Potassium in PDB 1ehy: X-Ray Structure of the Epoxide Hydrolase From Agrobacterium Radiobacter AD1
Enzymatic activity of X-Ray Structure of the Epoxide Hydrolase From Agrobacterium Radiobacter AD1
All present enzymatic activity of X-Ray Structure of the Epoxide Hydrolase From Agrobacterium Radiobacter AD1:
3.3.2.10;
Protein crystallography data
The structure of X-Ray Structure of the Epoxide Hydrolase From Agrobacterium Radiobacter AD1, PDB code: 1ehy
was solved by
M.Nardini,
I.S.Ridder,
H.J.Rozeboom,
K.H.Kalk,
R.Rink,
D.B.Janssen,
B.W.Dijkstra,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
25.00 /
2.10
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
146.624,
100.201,
96.879,
90.00,
100.68,
90.00
|
R / Rfree (%)
|
19 /
22.7
|
Potassium Binding Sites:
The binding sites of Potassium atom in the X-Ray Structure of the Epoxide Hydrolase From Agrobacterium Radiobacter AD1
(pdb code 1ehy). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the
X-Ray Structure of the Epoxide Hydrolase From Agrobacterium Radiobacter AD1, PDB code: 1ehy:
Jump to Potassium binding site number:
1;
2;
3;
4;
Potassium binding site 1 out
of 4 in 1ehy
Go back to
Potassium Binding Sites List in 1ehy
Potassium binding site 1 out
of 4 in the X-Ray Structure of the Epoxide Hydrolase From Agrobacterium Radiobacter AD1
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of X-Ray Structure of the Epoxide Hydrolase From Agrobacterium Radiobacter AD1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K295
b:36.6
occ:1.00
|
O
|
A:SER184
|
2.4
|
22.9
|
1.0
|
O
|
A:HOH411
|
2.6
|
31.2
|
1.0
|
O
|
A:ARG186
|
2.6
|
36.4
|
1.0
|
O
|
A:ASP181
|
2.8
|
30.1
|
1.0
|
O
|
A:HOH352
|
2.9
|
41.6
|
1.0
|
C
|
A:SER184
|
3.5
|
30.0
|
1.0
|
O
|
A:TYR185
|
3.5
|
37.2
|
1.0
|
C
|
A:ARG186
|
3.6
|
33.6
|
1.0
|
C
|
A:ASP181
|
3.8
|
27.4
|
1.0
|
C
|
A:TYR185
|
3.9
|
35.7
|
1.0
|
CA
|
A:ASP187
|
4.1
|
33.1
|
1.0
|
N
|
A:SER184
|
4.2
|
28.5
|
1.0
|
N
|
A:ASP187
|
4.2
|
33.1
|
1.0
|
CA
|
A:SER184
|
4.2
|
29.2
|
1.0
|
O
|
A:HIS182
|
4.3
|
25.4
|
1.0
|
CB
|
A:SER184
|
4.4
|
25.2
|
1.0
|
CA
|
A:HIS182
|
4.4
|
25.5
|
1.0
|
N
|
A:ARG186
|
4.4
|
35.3
|
1.0
|
O
|
A:HOH392
|
4.4
|
49.0
|
1.0
|
N
|
A:TYR185
|
4.4
|
30.9
|
1.0
|
O
|
A:ASP187
|
4.4
|
34.3
|
1.0
|
C
|
A:HIS182
|
4.4
|
24.5
|
1.0
|
