Zinc in PDB 3itm: Catalytic Domain of HPDE2A
Enzymatic activity of Catalytic Domain of HPDE2A
All present enzymatic activity of Catalytic Domain of HPDE2A:
3.1.4.17;
Protein crystallography data
The structure of Catalytic Domain of HPDE2A, PDB code: 3itm
was solved by
J.Pandit,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
2.49
|
Space group
|
P 61 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
108.017,
108.017,
515.563,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
22.7 /
28.6
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Catalytic Domain of HPDE2A
(pdb code 3itm). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Catalytic Domain of HPDE2A, PDB code: 3itm:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 3itm
Go back to
Zinc Binding Sites List in 3itm
Zinc binding site 1 out
of 4 in the Catalytic Domain of HPDE2A
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Catalytic Domain of HPDE2A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn1
b:33.9
occ:1.00
|
NE2
|
A:HIS660
|
1.9
|
29.3
|
1.0
|
OD2
|
A:ASP697
|
2.0
|
37.4
|
1.0
|
OD1
|
A:ASP808
|
2.0
|
45.3
|
1.0
|
NE2
|
A:HIS696
|
2.2
|
46.5
|
1.0
|
CE1
|
A:HIS660
|
2.8
|
33.6
|
1.0
|
CG
|
A:ASP808
|
3.0
|
44.6
|
1.0
|
CD2
|
A:HIS660
|
3.0
|
32.7
|
1.0
|
CG
|
A:ASP697
|
3.1
|
41.4
|
1.0
|
CE1
|
A:HIS696
|
3.2
|
45.2
|
1.0
|
CD2
|
A:HIS696
|
3.2
|
43.0
|
1.0
|
OG
|
A:SER721
|
3.2
|
43.1
|
1.0
|
OD2
|
A:ASP808
|
3.2
|
50.2
|
1.0
|
OD1
|
A:ASP697
|
3.6
|
37.8
|
1.0
|
ND1
|
A:HIS660
|
4.0
|
35.2
|
1.0
|
ND1
|
A:HIS656
|
4.1
|
40.0
|
1.0
|
CG
|
A:HIS660
|
4.1
|
35.4
|
1.0
|
CE1
|
A:HIS656
|
4.2
|
39.4
|
1.0
|
ND1
|
A:HIS696
|
4.3
|
45.0
|
1.0
|
CG
|
A:HIS696
|
4.3
|
45.4
|
1.0
|
CB
|
A:ASP808
|
4.3
|
41.3
|
1.0
|
CB
|
A:ASP697
|
4.4
|
41.2
|
1.0
|
CB
|
A:SER721
|
4.6
|
41.4
|
1.0
|
CG2
|
A:THR768
|
4.6
|
42.7
|
1.0
|
CG2
|
A:VAL664
|
4.9
|
41.4
|
1.0
|
CA
|
A:ASP808
|
4.9
|
42.4
|
1.0
|
|
Zinc binding site 2 out
of 4 in 3itm
Go back to
Zinc Binding Sites List in 3itm
Zinc binding site 2 out
of 4 in the Catalytic Domain of HPDE2A
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Catalytic Domain of HPDE2A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn2
b:30.9
occ:1.00
|
NE2
|
B:HIS660
|
1.9
|
32.3
|
1.0
|
OD1
|
B:ASP808
|
2.0
|
47.1
|
1.0
|
OD2
|
B:ASP697
|
2.1
|
39.3
|
1.0
|
NE2
|
B:HIS696
|
2.3
|
44.9
|
1.0
|
CE1
|
B:HIS660
|
2.8
|
34.1
|
1.0
|
CG
|
B:ASP808
|
2.9
|
45.8
|
1.0
|
CD2
|
B:HIS660
|
3.0
|
31.5
|
1.0
|
CD2
|
B:HIS696
|
3.1
|
41.3
|
1.0
|
CG
|
B:ASP697
|
3.1
|
41.8
|
1.0
|
OD2
|
B:ASP808
|
3.2
|
44.9
|
1.0
|
OG
|
B:SER721
|
3.3
|
46.5
|
1.0
|
CE1
|
B:HIS696
|
3.4
|
43.7
|
1.0
|
OD1
|
B:ASP697
|
3.6
|
39.1
|
1.0
|
ND1
|
B:HIS660
|
4.0
|
30.0
|
1.0
|
CD2
|
B:HIS656
|
4.0
|
37.2
|
1.0
|
CG
|
B:HIS660
|
4.1
|
33.5
|
1.0
|
CB
|
B:ASP808
|
4.3
|
42.0
|
1.0
|
CG
|
B:HIS696
|
4.3
|
41.5
|
1.0
|
CB
|
B:ASP697
|
4.4
|
40.8
|
1.0
|
ND1
|
B:HIS696
|
4.4
|
42.2
|
1.0
|
O
|
B:HOH44
|
4.5
|
33.6
|
1.0
