Zinc in PDB 5si5: Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide
Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide
All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide:
3.1.4.17;
Protein crystallography data
The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide, PDB code: 5si5
was solved by
C.Joseph,
J.Benz,
A.Flohr,
M.G.Rudolph,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.35 /
2.27
|
Space group
|
H 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
134.764,
134.764,
234.884,
90,
90,
120
|
R / Rfree (%)
|
18 /
22.4
|
Other elements in 5si5:
The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide
(pdb code 5si5). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide, PDB code: 5si5:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 5si5
Go back to
Zinc Binding Sites List in 5si5
Zinc binding site 1 out
of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn801
b:34.0
occ:1.00
|
OD2
|
A:ASP564
|
2.1
|
28.2
|
1.0
|
NE2
|
A:HIS529
|
2.1
|
28.6
|
1.0
|
OD1
|
A:ASP674
|
2.1
|
33.6
|
1.0
|
NE2
|
A:HIS563
|
2.1
|
28.1
|
1.0
|
O
|
A:HOH953
|
2.2
|
32.5
|
1.0
|
O
|
A:HOH970
|
2.3
|
27.9
|
1.0
|
CD2
|
A:HIS563
|
3.0
|
28.5
|
1.0
|
CG
|
A:ASP674
|
3.0
|
31.8
|
1.0
|
CD2
|
A:HIS529
|
3.1
|
28.7
|
1.0
|
CE1
|
A:HIS529
|
3.1
|
29.8
|
1.0
|
CG
|
A:ASP564
|
3.1
|
30.0
|
1.0
|
CE1
|
A:HIS563
|
3.2
|
30.5
|
1.0
|
OD2
|
A:ASP674
|
3.3
|
32.6
|
1.0
|
OD1
|
A:ASP564
|
3.7
|
27.6
|
1.0
|
MG
|
A:MG802
|
3.9
|
30.8
|
1.0
|
CD2
|
A:HIS525
|
4.2
|
30.9
|
1.0
|
CG
|
A:HIS563
|
4.2
|
29.5
|
1.0
|
ND1
|
A:HIS529
|
4.2
|
27.4
|
1.0
|
CG
|
A:HIS529
|
4.2
|
27.6
|
1.0
|
ND1
|
A:HIS563
|
4.2
|
28.9
|
1.0
|
CB
|
A:ASP564
|
4.3
|
28.4
|
1.0
|
O
|
A:HOH990
|
4.3
|
26.7
|
1.0
|
CB
|
A:ASP674
|
4.4
|
31.0
|
1.0
|
O
|
A:HOH963
|
4.4
|
32.4
|
1.0
|
NE2
|
A:HIS525
|
4.4
|
30.6
|
1.0
|
O
|
A:HOH930
|
4.6
|
26.2
|
1.0
|
O
|
A:ASP674
|
4.7
|
29.2
|
1.0
|
CG2
|
A:VAL533
|
4.7
|
25.8
|
1.0
|
CA
|
A:ASP674
|
4.8
|
28.4
|
1.0
|
|
Zinc binding site 2 out
of 4 in 5si5
Go back to
Zinc Binding Sites List in 5si5
Zinc binding site 2 out
of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn801
b:32.5
occ:1.00
|
O
|
B:HOH931
|
2.1
|
22.9
|
1.0
|
OD2
|
B:ASP564
|
2.1
|
29.4
|
1.0
|
NE2
|
B:HIS563
|
2.1
|
25.3
|
1.0
|
OD1
|
B:ASP674
|
2.1
|
32.7
|
1.0
|
NE2
|
B:HIS529
|
2.1
|
26.4
|
1.0
|
O
|
B:HOH953
|
2.5
|
36.3
|
1.0
|
CD2
|
B:HIS563
|
2.9
|
27.5
|
1.0
|
CG
|
B:ASP564
|
3.0
|
29.8
|
1.0
|
CG
|
B:ASP674
|
3.1
|
29.8
|
1.0
|
CD2
|
B:HIS529
|
3.1
|
26.8
|
1.0
|
CE1
|
B:HIS529
|
3.2
|
29.7
|
1.0
|
CE1
|
B:HIS563
|
3.2
|
28.7
|
1.0
|
OD2
|
B:ASP674
|
3.3
|
31.5
|
1.0
|
OD1
|
B:ASP564
|
3.5
|
26.5
|
1.0
|
MG
|
B:MG802
|
3.8
|
23.1
|
1.0
|
O
|
B:HOH987
|
4.1
|
17.9
|
1.0
|
CG
|
B:HIS563
|
4.1
|
25.5
|
1.0
|
CD2
|
B:HIS525
|
4.2
|
27.7
|
1.0
|
ND1
|
B:HIS563
|
4.2
|
24.6
|
1.0
|
CB
|
B:ASP564
|
4.2
|
