Chlorine in PDB 5ak6: Ligand Complex Structure of Soluble Epoxide Hydrolase
Enzymatic activity of Ligand Complex Structure of Soluble Epoxide Hydrolase
All present enzymatic activity of Ligand Complex Structure of Soluble Epoxide Hydrolase:
3.1.3.76;
3.3.2.10;
Protein crystallography data
The structure of Ligand Complex Structure of Soluble Epoxide Hydrolase, PDB code: 5ak6
was solved by
L.Oster,
S.Tapani,
Y.Xue,
H.Kack,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
80.48 /
2.15
|
Space group
|
P 65 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
91.738,
91.738,
245.273,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
20.38 /
24.82
|
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Ligand Complex Structure of Soluble Epoxide Hydrolase
(pdb code 5ak6). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the
Ligand Complex Structure of Soluble Epoxide Hydrolase, PDB code: 5ak6:
Jump to Chlorine binding site number:
1;
2;
3;
Chlorine binding site 1 out
of 3 in 5ak6
Go back to
Chlorine Binding Sites List in 5ak6
Chlorine binding site 1 out
of 3 in the Ligand Complex Structure of Soluble Epoxide Hydrolase
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Ligand Complex Structure of Soluble Epoxide Hydrolase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl1553
b:33.0
occ:1.00
|
CL7
|
A:YPN1553
|
0.0
|
33.0
|
1.0
|
C6
|
A:YPN1553
|
1.7
|
29.1
|
1.0
|
C1
|
A:YPN1553
|
2.7
|
28.3
|
1.0
|
C5
|
A:YPN1553
|
2.7
|
28.4
|
1.0
|
O
|
A:HOH2277
|
3.4
|
30.0
|
1.0
|
CH2
|
A:TRP336
|
3.7
|
20.0
|
1.0
|
N4
|
A:YPN1555
|
3.7
|
61.0
|
1.0
|
SD
|
A:MET469
|
3.8
|
31.1
|
1.0
|
C5
|
A:YPN1555
|
3.9
|
55.4
|
1.0
|
C2
|
A:YPN1553
|
4.0
|
26.4
|
1.0
|
N4
|
A:YPN1553
|
4.0
|
27.7
|
1.0
|
CE
|
A:MET469
|
4.1
|
27.2
|
1.0
|
C3
|
A:YPN1555
|
4.2
|
64.6
|
1.0
|
CZ2
|
A:TRP336
|
4.2
|
20.2
|
1.0
|
C9
|
A:YPN1555
|
4.2
|
69.9
|
1.0
|
CZ3
|
A:TRP336
|
4.3
|
19.2
|
1.0
|
C3
|
A:YPN1553
|
4.4
|
26.4
|
1.0
|
O
|
A:HOH2276
|
4.5
|
35.2
|
1.0
|
O1
|
A:PEG1551
|
4.5
|
66.0
|
1.0
|
C6
|
A:YPN1555
|
4.6
|
52.8
|
1.0
|
C2
|
A:PEG1551
|
4.7
|
66.5
|
1.0
|
NE2
|
A:GLN384
|
4.7
|
16.7
|
1.0
|
S8
|
A:YPN1555
|
4.8
|
69.6
|
1.0
|
C2
|
A:YPN1555
|
4.8
|
60.1
|
1.0
|
O2
|
A:PEG1551
|
4.9
|
66.1
|
1.0
|
C1
|
A:YPN1555
|
5.0
|
55.5
|
1.0
|
|
Chlorine binding site 2 out
of 3 in 5ak6
Go back to
Chlorine Binding Sites List in 5ak6
Chlorine binding site 2 out
of 3 in the Ligand Complex Structure of Soluble Epoxide Hydrolase
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Ligand Complex Structure of Soluble Epoxide Hydrolase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl1554