|
NE2
|
B:HIS656
|
4.5
|
39.4
|
1.0
|
CG2
|
B:THR768
|
4.5
|
43.2
|
1.0
|
CB
|
B:SER721
|
4.7
|
42.4
|
1.0
|
CG2
|
B:VAL664
|
4.9
|
41.6
|
1.0
|
CA
|
B:ASP808
|
5.0
|
42.4
|
1.0
|
|
Zinc binding site 3 out
of 4 in 3itm
Go back to
Zinc Binding Sites List in 3itm
Zinc binding site 3 out
of 4 in the Catalytic Domain of HPDE2A
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Catalytic Domain of HPDE2A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn3
b:42.3
occ:1.00
|
NE2
|
C:HIS660
|
2.0
|
36.5
|
1.0
|
OD2
|
C:ASP697
|
2.1
|
38.7
|
1.0
|
OD1
|
C:ASP808
|
2.1
|
47.8
|
1.0
|
NE2
|
C:HIS696
|
2.1
|
44.1
|
1.0
|
CE1
|
C:HIS660
|
2.9
|
37.8
|
1.0
|
CG
|
C:ASP808
|
2.9
|
45.2
|
1.0
|
CD2
|
C:HIS696
|
3.0
|
41.6
|
1.0
|
CD2
|
C:HIS660
|
3.1
|
36.9
|
1.0
|
OD2
|
C:ASP808
|
3.1
|
46.4
|
1.0
|
CG
|
C:ASP697
|
3.1
|
41.4
|
1.0
|
CE1
|
C:HIS696
|
3.2
|
41.3
|
1.0
|
OG
|
C:SER721
|
3.2
|
45.9
|
1.0
|
OD1
|
C:ASP697
|
3.5
|
40.4
|
1.0
|
ND1
|
C:HIS660
|
4.0
|
35.4
|
1.0
|
CG
|
C:HIS660
|
4.1
|
36.5
|
1.0
|
ND1
|
C:HIS656
|
4.2
|
40.7
|
1.0
|
CG
|
C:HIS696
|
4.2
|
40.7
|
1.0
|
CB
|
C:ASP808
|
4.2
|
42.0
|
1.0
|
ND1
|
C:HIS696
|
4.2
|
37.6
|
1.0
|
O
|
C:HOH32
|
4.3
|
31.9
|
1.0
|
CB
|
C:ASP697
|
4.5
|
40.5
|
1.0
|
CE1
|
C:HIS656
|
4.5
|
41.5
|
1.0
|
CG2
|
C:THR768
|
4.5
|
42.6
|
1.0
|
CB
|
C:SER721
|
4.7
|
42.2
|
1.0
|
CG2
|
C:VAL664
|
4.7
|
42.1
|
1.0
|
CA
|
C:ASP808
|
4.8
|
42.7
|
1.0
|
|
Zinc binding site 4 out
of 4 in 3itm
Go back to
Zinc Binding Sites List in 3itm
Zinc binding site 4 out
of 4 in the Catalytic Domain of HPDE2A
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Catalytic Domain of HPDE2A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn4
b:38.8
occ:1.00
|
NE2
|
D:HIS660
|
2.0
|
37.4
|
1.0
|
OD1
|
D:ASP808
|
2.0
|
43.7
|
1.0
|
OD2
|
D:ASP697
|
2.1
|
35.3
|
1.0
|
NE2
|
D:HIS696
|
2.2
|
40.3
|
1.0
|
CG
|
D:ASP808
|
2.8
|
44.0
|
1.0
|
OD2
|
D:ASP808
|
2.8
|
44.3
|
1.0
|
CD2
|
D:HIS660
|
2.9
|
36.1
|
1.0
|
CE1
|
D:HIS660
|
3.0
|
37.6
|
1.0
|
CD2
|
D:HIS696
|
3.0
|
39.9
|
1.0
|
CG
|
D:ASP697
|
3.1
|
40.2
|
1.0
|
CE1
|
D:HIS696
|
3.3
|
38.7
|
1.0
|
OG
|
D:SER721
|
3.4
|
43.1
|
1.0
|
OD1
|
D:ASP697
|
3.5
|
33.9
|
1.0
|
ND1
|
D:HIS660
|
4.1
|
37.8
|
1.0
|
CD2
|
D:HIS656
|
4.1
|
39.7
|
1.0
|
CG
|
D:HIS660
|
4.1
|
37.2
|
1.0
|
CG
|
D:HIS696
|
4.2
|
40.6
|
1.0
|
CB
|
D:ASP808
|
4.2
|
42.7
|
1.0
|
ND1
|
D:HIS696
|
4.3
|
37.2
|
1.0
|
CB
|
D:ASP697
|
4.5
|
40.5
|
1.0
|
NE2
|
D:HIS656
|
4.6
|
40.9
|
1.0
|
CG2
|
D:VAL664
|
4.6
|
43.2
|
1.0
|
CG2
|
D:THR768
|
4.6
|
43.4
|
1.0
|
CB
|
D:SER721
|
4.8
|
41.7
|
1.0
|
CA
|
D:ASP808
|
4.9
|
42.4
|
1.0
|
|
Reference:
J.Pandit,
M.D.Forman,
K.F.Fennell,
K.S.Dillman,
F.S.Menniti.
Mechanism For the Allosteric Regulation of Phosphodiesterase 2A Deduced From the X-Ray Structure of A Near Full-Length Construct. Proc.Natl.Acad.Sci.Usa V. 106 18225 2009.
ISSN: ISSN 0027-8424
PubMed: 19828435
DOI: 10.1073/PNAS.0907635106
Page generated: Sat Oct 26 07:20:00 2024
|