4.7
|
47.6
|
1.0
|
CB
|
A:THR633
|
4.8
|
41.8
|
1.0
|
CD
|
A:GLU592
|
4.8
|
43.7
|
1.0
|
CA
|
A:ASP564
|
4.8
|
40.1
|
1.0
|
O
|
A:HOH944
|
4.9
|
42.9
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 5sj9
Go back to
Magnesium Binding Sites List in 5sj9
Magnesium binding site 2 out
of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-3-Propan-2-Yl-[1,2, 4]Triazolo[4,3-A]Pyridine-8-Carboxamide
 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 N-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-3-Propan-2-Yl-[1,2, 4]Triazolo[4,3-A]Pyridine-8-Carboxamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg802
b:35.8
occ:1.00
|
O
|
B:HOH942
|
1.9
|
34.2
|
1.0
|
O
|
B:HOH923
|
1.9
|
33.2
|
1.0
|
O
|
B:HOH918
|
1.9
|
39.0
|
1.0
|
O
|
B:HOH947
|
2.0
|
31.9
|
1.0
|
O
|
B:HOH902
|
2.1
|
26.6
|
1.0
|
OD1
|
B:ASP564
|
2.1
|
44.8
|
1.0
|
CG
|
B:ASP564
|
3.1
|
42.3
|
1.0
|
OD2
|
B:ASP564
|
3.4
|
41.0
|
1.0
|
OE2
|
B:GLU592
|
3.8
|
43.6
|
1.0
|
ZN
|
B:ZN801
|
3.9
|
46.0
|
1.0
|
NE2
|
B:HIS595
|
3.9
|
39.3
|
1.0
|
OG1
|
B:THR633
|
4.2
|
41.3
|
1.0
|
CD2
|
B:HIS595
|
4.2
|
43.3
|
1.0
|
CD2
|
B:HIS563
|
4.3
|
40.1
|
1.0
|
O
|
B:HIS563
|
4.3
|
47.7
|
1.0
|
CD2
|
B:HIS567
|
4.4
|
42.1
|
1.0
|
CB
|
B:ASP564
|
4.5
|
40.7
|
1.0
|
O
|
B:THR633
|
4.5
|
36.0
|
1.0
|
NE2
|
B:HIS567
|
4.5
|
43.2
|
1.0
|
NE2
|
B:HIS563
|
4.6
|
39.6
|
1.0
|
CD2
|
B:HIS525
|
4.6
|
45.7
|
1.0
|
OD2
|
B:ASP674
|
4.6
|
37.3
|
1.0
|
CG
|
B:GLU592
|
4.7
|
41.1
|
1.0
|
CD
|
B:GLU592
|
4.7
|
40.7
|
1.0
|
CB
|
B:THR633
|
4.7
|
41.0
|
1.0
|
CA
|
B:ASP564
|
4.8
|
44.0
|
1.0
|
NE2
|
B:HIS525
|
4.8
|
40.0
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 5sj9
Go back to
Magnesium Binding Sites List in 5sj9
Magnesium binding site 3 out
of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-3-Propan-2-Yl-[1,2, 4]Triazolo[4,3-A]Pyridine-8-Carboxamide
 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 N-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-3-Propan-2-Yl-[1,2, 4]Triazolo[4,3-A]Pyridine-8-Carboxamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg802
b:39.6
occ:1.00
|
O
|
C:HOH918
|
1.9
|
37.5
|
1.0
|
O
|
C:HOH912
|
2.0
|
37.7
|
1.0
|
OD1
|
C:ASP564
|
2.0
|
36.6
|
1.0
|
O
|
C:HOH934
|
2.1
|
42.6
|
1.0
|
O
|
C:HOH923
|
2.1
|
30.0
|
1.0
|
O
|
C:HOH946
|
2.2
|
34.1
|
1.0
|
CG
|
C:ASP564
|
3.0
|
36.5
|
1.0
|
OD2
|
C:ASP564
|
3.3
|
37.9
|
1.0
|
ZN
|
C:ZN801