C
|
A:ASP187
|
4.5
|
33.8
|
1.0
|
N
|
A:HIS182
|
4.5
|
26.5
|
1.0
|
CA
|
A:TYR185
|
4.5
|
34.1
|
1.0
|
CA
|
A:ARG186
|
4.6
|
34.4
|
1.0
|
CB
|
A:ASP246
|
4.7
|
71.9
|
1.0
|
CA
|
A:ASP181
|
4.8
|
28.3
|
1.0
|
OD1
|
A:ASP187
|
4.8
|
38.1
|
1.0
|
|
Potassium binding site 2 out
of 4 in 1ehy
Go back to
Potassium Binding Sites List in 1ehy
Potassium binding site 2 out
of 4 in the X-Ray Structure of the Epoxide Hydrolase From Agrobacterium Radiobacter AD1
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of X-Ray Structure of the Epoxide Hydrolase From Agrobacterium Radiobacter AD1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K296
b:29.9
occ:1.00
|
O
|
B:ASP181
|
2.6
|
27.5
|
1.0
|
O
|
B:ARG186
|
2.7
|
31.8
|
1.0
|
O
|
B:SER184
|
2.7
|
25.4
|
1.0
|
O
|
B:HOH359
|
2.9
|
54.7
|
1.0
|
O
|
B:HOH440
|
3.0
|
31.1
|
1.0
|
C
|
B:SER184
|
3.6
|
23.4
|
1.0
|
C
|
B:ARG186
|
3.6
|
31.6
|
1.0
|
C
|
B:ASP181
|
3.7
|
26.7
|
1.0
|
O
|
B:TYR185
|
3.8
|
33.8
|
1.0
|
C
|
B:TYR185
|
4.0
|
30.7
|
1.0
|
O
|
B:ASP187
|
4.2
|
33.8
|
1.0
|
CA
|
B:ASP187
|
4.3
|
33.2
|
1.0
|
N
|
B:ARG186
|
4.3
|
31.4
|
1.0
|
O
|
B:HIS182
|
4.3
|
25.5
|
1.0
|
N
|
B:ASP187
|
4.4
|
30.9
|
1.0
|
O
|
B:HOH401
|
4.4
|
47.0
|
1.0
|
N
|
B:SER184
|
4.4
|
20.7
|
1.0
|
CA
|
B:SER184
|
4.4
|
21.2
|
1.0
|
CA
|
B:HIS182
|
4.4
|
26.6
|
1.0
|
N
|
B:TYR185
|
4.4
|
25.3
|
1.0
|
N
|
B:HIS182
|
4.4
|
25.4
|
1.0
|
C
|
B:HIS182
|
4.5
|
24.1
|
1.0
|
CA
|
B:TYR185
|
4.5
|
28.7
|
1.0
|
C
|
B:ASP187
|
4.5
|
33.7
|
1.0
|
CB
|
B:SER184
|
4.5
|
21.2
|
1.0
|
CA
|
B:ARG186
|
4.6
|
31.1
|
1.0
|
CA
|
B:ASP181
|
4.6
|
25.0
|
1.0
|
CB
|
B:ASP181
|
5.0
|
27.9
|
1.0
|
|
Potassium binding site 3 out
of 4 in 1ehy
Go back to
Potassium Binding Sites List in 1ehy
Potassium binding site 3 out
of 4 in the X-Ray Structure of the Epoxide Hydrolase From Agrobacterium Radiobacter AD1
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of X-Ray Structure of the Epoxide Hydrolase From Agrobacterium Radiobacter AD1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K297
b:33.3
occ:1.00
|
O
|
C:ARG186
|
2.6
|
32.7
|
1.0
|
O
|
C:ASP181
|
2.6
|
26.6
|
1.0
|
O
|
C:HOH559
|
2.8
|
36.0
|
1.0
|
O
|
C:SER184
|
2.9
|
26.7
|
1.0
|
O
|
C:TYR185
|
3.6
|
27.8
|
1.0
|
C
|
C:ARG186
|
3.6
|
31.9
|
1.0
|
C
|
C:ASP181
|
3.6
|
26.5
|
1.0
|
C
|
