Potassium in PDB 9gkw: Crystal Structure of Dimethoate Hydrolase (Dmha) of Rhizorhabdus Wittichii in Complex with Octanoic Acid
Protein crystallography data
The structure of Crystal Structure of Dimethoate Hydrolase (Dmha) of Rhizorhabdus Wittichii in Complex with Octanoic Acid, PDB code: 9gkw
was solved by
L.G.Graf,
S.Schulze,
G.J.Palm,
M.Lammers,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.10 /
2.10
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
131.616,
144.034,
92.959,
90,
92.12,
90
|
R / Rfree (%)
|
16.9 /
22.4
|
Other elements in 9gkw:
The structure of Crystal Structure of Dimethoate Hydrolase (Dmha) of Rhizorhabdus Wittichii in Complex with Octanoic Acid also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Crystal Structure of Dimethoate Hydrolase (Dmha) of Rhizorhabdus Wittichii in Complex with Octanoic Acid
(pdb code 9gkw). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 10 binding sites of Potassium where determined in the
Crystal Structure of Dimethoate Hydrolase (Dmha) of Rhizorhabdus Wittichii in Complex with Octanoic Acid, PDB code: 9gkw:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Potassium binding site 1 out
of 10 in 9gkw
Go back to
Potassium Binding Sites List in 9gkw
Potassium binding site 1 out
of 10 in the Crystal Structure of Dimethoate Hydrolase (Dmha) of Rhizorhabdus Wittichii in Complex with Octanoic Acid
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of Crystal Structure of Dimethoate Hydrolase (Dmha) of Rhizorhabdus Wittichii in Complex with Octanoic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K402
b:20.7
occ:1.00
|
O
|
A:VAL197
|
2.6
|
23.2
|
1.0
|
O
|
A:PHE191
|
2.7
|
22.2
|
1.0
|
O
|
A:HOH589
|
2.7
|
17.0
|
1.0
|
O
|
A:ARG194
|
2.8
|
14.3
|
1.0
|
O
|
A:TYR226
|
2.9
|
16.8
|
1.0
|
O
|
A:HOH587
|
3.1
|
22.7
|
1.0
|
C
|
A:TYR226
|
3.6
|
18.7
|
1.0
|
C
|
A:PHE191
|
3.6
|
17.3
|
1.0
|
CB
|
A:TYR226
|
3.7
|
14.7
|
1.0
|
CB
|
A:PHE191
|
3.8
|
13.8
|
1.0
|
C
|
A:VAL197
|
3.9
|
18.8
|
1.0
|
OG1
|
A:THR199
|
3.9
|
20.4
|
1.0
|
C
|
A:ARG194
|
4.0
|
25.6
|
1.0
|
CA
|
A:TYR226
|
4.3
|
16.6
|
1.0
|
CA
|
A:PHE191
|
4.4
|
15.6
|
1.0
|
N
|
A:ASN227
|
4.4
|
20.0
|
1.0
|
N
|
A:THR199
|
4.4
|
20.9
|
1.0
|
N
|
A:TYR192
|
4.5
|
20.5
|
1.0
|
N
|
A:ARG194
|
4.5
|
24.7
|
1.0
|
CA
|
A:TYR192
|
4.5
|
24.6
|
1.0
|
CA
|
A:LEU198
|
4.6
|
19.0
|
1.0
|
C
|
A:TYR192
|
4.6
|
21.8
|
1.0
|
CG2
