Zinc in PDB 4htx: Crystal Structure of PDE2 Catalytic Domain in Complex with BAY60-7550
Enzymatic activity of Crystal Structure of PDE2 Catalytic Domain in Complex with BAY60-7550
All present enzymatic activity of Crystal Structure of PDE2 Catalytic Domain in Complex with BAY60-7550:
3.1.4.17;
Protein crystallography data
The structure of Crystal Structure of PDE2 Catalytic Domain in Complex with BAY60-7550, PDB code: 4htx
was solved by
J.Zhu,
Q.Huang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
44.16 /
1.90
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
56.260,
73.820,
92.470,
109.59,
91.93,
90.88
|
R / Rfree (%)
|
17.3 /
22.7
|
Other elements in 4htx:
The structure of Crystal Structure of PDE2 Catalytic Domain in Complex with BAY60-7550 also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of PDE2 Catalytic Domain in Complex with BAY60-7550
(pdb code 4htx). 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 PDE2 Catalytic Domain in Complex with BAY60-7550, PDB code: 4htx:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 4htx
Go back to
Zinc Binding Sites List in 4htx
Zinc binding site 1 out
of 4 in the Crystal Structure of PDE2 Catalytic Domain in Complex with BAY60-7550
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 PDE2 Catalytic Domain in Complex with BAY60-7550 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1001
b:18.2
occ:1.00
|
O
|
A:HOH1297
|
2.1
|
15.6
|
1.0
|
OD2
|
A:ASP697
|
2.1
|
13.0
|
1.0
|
NE2
|
A:HIS696
|
2.2
|
12.0
|
1.0
|
OD1
|
A:ASP808
|
2.2
|
15.5
|
1.0
|
NE2
|
A:HIS660
|
2.3
|
10.8
|
1.0
|
O
|
A:HOH1117
|
2.4
|
15.8
|
1.0
|
CD2
|
A:HIS696
|
3.1
|
9.4
|
1.0
|
CG
|
A:ASP808
|
3.1
|
16.2
|
1.0
|
CG
|
A:ASP697
|
3.1
|
11.4
|
1.0
|
CE1
|
A:HIS696
|
3.2
|
17.4
|
1.0
|
CD2
|
A:HIS660
|
3.2
|
10.9
|
1.0
|
OD2
|
A:ASP808
|
3.3
|
23.1
|
1.0
|
CE1
|
A:HIS660
|
3.3
|
11.4
|
1.0
|
OD1
|
A:ASP697
|
3.6
|
9.7
|
1.0
|
MG
|
A:MG1002
|
3.8
|
14.2
|
1.0
|
CD2
|
A:HIS656
|
4.2
|
14.2
|
1.0
|
O
|
A:HOH1103
|
4.2
|
13.8
|
1.0
|
CG
|
A:HIS696
|
4.3
|
14.0
|
1.0
|
ND1
|
A:HIS696
|
4.3
|
9.3
|
1.0
|
O
|
A:HOH1110
|
4.3
|
16.9
|
1.0
|
ND1
|
A:HIS660
|
4.4
|
11.8
|
1.0
|
CG
|
A:HIS660
|
4.4
|
11.4
|
1.0
|
CB
|
A:ASP697
|
4.4
|
9.6
|
1.0
|
NE2
|
A:HIS656
|
4.4
|
16.3
|
1.0
|
CB
|
A:ASP808
|
4.5
|
15.8
|
1.0
|
O
|