C:SER184
|
3.7
|
26.1
|
1.0
|
C
|
C:TYR185
|
4.0
|
29.2
|
1.0
|
O
|
C:ASP187
|
4.2
|
35.5
|
1.0
|
CA
|
C:ASP187
|
4.2
|
35.4
|
1.0
|
CA
|
C:HIS182
|
4.3
|
26.2
|
1.0
|
N
|
C:ASP187
|
4.3
|
33.9
|
1.0
|
N
|
C:SER184
|
4.3
|
21.6
|
1.0
|
O
|
C:HIS182
|
4.4
|
29.6
|
1.0
|
N
|
C:HIS182
|
4.4
|
24.5
|
1.0
|
C
|
C:HIS182
|
4.4
|
25.9
|
1.0
|
CA
|
C:SER184
|
4.4
|
23.8
|
1.0
|
O
|
C:HOH601
|
4.4
|
44.9
|
1.0
|
C
|
C:ASP187
|
4.4
|
34.0
|
1.0
|
N
|
C:ARG186
|
4.5
|
28.7
|
1.0
|
N
|
C:TYR185
|
4.5
|
27.6
|
1.0
|
CB
|
C:SER184
|
4.6
|
21.2
|
1.0
|
CA
|
C:ASP181
|
4.6
|
28.1
|
1.0
|
CA
|
C:TYR185
|
4.6
|
29.0
|
1.0
|
CA
|
C:ARG186
|
4.6
|
28.7
|
1.0
|
|
Potassium binding site 4 out
of 4 in 1ehy
Go back to
Potassium Binding Sites List in 1ehy
Potassium binding site 4 out
of 4 in the X-Ray Structure of the Epoxide Hydrolase From Agrobacterium Radiobacter AD1
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of X-Ray Structure of the Epoxide Hydrolase From Agrobacterium Radiobacter AD1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K298
b:33.5
occ:1.00
|
O
|
D:SER184
|
2.6
|
28.4
|
1.0
|
O
|
D:ASP181
|
2.6
|
24.5
|
1.0
|
O
|
D:ARG186
|
2.7
|
28.2
|
1.0
|
O
|
D:TYR185
|
3.4
|
29.4
|
1.0
|
C
|
D:SER184
|
3.5
|
24.9
|
1.0
|
C
|
D:ASP181
|
3.7
|
23.0
|
1.0
|
C
|
D:ARG186
|
3.7
|
28.2
|
1.0
|
C
|
D:TYR185
|
3.9
|
29.1
|
1.0
|
O
|
D:ASP187
|
4.2
|
29.4
|
1.0
|
CA
|
D:ASP187
|
4.2
|
30.8
|
1.0
|
N
|
D:SER184
|
4.3
|
21.1
|
1.0
|
CA
|
D:SER184
|
4.3
|
22.6
|
1.0
|
N
|
D:TYR185
|
4.3
|
25.3
|
1.0
|
N
|
D:ASP187
|
4.4
|
28.9
|
1.0
|
CA
|
D:HIS182
|
4.4
|
25.8
|
1.0
|
O
|
D:HIS182
|
4.4
|
25.9
|
1.0
|
O
|
D:HOH382
|
4.4
|
67.0
|
1.0
|
N
|
D:HIS182
|
4.4
|
24.1
|
1.0
|
C
|
D:HIS182
|
4.4
|
26.0
|
1.0
|
CA
|
D:TYR185
|
4.5
|
30.9
|
1.0
|
C
|
D:ASP187
|
4.5
|
30.1
|
1.0
|
N
|
D:ARG186
|
4.5
|
27.9
|
1.0
|
CB
|
D:SER184
|
4.5
|
21.2
|
1.0
|
CA
|
D:ASP181
|
4.7
|
24.0
|
1.0
|
CA
|
D:ARG186
|
4.7
|
27.3
|
1.0
|
|
Reference:
M.Nardini,
I.S.Ridder,
H.J.Rozeboom,
K.H.Kalk,
R.Rink,
D.B.Janssen,
B.W.Dijkstra.
The X-Ray Structure of Epoxide Hydrolase From Agrobacterium Radiobacter AD1. An Enzyme to Detoxify Harmful Epoxides. J.Biol.Chem. V. 274 14579 1999.
ISSN: ISSN 0021-9258
PubMed: 10329649
DOI: 10.1074/JBC.274.21.14579
Page generated: Mon Aug 12 04:26:25 2024
|