Zinc 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:
Zinc Binding Sites:
The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the
Crystal Structure of Dimethoate Hydrolase (Dmha) of Rhizorhabdus Wittichii in Complex with Octanoic Acid, PDB code: 9gkw:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 9gkw
Go back to
Zinc Binding Sites List in 9gkw
Zinc binding site 1 out
of 4 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 Zinc with other atoms in the Zn 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:Zn405
b:19.5
occ:0.34
|
OD2
|
A:ASP268
|
2.0
|
16.5
|
1.0
|
O1
|
A:OCA401
|
2.1
|
17.4
|
0.9
|
O2
|
A:OCA401
|
2.1
|
20.1
|
0.9
|
C1
|
A:OCA401
|
2.2
|
28.8
|
0.9
|
ND1
|
A:HIS182
|
2.3
|
15.1
|
1.0
|
OD2
|
A:ASP180
|
2.3
|
13.4
|
1.0
|
OD1
|
A:ASP180
|
2.3
|
22.8
|
1.0
|
CG
|
A:ASP180
|
2.6
|
17.0
|
1.0
|
CE1
|
A:HIS182
|
3.1
|
18.9
|
1.0
|
CG
|
A:ASP268
|
3.1
|
20.9
|
1.0
|
CG
|
A:HIS182
|
3.3
|
17.2
|
1.0
|
C2
|
A:OCA401
|
3.5
|
27.0
|
0.9
|
OD1
|
A:ASP268
|
3.6
|
16.4
|
1.0
|
CB
|
A:HIS182
|
3.7
|
14.9
|
1.0
|
N
|
A:HIS182
|
4.0
|
15.1
|
1.0
|
NE2
|
A:HIS142
|
4.1
|
19.4
|
1.0
|
CB
|
A:ASP180
|
4.1
|
20.7
|
1.0
|
CA
|
A:GLY310
|
4.2
|
16.2
|
1.0
|
NE2
|
A:HIS182
|
4.3
|
16.5
|
1.0
|
N
|
A:VAL181
|
4.3
|
15.5
|
1.0
|
C3
|
A:OCA401
|
4.3
|
31.3
|
0.9
|
CE2
|
A:TYR312
|
4.3
|
15.7
|
1.0
|
CB
|
A:ASP268
|
4.4
|
17.1
|
1.0
|
OH
|
A:TYR312
|
4.4
|
23.7
|
1.0
|
CD2
|
A:HIS182
|
4.4
|
17.2
|
1.0
|
CG1
|
A:VAL181
|
4.4
|
13.1
|
1.0
|
N
|
A:GLY310
|
4.5
|
15.3
|
1.0
|
NE2
|
A:HIS143
|
4.5
|
20.1
|
1.0
|
CA
|
A:HIS182
|
4.5
|
18.4
|
1.0
|
CE1
|
A:HIS142
|
4.5
|
17.4
|
1.0
|
C
|
A:ASP180
|
4.8
|
19.9
|
1.0
|
CZ
|
A:TYR312
|
4.9
|
19.0
|
1.0
|
CA
|
A:ASP180
|
4.9
|
20.9
|
1.0
|
C
|
A:GLY310
|
4.9
|
20.9
|
1.0
|
C
|
A:VAL181
|
4.9
|
16.9
|
1.0
|
|
Zinc binding site 2 out
of 4 in 9gkw
Go back to
Zinc Binding Sites List in 9gkw
Zinc binding site 2 out
of 4 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 Zinc with other atoms in the Zn 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
|
B:Zn405
b:17.9
occ:0.37
|
OD1
|
B:ASP180
|
2.0
|
23.7
|
1.0
|
OD2
|
B:ASP268
|
2.0
|
24.2
|
1.0
|
O1
|
B:OCA401
|
2.1
|