|
3.7
|
44.4
|
1.0
|
O
|
C:HOH942
|
3.8
|
50.0
|
1.0
|
CD2
|
C:HIS563
|
4.1
|
35.7
|
1.0
|
NE2
|
C:HIS595
|
4.1
|
42.3
|
1.0
|
OE2
|
C:GLU592
|
4.2
|
44.5
|
1.0
|
OG1
|
C:THR633
|
4.2
|
40.1
|
1.0
|
CD2
|
C:HIS567
|
4.3
|
37.6
|
1.0
|
CB
|
C:ASP564
|
4.3
|
34.2
|
1.0
|
O
|
C:HIS563
|
4.3
|
41.3
|
1.0
|
O
|
C:HOH922
|
4.3
|
41.0
|
1.0
|
CD2
|
C:HIS595
|
4.4
|
43.9
|
1.0
|
OD2
|
C:ASP674
|
4.4
|
34.0
|
1.0
|
O
|
C:HOH950
|
4.4
|
58.5
|
1.0
|
NE2
|
C:HIS563
|
4.4
|
31.6
|
1.0
|
O
|
C:THR633
|
4.5
|
41.4
|
1.0
|
NE2
|
C:HIS567
|
4.5
|
39.1
|
1.0
|
CB
|
C:THR633
|
4.7
|
41.6
|
1.0
|
CA
|
C:ASP564
|
4.7
|
35.5
|
1.0
|
CD2
|
C:HIS525
|
4.7
|
42.9
|
1.0
|
NE2
|
C:HIS525
|
4.8
|
40.4
|
1.0
|
CG
|
C:GLU592
|
4.9
|
44.9
|
1.0
|
CD
|
C:GLU592
|
5.0
|
46.8
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 5sj9
Go back to
Magnesium Binding Sites List in 5sj9
Magnesium binding site 4 out
of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-3-Propan-2-Yl-[1,2, 4]Triazolo[4,3-A]Pyridine-8-Carboxamide
 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 N-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-3-Propan-2-Yl-[1,2, 4]Triazolo[4,3-A]Pyridine-8-Carboxamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg802
b:60.2
occ:1.00
|
O
|
D:HOH902
|
2.0
|
54.9
|
1.0
|
O
|
D:HOH901
|
2.0
|
57.5
|
1.0
|
O
|
D:HOH911
|
2.1
|
44.3
|
1.0
|
O
|
D:HOH912
|
2.1
|
51.4
|
1.0
|
O
|
D:HOH913
|
2.1
|
46.9
|
1.0
|
OD1
|
D:ASP564
|
2.2
|
56.1
|
1.0
|
CG
|
D:ASP564
|
3.1
|
54.7
|
1.0
|
OD2
|
D:ASP564
|
3.5
|
71.4
|
1.0
|
NE2
|
D:HIS595
|
3.8
|
60.6
|
1.0
|
OE2
|
D:GLU592
|
3.9
|
55.4
|
1.0
|
ZN
|
D:ZN801
|
3.9
|
60.5
|
1.0
|
O
|
D:HOH904
|
4.0
|
52.9
|
1.0
|
CD2
|
D:HIS595
|
4.1
|
63.5
|
1.0
|
O
|
D:HIS563
|
4.1
|
56.3
|
1.0
|
CD2
|
D:HIS563
|
4.3
|
52.5
|
1.0
|
OG1
|
D:THR633
|
4.3
|
61.6
|
1.0
|
CD2
|
D:HIS567
|
4.3
|
58.3
|
1.0
|
CB
|
D:ASP564
|
4.4
|
54.0
|
1.0
|
CA
|
D:ASP564
|
4.6
|
49.9
|
1.0
|
O
|
D:THR633
|
4.7
|
62.8
|
1.0
|
CD2
|
D:HIS525
|
4.7
|
68.4
|
1.0
|
CB
|
D:THR633
|
4.7
|
57.3
|
1.0
|
CD
|
D:GLU592
|
4.7
|
56.5
|
1.0
|
NE2
|
D:HIS567
|
4.7
|
63.1
|
1.0
|
NE2
|
D:HIS563
|
4.7
|
47.0
|
1.0
|
OD2
|
D:ASP674
|
4.8
|
62.2
|
1.0
|
CG
|
D:GLU592
|
4.8
|
54.7
|
1.0
|
NE2
|
D:HIS525
|
4.9
|
66.4
|
1.0
|
CE1
|
D:HIS595
|
4.9
|
60.1
|
1.0
|
C
|
D:HIS563
|
5.0
|
54.1
|
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 04:19:32 2024
|