|
A:THR199
|
4.7
|
22.0
|
1.0
|
N
|
A:LEU198
|
4.7
|
18.6
|
1.0
|
O
|
A:TYR192
|
4.7
|
26.7
|
1.0
|
CA
|
A:ARG194
|
4.7
|
24.3
|
1.0
|
O
|
A:GLY223
|
4.7
|
22.9
|
1.0
|
CA
|
A:ASN227
|
4.8
|
18.2
|
1.0
|
CA
|
A:VAL197
|
4.8
|
19.0
|
1.0
|
CB
|
A:ASN227
|
4.9
|
19.9
|
1.0
|
CB
|
A:THR199
|
4.9
|
23.4
|
1.0
|
CB
|
A:ARG194
|
4.9
|
22.0
|
1.0
|
C
|
A:LEU198
|
5.0
|
17.9
|
1.0
|
CB
|
A:VAL197
|
5.0
|
23.2
|
1.0
|
CA
|
A:GLY223
|
5.0
|
24.9
|
1.0
|
N
|
A:ALA195
|
5.0
|
23.4
|
1.0
|
|
Potassium binding site 2 out
of 10 in 9gkw
Go back to
Potassium Binding Sites List in 9gkw
Potassium binding site 2 out
of 10 in the Crystal Structure of Dimethoate Hydrolase (Dmha) of Rhizorhabdus Wittichii in Complex with Octanoic Acid
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of Crystal Structure of Dimethoate Hydrolase (Dmha) of Rhizorhabdus Wittichii in Complex with Octanoic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K403
b:16.1
occ:1.00
|
O
|
A:ASP180
|
2.6
|
17.0
|
1.0
|
O
|
A:ILE202
|
2.6
|
17.6
|
1.0
|
O
|
A:HIS182
|
2.7
|
13.4
|
1.0
|
OD1
|
A:ASP178
|
2.8
|
18.0
|
1.0
|
O
|
A:ASP178
|
2.9
|
16.9
|
1.0
|
OG
|
A:SER201
|
3.0
|
18.0
|
1.0
|
CG
|
A:ASP178
|
3.2
|
17.4
|
1.0
|
C
|
A:ILE202
|
3.6
|
16.1
|
1.0
|
C
|
A:ASP180
|
3.6
|
19.9
|
1.0
|
C
|
A:ASP178
|
3.6
|
13.6
|
1.0
|
C
|
A:HIS182
|
3.7
|
19.9
|
1.0
|
OD2
|
A:ASP178
|
3.7
|
19.1
|
1.0
|
CB
|
A:ASP178
|
3.8
|
14.2
|
1.0
|
N
|
A:ILE202
|
3.8
|
11.3
|
1.0
|
CB
|
A:HIS203
|
3.9
|
11.6
|
1.0
|
N
|
A:ASP180
|
4.0
|
18.8
|
1.0
|
CB
|
A:SER201
|
4.0
|
13.3
|
1.0
|
N
|
A:GLY184
|
4.0
|
17.0
|
1.0
|
CA
|
A:SER201
|
4.2
|
20.4
|
1.0
|
CA
|
A:HIS183
|
4.2
|
18.1
|
1.0
|
CA
|
A:ASP180
|
4.2
|
20.9
|
1.0
|
C
|
A:SER201
|
4.3
|
17.4
|
1.0
|
CA
|
A:ASP178
|
4.3
|
14.8
|
1.0
|
N
|
A:HIS182
|
4.3
|
15.1
|
1.0
|
C
|
A:TRP179
|
4.3
|
19.7
|
1.0
|
N
|
A:HIS183
|
4.4
|
17.8
|
1.0
|
N
|
A:TRP179
|
4.4
|
14.7
|
1.0
|
CA
|
A:HIS203
|
4.4
|
19.8
|
1.0
|
CA
|
A:ILE202
|
4.4
|
14.6
|
1.0
|
ND1
|
A:HIS203
|
4.4
|
17.1
|
1.0
|
N
|
A:HIS203
|
4.4
|
17.2
|
1.0
|
C
|
A:HIS183
|
4.4
|
18.8
|
1.0
|
CA
|
A:TRP179
|
4.5
|
13.9
|
1.0
|
CB
|
A:ASP180
|
4.5
|
20.7
|
1.0
|
C
|
A:VAL181
|
4.6
|
16.9
|
1.0
|
CG
|
A:HIS203
|
4.6
|
18.2
|
1.0
|
O
|
A:HOH594
|
4.6
|
16.0
|
1.0
|
CE1
|
A:HIS142
|
4.6
|
17.4
|
1.0
|
CA
|
A:HIS182
|
4.6
|
18.4
|
1.0
|
N
|
A:VAL181
|
4.7
|
15.5
|
1.0
|
OD1
|
A:ASP180
|
4.8
|
22.8
|
1.0
|