29.8
|
1.0
|
CG
|
B:HIS529
|
4.3
|
26.7
|
1.0
|
ND1
|
B:HIS529
|
4.3
|
27.2
|
1.0
|
CB
|
B:ASP674
|
4.4
|
30.1
|
1.0
|
NE2
|
B:HIS525
|
4.4
|
29.8
|
1.0
|
O
|
B:HOH940
|
4.5
|
29.6
|
1.0
|
O
|
B:HOH934
|
4.6
|
29.3
|
1.0
|
CG2
|
B:VAL533
|
4.7
|
30.9
|
1.0
|
O
|
B:ASP674
|
4.8
|
30.9
|
1.0
|
CA
|
B:ASP674
|
4.8
|
29.1
|
1.0
|
|
Zinc binding site 3 out
of 4 in 5si5
Go back to
Zinc Binding Sites List in 5si5
Zinc binding site 3 out
of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn801
b:35.1
occ:1.00
|
OD2
|
C:ASP564
|
2.1
|
29.6
|
1.0
|
NE2
|
C:HIS529
|
2.1
|
29.3
|
1.0
|
O
|
C:HOH920
|
2.1
|
22.3
|
1.0
|
OD1
|
C:ASP674
|
2.1
|
30.5
|
1.0
|
NE2
|
C:HIS563
|
2.2
|
30.4
|
1.0
|
O
|
C:HOH960
|
2.3
|
37.9
|
1.0
|
CG
|
C:ASP674
|
3.0
|
29.4
|
1.0
|
CE1
|
C:HIS529
|
3.1
|
29.7
|
1.0
|
CD2
|
C:HIS563
|
3.1
|
28.9
|
1.0
|
CD2
|
C:HIS529
|
3.1
|
28.7
|
1.0
|
CG
|
C:ASP564
|
3.2
|
31.2
|
1.0
|
OD2
|
C:ASP674
|
3.2
|
32.5
|
1.0
|
CE1
|
C:HIS563
|
3.2
|
30.2
|
1.0
|
OD1
|
C:ASP564
|
3.7
|
30.4
|
1.0
|
MG
|
C:MG802
|
3.8
|
28.0
|
1.0
|
CD2
|
C:HIS525
|
4.1
|
34.5
|
1.0
|
ND1
|
C:HIS529
|
4.2
|
25.8
|
1.0
|
CG
|
C:HIS529
|
4.2
|
28.8
|
1.0
|
O
|
C:HOH989
|
4.2
|
24.6
|
1.0
|
CG
|
C:HIS563
|
4.3
|
29.2
|
1.0
|
ND1
|
C:HIS563
|
4.3
|
29.9
|
1.0
|
CB
|
C:ASP564
|
4.3
|
29.9
|
1.0
|
CB
|
C:ASP674
|
4.4
|
28.9
|
1.0
|
O
|
C:HOH955
|
4.4
|
33.5
|
1.0
|
NE2
|
C:HIS525
|
4.4
|
34.4
|
1.0
|
O
|
C:HOH979
|
4.6
|
47.5
|
1.0
|
O
|
C:HOH919
|
4.6
|
29.6
|
1.0
|
O
|
C:ASP674
|
4.7
|
30.5
|
1.0
|
CG2
|
C:VAL533
|
4.7
|
29.2
|
1.0
|
CA
|
C:ASP674
|
4.8
|
30.3
|
1.0
|
|
Zinc binding site 4 out
of 4 in 5si5
Go back to
Zinc Binding Sites List in 5si5
Zinc binding site 4 out
of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn801
b:48.1
occ:1.00
|
NE2
|
D:HIS563
|
2.0
|
32.7
|
1.0
|
O
|
D:HOH918
|
2.1
|
36.8
|
1.0
|
OD1
|
D:ASP674
|
2.2
|
39.9
|
1.0
|
NE2
|
D:HIS529
|
2.2
|
39.1
|
1.0
|
OD2
|
D:ASP564
|
2.3
|
45.8
|
1.0
|
O
|
D:HOH935
|
2.3
|
44.3
|
1.0
|
CD2
|
D:HIS563
|
2.9
|
35.9
|
1.0
|
CG
|
D:ASP674
|
3.1
|
44.1
|
1.0
|
CE1
|
D:HIS563
|
3.1
|
34.6
|
1.0
|
CG
|
D:ASP564
|
3.2
|
41.8
|
1.0
|
CE1
|
D:HIS529
|
3.2
|
40.7
|
1.0
|
CD2
|
D:HIS529
|
3.2
|
41.1
|
1.0
|
OD2
|
D:ASP674
|
3.3
|
42.8
|
1.0
|
OD1
|
D:ASP564
|
3.6
|
39.3
|
1.0
|
MG
|
D:MG802
|
3.8
|
48.6
|
1.0
|
CG
|
D:HIS563
|
4.1
|
35.2
|
1.0
|
ND1
|
D:HIS563
|
4.2
|
34.7
|
1.0
|
O
|
D:HOH938
|
4.2
|
36.6
|
1.0
|
CD2
|
D:HIS525
|
4.3
|
51.8
|
1.0
|
CB
|
D:ASP564
|
4.3
|
40.3
|
1.0
|
ND1
|
D:HIS529
|
4.3
|
42.9
|
1.0
|
CG
|
D:HIS529
|
4.3
|
38.6
|
1.0
|
CB
|
D:ASP674
|
4.4
|
46.2
|
1.0
|
O
|
D:HOH925
|
4.4
|
44.8
|
1.0
|
O
|
D:ASP674
|
4.6
|
45.0
|
1.0
|
NE2
|
D:HIS525
|
4.6
|
48.4
|
1.0
|
O
|
D:HOH911
|
4.7
|
36.8
|
1.0
|
CG2
|
D:VAL533
|
4.8
|
50.3
|
1.0
|
CA
|
D:ASP674
|
4.8
|
47.8
|
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 Oct 28 05:41:13 2024
|