A:HOH1299
|
4.5
|
35.3
|
1.0
|
O
|
A:HOH1261
|
4.7
|
13.3
|
1.0
|
CG2
|
A:VAL664
|
4.9
|
11.2
|
1.0
|
CA
|
A:ASP808
|
5.0
|
14.4
|
1.0
|
|
Zinc binding site 2 out
of 4 in 4htx
Go back to
Zinc Binding Sites List in 4htx
Zinc binding site 2 out
of 4 in the Crystal Structure of PDE2 Catalytic Domain in Complex with BAY60-7550
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 PDE2 Catalytic Domain in Complex with BAY60-7550 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn1001
b:19.3
occ:1.00
|
OD2
|
B:ASP697
|
2.1
|
15.0
|
1.0
|
OD1
|
B:ASP808
|
2.1
|
16.0
|
1.0
|
NE2
|
B:HIS696
|
2.2
|
14.5
|
1.0
|
NE2
|
B:HIS660
|
2.2
|
18.4
|
1.0
|
O
|
B:HOH1219
|
2.2
|
12.3
|
1.0
|
O
|
B:HOH1133
|
2.5
|
19.6
|
1.0
|
CG
|
B:ASP808
|
3.0
|
25.8
|
1.0
|
CD2
|
B:HIS696
|
3.0
|
10.4
|
1.0
|
CG
|
B:ASP697
|
3.2
|
13.6
|
1.0
|
CD2
|
B:HIS660
|
3.2
|
20.1
|
1.0
|
CE1
|
B:HIS696
|
3.2
|
12.0
|
1.0
|
OD2
|
B:ASP808
|
3.2
|
31.9
|
1.0
|
CE1
|
B:HIS660
|
3.3
|
13.5
|
1.0
|
OD1
|
B:ASP697
|
3.7
|
11.4
|
1.0
|
MG
|
B:MG1002
|
3.8
|
13.5
|
1.0
|
O
|
B:HOH1101
|
4.0
|
12.6
|
1.0
|
O
|
B:HOH1124
|
4.1
|
23.9
|
1.0
|
CG
|
B:HIS696
|
4.2
|
12.5
|
1.0
|
CD2
|
B:HIS656
|
4.3
|
20.5
|
1.0
|
ND1
|
B:HIS696
|
4.3
|
9.9
|
1.0
|
CB
|
B:ASP697
|
4.3
|
10.4
|
1.0
|
CG
|
B:HIS660
|
4.3
|
19.2
|
1.0
|
ND1
|
B:HIS660
|
4.3
|
13.7
|
1.0
|
CB
|
B:ASP808
|
4.4
|
15.6
|
1.0
|
NE2
|
B:HIS656
|
4.5
|
21.8
|
1.0
|
O
|
B:HOH1103
|
4.7
|
14.4
|
1.0
|
CG2
|
B:VAL664
|
4.9
|
10.9
|
1.0
|
O
|
B:HOH1137
|
4.9
|
39.1
|
1.0
|
CA
|
B:ASP808
|
4.9
|
17.8
|
1.0
|
|
Zinc binding site 3 out
of 4 in 4htx
Go back to
Zinc Binding Sites List in 4htx
Zinc binding site 3 out
of 4 in the Crystal Structure of PDE2 Catalytic Domain in Complex with BAY60-7550
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 PDE2 Catalytic Domain in Complex with BAY60-7550 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn1001
b:23.1
occ:1.00
|
OD1
|
C:ASP808
|
2.0
|
19.9
|
1.0
|
OD2
|
C:ASP697
|
2.1
|
19.3
|
1.0
|
NE2
|
C:HIS696
|
2.1
|
15.1
|
1.0
|
NE2
|
C:HIS660
|
2.3
|
17.6
|
1.0
|
O
|
C:HOH1105
|
2.3
|
21.8
|
1.0
|
O
|
C:HOH1120
|
2.4
|
20.8
|
1.0
|
CG
|
C:ASP808
|
3.0
|
24.1
|
1.0
|
CD2
|
C:HIS696
|
3.0
|
14.9
|
1.0
|
CE1
|
C:HIS696
|
3.1
|
18.9
|
1.0
|
CG
|
C:ASP697
|
3.2
|
18.3
|
1.0
|
CD2
|
C:HIS660
|
3.2
|
16.3