ND1
|
A:HIS142
|
4.8
|
14.0
|
1.0
|
CA
|
A:GLY184
|
4.9
|
16.9
|
1.0
|
CA
|
A:VAL181
|
4.9
|
15.7
|
1.0
|
|
Potassium binding site 3 out
of 10 in 9gkw
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Potassium Binding Sites List in 9gkw
Potassium binding site 3 out
of 10 in the Crystal Structure of Dimethoate Hydrolase (Dmha) of Rhizorhabdus Wittichii in Complex with Octanoic Acid
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of Crystal Structure of Dimethoate Hydrolase (Dmha) of Rhizorhabdus Wittichii in Complex with Octanoic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K404
b:50.8
occ:1.00
|
OG1
|
A:THR187
|
2.6
|
24.5
|
1.0
|
O
|
A:HOH596
|
2.7
|
21.4
|
1.0
|
O
|
A:HOH676
|
3.0
|
17.0
|
1.0
|
CD
|
A:PRO159
|
3.1
|
13.8
|
1.0
|
CA
|
A:HIS142
|
3.1
|
16.8
|
1.0
|
N
|
A:THR187
|
3.6
|
21.8
|
1.0
|
CG
|
A:PRO159
|
3.6
|
21.4
|
1.0
|
CB
|
A:THR187
|
3.6
|
22.5
|
1.0
|
CB
|
A:HIS142
|
3.7
|
12.7
|
1.0
|
O
|
A:GLY141
|
3.8
|
16.4
|
1.0
|
CA
|
A:THR187
|
3.8
|
20.9
|
1.0
|
N
|
A:HIS142
|
3.9
|
12.3
|
1.0
|
C
|
A:HIS142
|
4.0
|
18.6
|
1.0
|
O
|
A:HIS142
|
4.0
|
18.4
|
1.0
|
CG2
|
A:THR187
|
4.0
|
23.1
|
1.0
|
C
|
A:GLY141
|
4.0
|
15.3
|
1.0
|
O
|
A:HOH510
|
4.3
|
17.7
|
1.0
|
CB
|
A:ILE158
|
4.3
|
13.1
|
1.0
|
C
|
A:GLY186
|
4.4
|
20.6
|
1.0
|
N
|
A:PRO159
|
4.4
|
22.8
|
1.0
|
N
|
A:ILE158
|
4.6
|
18.9
|
1.0
|
CA
|
A:ILE158
|
4.9
|
18.0
|
1.0
|
CA
|
A:GLY186
|
4.9
|
17.8
|
1.0
|
CB
|
A:ALA156
|
4.9
|
18.4
|
1.0
|
CA
|
A:ALA156
|
4.9
|
20.4
|
1.0
|
CG1
|
A:ILE158
|
5.0
|
16.2
|
1.0
|
C
|
A:ALA156
|
5.0
|
17.0
|
1.0
|
|
Potassium binding site 4 out
of 10 in 9gkw
Go back to
Potassium Binding Sites List in 9gkw
Potassium binding site 4 out
of 10 in the Crystal Structure of Dimethoate Hydrolase (Dmha) of Rhizorhabdus Wittichii in Complex with Octanoic Acid
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of Crystal Structure of Dimethoate Hydrolase (Dmha) of Rhizorhabdus Wittichii in Complex with Octanoic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K402
b:23.2
occ:1.00
|
O
|
B:VAL197
|
2.6
|
22.4
|
1.0
|
O
|
B:HOH648
|
2.6
|
22.9
|
1.0
|
O
|
B:HOH645
|
2.7
|
22.1
|
1.0
|
O
|
B:PHE191
|
2.8
|
25.5
|
1.0
|
O
|
B:TYR226
|
2.8
|
24.3
|
1.0
|
O
|
B:ARG194
|
3.0
|
29.9
|
1.0
|
C
|
B:TYR226
|
3.6
|
24.4
|
1.0
|
C
|
B:PHE191
|
3.7
|
20.8
|
1.0
|
CB
|
B:TYR226
|
3.7
|
27.4
|
1.0
|
CB
|
B:PHE191
|
3.8
|
21.3
|
1.0
|
OG1
|