29.9
|
1.0
|
ND1
|
B:HIS182
|
2.2
|
17.4
|
1.0
|
C1
|
B:OCA401
|
2.3
|
33.3
|
1.0
|
O2
|
B:OCA401
|
2.3
|
29.6
|
1.0
|
OD2
|
B:ASP180
|
2.4
|
13.5
|
1.0
|
CG
|
B:ASP180
|
2.5
|
21.4
|
1.0
|
CG
|
B:ASP268
|
3.0
|
22.1
|
1.0
|
CE1
|
B:HIS182
|
3.1
|
20.1
|
1.0
|
CG
|
B:HIS182
|
3.3
|
21.7
|
1.0
|
OD1
|
B:ASP268
|
3.4
|
19.2
|
1.0
|
C2
|
B:OCA401
|
3.6
|
28.9
|
1.0
|
CB
|
B:HIS182
|
3.7
|
16.6
|
1.0
|
N
|
B:HIS182
|
3.8
|
17.7
|
1.0
|
NE2
|
B:HIS142
|
4.0
|
23.6
|
1.0
|
C3
|
B:OCA401
|
4.0
|
28.6
|
1.0
|
CB
|
B:ASP180
|
4.0
|
18.6
|
1.0
|
N
|
B:VAL181
|
4.1
|
19.6
|
1.0
|
CA
|
B:GLY310
|
4.1
|
24.5
|
1.0
|
CG1
|
B:VAL181
|
4.2
|
19.5
|
1.0
|
NE2
|
B:HIS182
|
4.3
|
17.0
|
1.0
|
CB
|
B:ASP268
|
4.4
|
14.5
|
1.0
|
OH
|
B:TYR312
|
4.4
|
24.9
|
1.0
|
CA
|
B:HIS182
|
4.4
|
18.8
|
1.0
|
CE1
|
B:HIS142
|
4.4
|
19.0
|
1.0
|
CD2
|
B:HIS182
|
4.4
|
16.0
|
1.0
|
CE2
|
B:TYR312
|
4.4
|
17.8
|
1.0
|
N
|
B:GLY310
|
4.5
|
22.8
|
1.0
|
NE2
|
B:HIS143
|
4.6
|
21.0
|
1.0
|
C
|
B:ASP180
|
4.6
|
23.2
|
1.0
|
C
|
B:VAL181
|
4.7
|
19.9
|
1.0
|
CA
|
B:ASP180
|
4.7
|
18.4
|
1.0
|
CA
|
B:VAL181
|
4.8
|
20.4
|
1.0
|
CZ
|
B:TYR312
|
4.9
|
26.7
|
1.0
|
C
|
B:GLY310
|
5.0
|
24.9
|
1.0
|
|
Zinc binding site 3 out
of 4 in 9gkw
Go back to
Zinc Binding Sites List in 9gkw
Zinc binding site 3 out
of 4 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 Zinc with other atoms in the Zn 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
|
C:Zn405
b:22.1
occ:0.43
|
OD1
|
C:ASP180
|
2.0
|
18.6
|
1.0
|
OD2
|
C:ASP268
|
2.0
|
20.1
|
1.0
|
C1
|
C:OCA401
|
2.2
|
37.5
|
0.9
|
O2
|
C:OCA401
|
2.2
|
29.5
|
0.9
|
O1
|
C:OCA401
|
2.3
|
30.9
|
0.9
|
ND1
|
C:HIS182
|
2.3
|
21.3
|
1.0
|
OD2
|
C:ASP180
|
2.4
|
17.6
|
1.0
|
CG
|
C:ASP180
|
2.5
|
18.3
|
1.0
|
CG
|
C:ASP268
|
3.1
|
19.8
|
1.0
|
CE1
|
C:HIS182
|
3.2
|
20.1
|
1.0
|
C2
|
C:OCA401
|
3.3
|
23.1
|
0.9
|
CG
|
C:HIS182
|
3.3
|
20.4
|
1.0
|
OD1
|
C:ASP268
|
3.5
|
19.8
|
1.0
|
CB
|
C:HIS182
|
3.7
|
15.5
|
1.0
|
N
|
C:HIS182
|
3.9
|
17.1
|
1.0
|
NE2
|
C:HIS142
|
4.0
|
17.8
|
1.0
|
CB
|
C:ASP180
|
4.0
|
15.9
|
1.0
|
CA
|
C:GLY310
|
4.1
|
18.6
|
1.0
|
N
|
C:VAL181
|
4.2
|
18.3
|
1.0
|
CG1
|
C:VAL181
|
4.2
|
16.8
|
1.0
|
NE2
|