b:42.4
occ:1.00
|
CL7
|
A:YPN1554
|
0.0
|
42.4
|
1.0
|
C6
|
A:YPN1554
|
1.7
|
39.6
|
1.0
|
C5
|
A:YPN1554
|
2.7
|
37.5
|
1.0
|
C1
|
A:YPN1554
|
2.7
|
35.2
|
1.0
|
CE1
|
A:HIS524
|
3.2
|
19.7
|
1.0
|
ND1
|
A:HIS524
|
3.4
|
21.1
|
1.0
|
OH
|
A:TYR383
|
3.4
|
25.5
|
1.0
|
CB
|
A:VAL498
|
3.6
|
27.8
|
1.0
|
CG1
|
A:VAL498
|
3.6
|
26.4
|
1.0
|
OD1
|
A:ASP335
|
3.7
|
24.3
|
1.0
|
NE2
|
A:HIS524
|
3.8
|
19.7
|
1.0
|
O
|
A:HOH2159
|
3.8
|
37.2
|
1.0
|
C9
|
A:YPN1553
|
3.9
|
23.6
|
1.0
|
CG
|
A:LEU499
|
3.9
|
25.3
|
1.0
|
O11
|
A:YPN1553
|
3.9
|
27.8
|
1.0
|
N4
|
A:YPN1554
|
4.0
|
39.2
|
1.0
|
C2
|
A:YPN1554
|
4.0
|
34.0
|
1.0
|
CD1
|
A:LEU499
|
4.0
|
24.2
|
1.0
|
CG
|
A:HIS524
|
4.1
|
19.9
|
1.0
|
CG2
|
A:VAL498
|
4.2
|
27.2
|
1.0
|
CD2
|
A:HIS524
|
4.3
|
20.6
|
1.0
|
OD1
|
A:ASP496
|
4.4
|
26.9
|
1.0
|
C3
|
A:YPN1554
|
4.4
|
39.5
|
1.0
|
CZ
|
A:TYR383
|
4.4
|
30.1
|
1.0
|
C10
|
A:YPN1553
|
4.5
|
27.3
|
1.0
|
CD2
|
A:LEU499
|
4.7
|
24.3
|
1.0
|
N
|
A:LEU499
|
4.7
|
24.3
|
1.0
|
OD2
|
A:ASP496
|
4.8
|
28.3
|
1.0
|
CA
|
A:VAL498
|
4.9
|
24.6
|
1.0
|
CG
|
A:ASP335
|
5.0
|
22.1
|
1.0
|
|
Chlorine binding site 3 out
of 3 in 5ak6
Go back to
Chlorine Binding Sites List in 5ak6
Chlorine binding site 3 out
of 3 in the Ligand Complex Structure of Soluble Epoxide Hydrolase
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Ligand Complex Structure of Soluble Epoxide Hydrolase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl1555
b:50.5
occ:1.00
|
CL7
|
A:YPN1555
|
0.0
|
50.5
|
1.0
|
C6
|
A:YPN1555
|
1.7
|
52.8
|
1.0
|
C5
|
A:YPN1555
|
2.7
|
55.4
|
1.0
|
C1
|
A:YPN1555
|
2.7
|
55.5
|
1.0
|
CD2
|
A:LEU499
|
3.5
|
24.3
|
1.0
|
CE
|
A:MET503
|
3.7
|
40.9
|
1.0
|
C2
|
A:YPN1553
|
3.7
|
26.4
|
1.0
|
C3
|
A:YPN1553
|
3.9
|
26.4
|
1.0
|
N4
|
A:YPN1555
|
3.9
|
61.0
|
1.0
|
C2
|
A:YPN1555
|
4.0
|
60.1
|
1.0
|
CD
|
A:PRO361
|
4.0
|
23.1
|
1.0
|
C1
|
A:YPN1553
|
4.0
|
28.3
|
1.0
|
CG2
|
A:THR360
|
4.2
|
17.5
|
1.0
|
CZ
|
A:PHE381
|
4.3
|
38.1
|
1.0
|
N4
|
A:YPN1553
|
4.3
|
27.7
|
1.0
|
CE2
|
A:PHE381
|
4.4
|
37.8
|
1.0
|
C3
|
A:YPN1555
|
4.4
|
64.6
|
1.0
|
C6
|
A:YPN1553
|
4.4
|
29.1
|
1.0
|
S8
|
A:YPN1553
|
4.5
|
27.6
|
1.0
|
CG
|
A:PRO361
|
4.5
|
26.1
|
1.0
|
C5
|
A:YPN1553
|
4.6
|
28.4
|
1.0
|
SD
|
A:MET503
|
4.8
|
45.1
|
1.0
|
CG
|
A:LEU499
|
5.0
|
25.3
|
1.0
|
|
Reference:
L.Oster,
S.Tapani,
Y.Xue,
H.Kack.
Successful Generation of Structural Information For Fragment-Based Drug Discovery. Drug Discov Today 2015.
ISSN: ESSN 1878-5832
PubMed: 25931264
DOI: 10.1016/J.DRUDIS.2015.04.005
Page generated: Fri Jul 26 05:17:31 2024
|