B:THR199
|
3.8
|
21.4
|
1.0
|
C
|
B:VAL197
|
3.8
|
27.7
|
1.0
|
C
|
B:ARG194
|
4.2
|
28.5
|
1.0
|
CA
|
B:TYR226
|
4.3
|
27.7
|
1.0
|
N
|
B:THR199
|
4.3
|
16.7
|
1.0
|
CA
|
B:PHE191
|
4.4
|
26.5
|
1.0
|
N
|
B:ASN227
|
4.4
|
19.3
|
1.0
|
N
|
B:TYR192
|
4.5
|
25.5
|
1.0
|
CA
|
B:LEU198
|
4.5
|
26.2
|
1.0
|
CA
|
B:TYR192
|
4.5
|
24.8
|
1.0
|
CG2
|
B:THR199
|
4.6
|
21.1
|
1.0
|
N
|
B:LEU198
|
4.6
|
28.8
|
1.0
|
O
|
B:TYR192
|
4.6
|
23.8
|
1.0
|
C
|
B:TYR192
|
4.6
|
28.3
|
1.0
|
N
|
B:ARG194
|
4.6
|
24.1
|
1.0
|
CB
|
B:THR199
|
4.7
|
19.9
|
1.0
|
CB
|
B:ASN227
|
4.7
|
23.3
|
1.0
|
CA
|
B:ASN227
|
4.8
|
20.1
|
1.0
|
O
|
B:GLY223
|
4.8
|
28.4
|
1.0
|
C
|
B:LEU198
|
4.8
|
24.1
|
1.0
|
CA
|
B:VAL197
|
4.9
|
26.2
|
1.0
|
CA
|
B:ARG194
|
4.9
|
33.9
|
1.0
|
CB
|
B:VAL197
|
5.0
|
27.8
|
1.0
|
|
Potassium binding site 5 out
of 10 in 9gkw
Go back to
Potassium Binding Sites List in 9gkw
Potassium binding site 5 out
of 10 in the Crystal Structure of Dimethoate Hydrolase (Dmha) of Rhizorhabdus Wittichii in Complex with Octanoic Acid
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 5 of Crystal Structure of Dimethoate Hydrolase (Dmha) of Rhizorhabdus Wittichii in Complex with Octanoic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K403
b:20.6
occ:1.00
|
O
|
B:ASP180
|
2.5
|
19.4
|
1.0
|
O
|
B:HIS182
|
2.6
|
20.3
|
1.0
|
OD1
|
B:ASP178
|
2.7
|
19.4
|
1.0
|
O
|
B:ASP178
|
2.8
|
18.4
|
1.0
|
O
|
B:ILE202
|
2.8
|
16.0
|
1.0
|
OG
|
B:SER201
|
3.0
|
17.2
|
1.0
|
CG
|
B:ASP178
|
3.1
|
14.9
|
1.0
|
C
|
B:ASP178
|
3.5
|
19.4
|
1.0
|
C
|
B:ASP180
|
3.6
|
23.2
|
1.0
|
C
|
B:ILE202
|
3.6
|
21.6
|
1.0
|
OD2
|
B:ASP178
|
3.7
|
20.5
|
1.0
|
C
|
B:HIS182
|
3.7
|
19.8
|
1.0
|
CB
|
B:ASP178
|
3.8
|
17.6
|
1.0
|
N
|
B:ILE202
|
3.8
|
22.0
|
1.0
|
N
|
B:ASP180
|
4.0
|
18.1
|
1.0
|
CB
|
B:HIS203
|
4.0
|
16.9
|
1.0
|
CB
|
B:SER201
|
4.1
|
17.7
|
1.0
|
N
|
B:GLY184
|
4.1
|
22.5
|
1.0
|
CA
|
B:SER201
|
4.2
|
21.8
|
1.0
|
CA
|
B:ASP180
|
4.2
|
18.4
|
1.0
|
N
|
B:TRP179
|
4.2
|
23.1
|
1.0
|
C
|
B:TRP179
|
4.3
|
21.8
|
1.0
|
CA
|
B:ASP178
|
4.3
|
21.9
|
1.0
|
C
|
B:SER201
|
4.3
|
22.6
|
1.0
|
CA
|
B:TRP179
|
4.3
|
20.5
|
1.0
|
CA
|
B:HIS183
|
4.4
|
20.0
|
1.0
|
CB
|
B:ASP180
|
4.4
|
18.6
|
1.0
|
CA
|
B:ILE202
|
4.4
|
20.9
|
1.0
|
N
|
B:HIS182
|
4.4
|
17.7
|
1.0
|
CA
|
B:HIS203
|
4.4
|
20.6
|
1.0
|
N
|
B:HIS183
|
4.4
|
16.4
|
1.0
|
N
|
B:HIS203
|
4.5
|
16.0
|
1.0
|
ND1
|