|
1.0
|
OD2
|
C:ASP808
|
3.2
|
27.3
|
1.0
|
CE1
|
C:HIS660
|
3.3
|
15.9
|
1.0
|
OD1
|
C:ASP697
|
3.7
|
14.0
|
1.0
|
MG
|
C:MG1002
|
3.8
|
16.0
|
1.0
|
O
|
C:HOH1110
|
4.2
|
21.0
|
1.0
|
O
|
C:HOH1103
|
4.2
|
11.7
|
1.0
|
CG
|
C:HIS696
|
4.2
|
19.3
|
1.0
|
ND1
|
C:HIS696
|
4.2
|
18.9
|
1.0
|
CD2
|
C:HIS656
|
4.2
|
18.9
|
1.0
|
CG
|
C:HIS660
|
4.4
|
22.1
|
1.0
|
ND1
|
C:HIS660
|
4.4
|
16.4
|
1.0
|
CB
|
C:ASP697
|
4.4
|
18.3
|
1.0
|
CB
|
C:ASP808
|
4.4
|
20.4
|
1.0
|
NE2
|
C:HIS656
|
4.5
|
18.7
|
1.0
|
O
|
C:HOH1104
|
4.8
|
17.2
|
1.0
|
CA
|
C:ASP808
|
4.9
|
24.7
|
1.0
|
CG2
|
C:VAL664
|
4.9
|
18.3
|
1.0
|
|
Zinc binding site 4 out
of 4 in 4htx
Go back to
Zinc Binding Sites List in 4htx
Zinc binding site 4 out
of 4 in the Crystal Structure of PDE2 Catalytic Domain in Complex with BAY60-7550
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 PDE2 Catalytic Domain in Complex with BAY60-7550 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn1001
b:23.9
occ:1.00
|
OD2
|
D:ASP697
|
2.1
|
17.4
|
1.0
|
O
|
D:HOH1238
|
2.1
|
18.9
|
1.0
|
OD1
|
D:ASP808
|
2.2
|
25.2
|
1.0
|
NE2
|
D:HIS696
|
2.2
|
16.6
|
1.0
|
NE2
|
D:HIS660
|
2.2
|
17.3
|
1.0
|
O
|
D:HOH1106
|
2.3
|
26.3
|
1.0
|
CD2
|
D:HIS696
|
3.0
|
16.0
|
1.0
|
CG
|
D:ASP808
|
3.0
|
23.1
|
1.0
|
CG
|
D:ASP697
|
3.1
|
18.4
|
1.0
|
CE1
|
D:HIS660
|
3.2
|
14.9
|
1.0
|
CD2
|
D:HIS660
|
3.2
|
16.5
|
1.0
|
OD2
|
D:ASP808
|
3.2
|
32.9
|
1.0
|
CE1
|
D:HIS696
|
3.3
|
16.8
|
1.0
|
OD1
|
D:ASP697
|
3.6
|
16.6
|
1.0
|
MG
|
D:MG1002
|
3.8
|
15.3
|
1.0
|
CD2
|
D:HIS656
|
4.1
|
20.5
|
1.0
|
O
|
D:HOH1237
|
4.1
|
15.4
|
1.0
|
CG
|
D:HIS696
|
4.2
|
22.4
|
1.0
|
NE2
|
D:HIS656
|
4.3
|
23.9
|
1.0
|
O
|
D:HOH1158
|
4.3
|
23.3
|
1.0
|
ND1
|
D:HIS660
|
4.3
|
16.1
|
1.0
|
ND1
|
D:HIS696
|
4.3
|
19.7
|
1.0
|
CG
|
D:HIS660
|
4.3
|
21.2
|
1.0
|
CB
|
D:ASP697
|
4.3
|
20.2
|
1.0
|
CB
|
D:ASP808
|
4.5
|
19.7
|
1.0
|
O
|
D:HOH1105
|
4.7
|
15.5
|
1.0
|
CA
|
D:ASP808
|
4.9
|
19.6
|
1.0
|
|
Reference:
J.Zhu,
Q.Yang,
D.Dai,
Q.Huang.
X-Ray Crystal Structure of Phosphodiesterase 2 in Complex with A Highly Selective, Nanomolar Inhibitor Reveals A Binding-Induced Pocket Important For Selectivity. J.Am.Chem.Soc. V. 135 11708 2013.
ISSN: ISSN 0002-7863
PubMed: 23899287
DOI: 10.1021/JA404449G
Page generated: Sun Oct 27 00:17:39 2024
|