C:HIS182
|
4.3
|
17.0
|
1.0
|
CB
|
C:ASP268
|
4.4
|
18.7
|
1.0
|
CE1
|
C:HIS142
|
4.4
|
18.2
|
1.0
|
CE2
|
C:TYR312
|
4.4
|
21.9
|
1.0
|
CA
|
C:HIS182
|
4.4
|
20.6
|
1.0
|
OH
|
C:TYR312
|
4.4
|
26.8
|
1.0
|
CD2
|
C:HIS182
|
4.4
|
20.3
|
1.0
|
N
|
C:GLY310
|
4.5
|
20.3
|
1.0
|
NE2
|
C:HIS143
|
4.6
|
24.2
|
1.0
|
C
|
C:ASP180
|
4.7
|
19.8
|
1.0
|
C3
|
C:OCA401
|
4.7
|
30.0
|
0.9
|
CA
|
C:ASP180
|
4.8
|
20.2
|
1.0
|
C
|
C:VAL181
|
4.8
|
22.3
|
1.0
|
C
|
C:GLY310
|
4.9
|
21.2
|
1.0
|
CZ
|
C:TYR312
|
4.9
|
21.3
|
1.0
|
CA
|
C:VAL181
|
4.9
|
19.4
|
1.0
|
|
Zinc binding site 4 out
of 4 in 9gkw
Go back to
Zinc Binding Sites List in 9gkw
Zinc binding site 4 out
of 4 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 Zinc with other atoms in the Zn 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
|
D:Zn406
b:22.1
occ:0.41
|
OD1
|
D:ASP180
|
2.0
|
16.7
|
1.0
|
OD2
|
D:ASP268
|
2.0
|
13.9
|
1.0
|
ND1
|
D:HIS182
|
2.3
|
24.1
|
1.0
|
C1
|
D:OCA403
|
2.4
|
35.8
|
0.9
|
O1
|
D:OCA403
|
2.4
|
25.5
|
0.9
|
O2
|
D:OCA403
|
2.5
|
33.4
|
0.9
|
OD2
|
D:ASP180
|
2.6
|
23.5
|
1.0
|
CG
|
D:ASP180
|
2.6
|
16.9
|
1.0
|
CG
|
D:ASP268
|
3.1
|
18.1
|
1.0
|
CE1
|
D:HIS182
|
3.2
|
25.7
|
1.0
|
CG
|
D:HIS182
|
3.3
|
21.3
|
1.0
|
C2
|
D:OCA403
|
3.4
|
27.9
|
0.9
|
OD1
|
D:ASP268
|
3.4
|
18.3
|
1.0
|
CB
|
D:HIS182
|
3.6
|
15.7
|
1.0
|
N
|
D:HIS182
|
3.9
|
17.6
|
1.0
|
NE2
|
D:HIS142
|
4.0
|
19.5
|
1.0
|
CB
|
D:ASP180
|
4.1
|
16.1
|
1.0
|
N
|
D:VAL181
|
4.1
|
17.9
|
1.0
|
CA
|
D:GLY310
|
4.1
|
17.7
|
1.0
|
CG1
|
D:VAL181
|
4.2
|
10.7
|
1.0
|
CE2
|
D:TYR312
|
4.3
|
17.7
|
1.0
|
NE2
|
D:HIS182
|
4.3
|
22.3
|
1.0
|
CB
|
D:ASP268
|
4.4
|
14.4
|
1.0
|
CA
|
D:HIS182
|
4.4
|
17.9
|
1.0
|
CD2
|
D:HIS182
|
4.4
|
20.6
|
1.0
|
CE1
|
D:HIS142
|
4.4
|
17.4
|
1.0
|
N
|
D:GLY310
|
4.5
|
16.2
|
1.0
|
NE2
|
D:HIS143
|
4.5
|
20.7
|
1.0
|
OH
|
D:TYR312
|
4.6
|
19.8
|
1.0
|
C
|
D:ASP180
|
4.6
|
22.5
|
1.0
|
C3
|
D:OCA403
|
4.7
|
27.6
|
0.9
|
CA
|
D:ASP180
|
4.8
|
20.2
|
1.0
|
C
|
D:VAL181
|
4.8
|
18.0
|
1.0
|
CA
|
D:VAL181
|
4.9
|
15.9
|
1.0
|
C
|
D:GLY310
|
4.9
|
18.1
|
1.0
|
CZ
|
D:TYR312
|
5.0
|
26.1
|
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 13:59:30 2024
|