B:HIS203
|
4.5
|
19.3
|
1.0
|
C
|
B:HIS183
|
4.6
|
22.1
|
1.0
|
O
|
B:HOH560
|
4.6
|
13.2
|
1.0
|
CE1
|
B:HIS142
|
4.6
|
19.0
|
1.0
|
N
|
B:VAL181
|
4.7
|
19.6
|
1.0
|
CA
|
B:HIS182
|
4.7
|
18.8
|
1.0
|
C
|
B:VAL181
|
4.7
|
19.9
|
1.0
|
CG
|
B:HIS203
|
4.7
|
18.7
|
1.0
|
ND1
|
B:HIS142
|
4.8
|
26.0
|
1.0
|
OD1
|
B:ASP180
|
4.9
|
23.7
|
1.0
|
CA
|
B:VAL181
|
5.0
|
20.4
|
1.0
|
O
|
B:TRP179
|
5.0
|
20.1
|
1.0
|
|
Potassium binding site 6 out
of 10 in 9gkw
Go back to
Potassium Binding Sites List in 9gkw
Potassium binding site 6 out
of 10 in the Crystal Structure of Dimethoate Hydrolase (Dmha) of Rhizorhabdus Wittichii in Complex with Octanoic Acid
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 6 of Crystal Structure of Dimethoate Hydrolase (Dmha) of Rhizorhabdus Wittichii in Complex with Octanoic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K404
b:50.1
occ:1.00
|
OG1
|
B:THR187
|
2.7
|
27.0
|
1.0
|
CD
|
B:PRO159
|
2.9
|
22.5
|
1.0
|
O
|
B:HOH525
|
3.0
|
22.9
|
1.0
|
O
|
B:HOH604
|
3.1
|
19.0
|
1.0
|
CG2
|
B:THR187
|
3.4
|
16.8
|
1.0
|
CB
|
B:THR187
|
3.4
|
17.3
|
1.0
|
CA
|
B:HIS142
|
3.4
|
18.7
|
1.0
|
CG
|
B:PRO159
|
3.5
|
20.0
|
1.0
|
N
|
B:THR187
|
3.7
|
20.0
|
1.0
|
CA
|
B:THR187
|
3.8
|
16.5
|
1.0
|
CB
|
B:ILE158
|
3.8
|
19.5
|
1.0
|
CB
|
B:HIS142
|
3.9
|
20.2
|
1.0
|
O
|
B:GLY141
|
4.0
|
17.0
|
1.0
|
N
|
B:HIS142
|
4.2
|
20.1
|
1.0
|
N
|
B:PRO159
|
4.2
|
17.5
|
1.0
|
C
|
B:GLY141
|
4.3
|
21.3
|
1.0
|
O
|
B:HIS142
|
4.3
|
20.2
|
1.0
|
O
|
B:HOH523
|
4.3
|
21.1
|
1.0
|
N
|
B:ILE158
|
4.3
|
17.0
|
1.0
|
C
|
B:HIS142
|
4.3
|
20.1
|
1.0
|
CG2
|
B:ILE158
|
4.5
|
19.1
|
1.0
|
CA
|
B:ILE158
|
4.5
|
17.9
|
1.0
|
C
|
B:GLY186
|
4.6
|
22.1
|
1.0
|
CG1
|
B:ILE158
|
4.7
|
17.1
|
1.0
|
C
|
B:ILE158
|
4.8
|
20.5
|
1.0
|
CD1
|
B:ILE158
|
4.8
|
15.6
|
1.0
|
OE2
|
B:GLU309
|
4.9
|
20.8
|
1.0
|
CB
|
B:PRO159
|
4.9
|
22.1
|
1.0
|
|
Potassium binding site 7 out
of 10 in 9gkw
Go back to
Potassium Binding Sites List in 9gkw
Potassium binding site 7 out
of 10 in the Crystal Structure of Dimethoate Hydrolase (Dmha) of Rhizorhabdus Wittichii in Complex with Octanoic Acid
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 7 of Crystal Structure of Dimethoate Hydrolase (Dmha) of Rhizorhabdus Wittichii in Complex with Octanoic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K403
b:23.2
occ:1.00
|
O
|
C:PHE191
|
2.6
|
21.8
|
1.0
|
O
|
C:VAL197
|
2.6
|
22.2
|
1.0
|
O
|
C:ARG194
|
2.8
|
25.1
|
1.0
|
O
|
C:HOH1152
|
2.9
|
23.6
|
1.0
|
O
|
C:TYR226
|
2.9
|
21.4
|
1.0
|
O
|
C:HOH1223
|
3.0
|
15.5
|
1.0
|
C
|
C:PHE191
|
3.6
|
22.1
|
1.0
|
C
|
C:TYR226
|
3.7
|
24.7
|
1.0
|
CB
|
C:PHE191
|
3.8
|
21.1
|
1.0
|
CB
|
C:TYR226
|
3.8
|
23.4
|
1.0
|
C
|
C:VAL197
|
3.8
|
21.2
|
1.0
|
C
|
C:ARG194
|
4.0
|
28.0
|
1.0
|
OG1
|
C:THR199
|
4.0
|
26.8
|
1.0
|
CG2
|
C:THR199
|
4.2
|
25.6
|
1.0
|
CA
|
C:PHE191
|
4.3
|
22.3
|
1.0
|
N
|
C:ARG194
|
4.4
|
23.0
|
1.0
|
CA
|
C:TYR226
|
4.4
|
23.8
|
1.0
|
N
|
C:THR199
|
4.4
|
23.1
|
1.0
|
N
|
C:TYR192
|
4.5
|
20.4
|
1.0
|
CA
|
C:TYR192
|
4.5
|
24.0
|
1.0
|
N
|
C:ASN227
|
4.5
|
20.6
|
1.0
|
C
|
C:TYR192
|
4.6
|
28.9
|
1.0
|
O
|
C:TYR192
|
4.6
|
26.4
|
1.0
|
CA
|
C:ARG194
|
4.6
|
26.2
|
1.0
|
CA
|
C:LEU198
|
4.6
|
20.4
|
1.0
|
N
|
C:LEU198
|
4.7
|
17.8
|
1.0
|
CB
|
C:THR199
|
4.7
|
22.7
|
1.0
|
CA
|
C:VAL197
|
4.8
|
16.2
|
1.0
|
O
|
C:GLY223
|
4.8
|
22.2
|
1.0
|
CB
|
C:ARG194
|
4.9
|
26.4
|
1.0
|
CB
|
C:ASN227
|
4.9
|
18.9
|
1.0
|
CA
|
C:ASN227
|
4.9
|
21.7
|
1.0
|
CB
|
C:VAL197
|
4.9
|
14.8
|
1.0
|
N
|
C:VAL197
|
5.0
|
19.1
|
1.0
|
C
|
C:LEU198
|
5.0
|
25.4
|
1.0
|
|
Potassium binding site 8 out
of 10 in 9gkw
Go back to
Potassium Binding Sites List in 9gkw
Potassium binding site 8 out
of 10 in the Crystal Structure of Dimethoate Hydrolase (Dmha) of Rhizorhabdus Wittichii in Complex with Octanoic Acid
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 8 of Crystal Structure of Dimethoate Hydrolase (Dmha) of Rhizorhabdus Wittichii in Complex with Octanoic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K404
b:19.3
occ:1.00
|
O
|
C:ASP180
|
2.5
|
18.5
|
1.0
|
OD1
|
C:ASP178
|
2.6
|
13.0
|
1.0
|
O
|
C:HIS182
|
2.7
|
18.7
|
1.0
|
O
|
C:ILE202
|
2.7
|
20.4
|
1.0
|
O
|
C:ASP178
|
2.8
|
17.9
|
1.0
|
OG
|
C:SER201
|
2.8
|
13.5
|
1.0
|
CG
|
C:ASP178
|
3.1
|
16.6
|
1.0
|
C
|
C:ASP178
|
3.5
|
19.2
|
1.0
|
C
|
C:ASP180
|
3.6
|
19.8
|
1.0
|
C
|
C:ILE202
|
3.6
|
13.3
|
1.0
|
C
|
C:HIS182
|
3.7
|
18.3
|
1.0
|
CB
|
C:ASP178
|
3.7
|
17.2
|
1.0
|
OD2
|
C:ASP178
|
3.7
|
14.9
|
1.0
|
N
|
C:ILE202
|
3.8
|
17.0
|
1.0
|
N
|
C:ASP180
|
3.9
|
18.2
|
1.0
|
CB
|
C:SER201
|
3.9
|
15.9
|
1.0
|
CB
|
C:HIS203
|
4.0
|
13.3
|
1.0
|
N
|
C:GLY184
|
4.0
|
16.4
|
1.0
|
CA
|
C:SER201
|
4.1
|
21.1
|
1.0
|
N
|
C:TRP179
|
4.2
|
17.6
|
1.0
|
CA
|
C:ASP180
|
4.2
|
20.2
|
1.0
|
CA
|
C:ASP178
|
4.2
|
16.6
|
1.0
|
CA
|
C:HIS183
|
4.3
|
16.3
|
1.0
|
C
|
C:TRP179
|
4.3
|
20.2
|
1.0
|
C
|
C:SER201
|
4.3
|
19.7
|
1.0
|
CA
|
C:TRP179
|
4.3
|
16.9
|
1.0
|
CB
|
C:ASP180
|
4.3
|
15.9
|
1.0
|
N
|
C:HIS182
|
4.4
|
17.1
|
1.0
|
CA
|
C:ILE202
|
4.4
|
16.9
|
1.0
|
N
|
C:HIS183
|
4.4
|
14.8
|
1.0
|
O
|
C:HOH1153
|
4.4
|
19.0
|
1.0
|
C
|
C:HIS183
|
4.4
|
17.2
|
1.0
|
CA
|
C:HIS203
|
4.4
|
16.8
|
1.0
|
N
|
C:HIS203
|
4.5
|
18.3
|
1.0
|
ND1
|
C:HIS203
|
4.5
|
19.5
|
1.0
|
CE1
|
C:HIS142
|
4.6
|
18.2
|
1.0
|
CA
|
C:HIS182
|
4.7
|
20.6
|
1.0
|
C
|
C:VAL181
|
4.7
|
22.3
|
1.0
|
CG
|
C:HIS203
|
4.7
|
23.2
|
1.0
|
N
|
C:VAL181
|
4.7
|
18.3
|
1.0
|
ND1
|
C:HIS142
|
4.7
|
17.5
|
1.0
|
OD1
|
C:ASP180
|
4.9
|
18.6
|
1.0
|
CA
|
C:GLY184
|
5.0
|
12.7
|
1.0
|
|
Potassium binding site 9 out
of 10 in 9gkw
Go back to
Potassium Binding Sites List in 9gkw
Potassium binding site 9 out
of 10 in the Crystal Structure of Dimethoate Hydrolase (Dmha) of Rhizorhabdus Wittichii in Complex with Octanoic Acid
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 9 of Crystal Structure of Dimethoate Hydrolase (Dmha) of Rhizorhabdus Wittichii in Complex with Octanoic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K404
b:20.2
occ:1.00
|
O
|
D:HOH643
|
2.5
|
17.2
|
1.0
|
O
|
D:VAL197
|
2.7
|
17.6
|
1.0
|
O
|
D:PHE191
|
2.7
|
17.9
|
1.0
|
O
|
D:ARG194
|
2.9
|
21.1
|
1.0
|
O
|
D:TYR226
|
2.9
|
22.1
|
1.0
|
O
|
D:HOH633
|
2.9
|
17.2
|
1.0
|
C
|
D:PHE191
|
3.6
|
23.4
|
1.0
|
C
|
D:TYR226
|
3.6
|
19.8
|
1.0
|
CB
|
D:TYR226
|
3.7
|
22.6
|
1.0
|
OG1
|
D:THR199
|
3.9
|
17.6
|
1.0
|
CB
|
D:PHE191
|
3.9
|
14.1
|
1.0
|
C
|
D:VAL197
|
4.0
|
16.9
|
1.0
|
C
|
D:ARG194
|
4.1
|
21.5
|
1.0
|
CA
|
D:TYR226
|
4.3
|
23.0
|
1.0
|
CA
|
D:TYR192
|
4.4
|
19.5
|
1.0
|
CA
|
D:PHE191
|
4.4
|
20.1
|
1.0
|
N
|
D:ASN227
|
4.4
|
20.4
|
1.0
|
N
|
D:TYR192
|
4.4
|
20.5
|
1.0
|
N
|
D:ARG194
|
4.4
|
21.9
|
1.0
|
O
|
D:TYR192
|
4.5
|
23.2
|
1.0
|
C
|
D:TYR192
|
4.5
|
25.3
|
1.0
|
N
|
D:THR199
|
4.5
|
21.2
|
1.0
|
CG2
|
D:THR199
|
4.7
|
19.3
|
1.0
|
O
|
D:GLY223
|
4.7
|
24.3
|
1.0
|
CA
|
D:ARG194
|
4.7
|
28.5
|
1.0
|
CB
|
D:ASN227
|
4.7
|
15.5
|
1.0
|
CA
|
D:LEU198
|
4.8
|
17.7
|
1.0
|
CA
|
D:ASN227
|
4.8
|
22.9
|
1.0
|
CB
|
D:THR199
|
4.8
|
17.8
|
1.0
|
N
|
D:LEU198
|
4.8
|
26.7
|
1.0
|
CA
|
D:VAL197
|
4.9
|
24.9
|
1.0
|
CB
|
D:ARG194
|
4.9
|
22.4
|
1.0
|
|
Potassium binding site 10 out
of 10 in 9gkw
Go back to
Potassium Binding Sites List in 9gkw
Potassium binding site 10 out
of 10 in the Crystal Structure of Dimethoate Hydrolase (Dmha) of Rhizorhabdus Wittichii in Complex with Octanoic Acid
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 10 of Crystal Structure of Dimethoate Hydrolase (Dmha) of Rhizorhabdus Wittichii in Complex with Octanoic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K405
b:17.1
occ:1.00
|
O
|
D:ASP180
|
2.5
|
18.6
|
1.0
|
O
|
D:HIS182
|
2.6
|
16.1
|
1.0
|
OD1
|
D:ASP178
|
2.7
|
18.5
|
1.0
|
O
|
D:ILE202
|
2.8
|
20.2
|
1.0
|
OG
|
D:SER201
|
2.9
|
19.6
|
1.0
|
O
|
D:ASP178
|
2.9
|
17.6
|
1.0
|
CG
|
D:ASP178
|
3.1
|
21.0
|
1.0
|
C
|
D:ASP178
|
3.6
|
15.4
|
1.0
|
C
|
D:ASP180
|
3.6
|
22.5
|
1.0
|
OD2
|
D:ASP178
|
3.7
|
19.9
|
1.0
|
C
|
D:HIS182
|
3.7
|
19.7
|
1.0
|
C
|
D:ILE202
|
3.7
|
24.0
|
1.0
|
N
|
D:ILE202
|
3.8
|
16.1
|
1.0
|
CB
|
D:ASP178
|
3.8
|
16.4
|
1.0
|
CB
|
D:HIS203
|
4.0
|
14.2
|
1.0
|
CB
|
D:SER201
|
4.0
|
22.8
|
1.0
|
N
|
D:GLY184
|
4.1
|
16.3
|
1.0
|
N
|
D:ASP180
|
4.1
|
18.1
|
1.0
|
CA
|
D:SER201
|
4.2
|
20.4
|
1.0
|
CA
|
D:HIS183
|
4.3
|
18.3
|
1.0
|
CA
|
D:ASP180
|
4.3
|
20.2
|
1.0
|
N
|
D:HIS182
|
4.3
|
17.6
|
1.0
|
N
|
D:TRP179
|
4.3
|
16.5
|
1.0
|
CA
|
D:ASP178
|
4.3
|
18.2
|
1.0
|
C
|
D:SER201
|
4.3
|
24.2
|
1.0
|
C
|
D:TRP179
|
4.4
|
18.3
|
1.0
|
N
|
D:HIS183
|
4.4
|
16.4
|
1.0
|
ND1
|
D:HIS203
|
4.4
|
17.5
|
1.0
|
CB
|
D:ASP180
|
4.4
|
16.1
|
1.0
|
CA
|
D:TRP179
|
4.4
|
17.5
|
1.0
|
CA
|
D:ILE202
|
4.4
|
19.1
|
1.0
|
CA
|
D:HIS203
|
4.5
|
18.2
|
1.0
|
C
|
D:HIS183
|
4.5
|
15.5
|
1.0
|
N
|
D:HIS203
|
4.5
|
18.9
|
1.0
|
CE1
|
D:HIS142
|
4.5
|
17.4
|
1.0
|
C
|
D:VAL181
|
4.6
|
18.0
|
1.0
|
CG
|
D:HIS203
|
4.7
|
21.9
|
1.0
|
CA
|
D:HIS182
|
4.7
|
17.9
|
1.0
|
ND1
|
D:HIS142
|
4.7
|
18.7
|
1.0
|
N
|
D:VAL181
|
4.7
|
17.9
|
1.0
|
O
|
D:HOH605
|
4.7
|
13.3
|
1.0
|
CA
|
D:GLY184
|
4.9
|
17.6
|
1.0
|
CA
|
D:VAL181
|
5.0
|
15.9
|
1.0
|
OD1
|
D:ASP180
|
5.0
|
16.7
|
1.0
|
|
Reference:
L.G.Graf,
C.Moreno-Yruela,
C.Qin,
S.Schulze,
G.J.Palm,
O.Schmoeker,
N.Wang,
D.Hocking,
L.Jebeli,
B.Girbardt,
L.Berndt,
D.M.Weis,
M.Janetzky,
D.Zuehlke,
S.Sievers,
R.A.Strugnell,
C.A.Olsen,
K.Hofmann,
M.Lammers.
Distribution and Diversity of Classical Deacylases in Bacteria Nature Communications 2024.
Page generated: Wed Nov 13 11:17:29 2024
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