Zinc in PDB 9gkx: Crystal Structure of Rhizorhabdus Wittichii Dimethoate Hydrolase (Dmha) in Complex with Saha
Protein crystallography data
The structure of Crystal Structure of Rhizorhabdus Wittichii Dimethoate Hydrolase (Dmha) in Complex with Saha, PDB code: 9gkx
was solved by
L.G.Graf,
M.Lammers,
S.Schulze,
G.J.Palm,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.31 /
1.75
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
132.12,
144.96,
92.66,
90,
91.81,
90
|
R / Rfree (%)
|
16.3 /
19
|
Other elements in 9gkx:
The structure of Crystal Structure of Rhizorhabdus Wittichii Dimethoate Hydrolase (Dmha) in Complex with Saha also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Rhizorhabdus Wittichii Dimethoate Hydrolase (Dmha) in Complex with Saha
(pdb code 9gkx). 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 Rhizorhabdus Wittichii Dimethoate Hydrolase (Dmha) in Complex with Saha, PDB code: 9gkx:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 9gkx
Go back to
Zinc Binding Sites List in 9gkx
Zinc binding site 1 out
of 4 in the Crystal Structure of Rhizorhabdus Wittichii Dimethoate Hydrolase (Dmha) in Complex with Saha
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 Rhizorhabdus Wittichii Dimethoate Hydrolase (Dmha) in Complex with Saha within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:18.7
occ:0.50
|
O1
|
A:SHH401
|
2.0
|
22.7
|
0.5
|
OD1
|
A:ASP180
|
2.2
|
13.7
|
1.0
|
OD2
|
A:ASP268
|
2.2
|
14.4
|
1.0
|
ND1
|
A:HIS182
|
2.3
|
14.8
|
1.0
|
O2
|
A:SHH401
|
2.5
|
11.7
|
0.5
|
OD2
|
A:ASP180
|
2.5
|
13.6
|
1.0
|
N1
|
A:SHH401
|
2.6
|
14.6
|
0.5
|
CG
|
A:ASP180
|
2.7
|
14.7
|
1.0
|
C1
|
A:SHH401
|
2.7
|
15.9
|
0.5
|
CG
|
A:ASP268
|
3.2
|
17.0
|
1.0
|
CE1
|
A:HIS182
|
3.2
|
17.1
|
1.0
|
CG
|
A:HIS182
|
3.3
|
14.8
|
1.0
|
OD1
|
A:ASP268
|
3.5
|
12.8
|
1.0
|
CB
|
A:HIS182
|
3.7
|
12.6
|
1.0
|
N
|
A:HIS182
|
4.0
|
12.1
|
1.0
|
NE2
|
A:HIS142
|
4.1
|
15.5
|
1.0
|
C2
|
A:SHH401
|
4.1
|
17.7
|
0.5
|
CA
|
A:GLY310
|
4.1
|
13.7
|
1.0
|
CB
|
A:ASP180
|
4.2
|
11.2
|
1.0
|
CG1
|
A:VAL181
|
4.2
|
12.2
|
1.0
|
N
|
A:VAL181
|
4.3
|
13.8
|
1.0
|
NE2
|
A:HIS182
|
4.3
|
15.1
|
1.0
|
CE2
|
A:TYR312
|
4.3
|
15.1
|
1.0
|
C3
|
A:SHH401
|
4.4
|
17.5
|
0.5
|
CD2
|
A:HIS182
|
4.4
|
16.0
|
1.0
|
CA
|
A:HIS182
|
4.5
|
11.6
|
1.0
|
N
|
A:GLY310
|
4.5
|
16.4
|
1.0
|
CB
|
A:ASP268
|
4.5
|
14.1
|
1.0
|
OH
|
A:TYR312
|
4.5
|
16.8
|
1.0
|
CE1
|
A:HIS142
|
4.5
|
15.2
|
1.0
|
NE2
|
A:HIS143
|
4.6
|
16.5
|
1.0
|
C
|
A:ASP180
|
4.8
|
15.5
|
1.0
|
CA
|
A:ASP180
|
4.8
|
12.7
|
1.0
|
C
|
A:VAL181
|
4.9
|
15.6
|
1.0
|
C
|
A:GLY310
|
4.9
|
15.2
|
1.0
|
CZ
|
A:TYR312
|
4.9
|
17.6
|
1.0
|
CA
|
A:VAL181
|
5.0
|
13.6
|
1.0
|
|
Zinc binding site 2 out
of 4 in 9gkx
Go back to
Zinc Binding Sites List in 9gkx
Zinc binding site 2 out
of 4 in the Crystal Structure of Rhizorhabdus Wittichii Dimethoate Hydrolase (Dmha) in Complex with Saha
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 Rhizorhabdus Wittichii Dimethoate Hydrolase (Dmha) in Complex with Saha within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn402
b:19.1
occ:0.50
|
OD2
|
B:ASP268
|
2.2
|
14.3
|
1.0
|
OD1
|
B:ASP180
|
2.2
|
12.9
|
1.0
|
O1
|
B:OCA401
|
2.3
|
23.9
|
1.0
|
ND1
|
B:HIS182
|
2.3
|
13.7
|
1.0
|
O2
|
B:OCA401
|
2.4
|
22.5
|
1.0
|
C1
|
B:OCA401
|
2.5
|
23.7
|
1.0
|
OD2
|
B:ASP180
|
2.6
|
14.4
|
1.0
|
CG
|
B:ASP180
|
2.7
|
14.1
|
1.0
|
CG
|
B:ASP268
|
3.2
|
14.2
|
1.0
|
CE1
|
B:HIS182
|
3.2
|
14.4
|
1.0
|
CG
|
B:HIS182
|
3.4
|
13.5
|
1.0
|
OD1
|
B:ASP268
|
3.5
|
12.8
|
1.0
|
CB
|
B:HIS182
|
3.8
|
14.8
|
1.0
|
C2
|
B:OCA401
|
3.9
|
26.9
|
1.0
|
CA
|
B:GLY310
|
4.0
|
14.6
|
1.0
|
N
|
B:HIS182
|
4.0
|
11.8
|
1.0
|
NE2
|
B:HIS142
|
4.1
|
15.2
|
1.0
|
CB
|
B:ASP180
|
4.2
|
14.5
|
1.0
|
N
|
B:VAL181
|
4.3
|
15.2
|
1.0
|
CG1
|
B:VAL181
|
4.3
|
10.6
|
1.0
|
C3
|
B:OCA401
|
4.3
|
25.5
|
1.0
|
CE2
|
B:TYR312
|
4.3
|
13.9
|
1.0
|
NE2
|
B:HIS182
|
4.3
|
13.1
|
1.0
|
N
|
B:GLY310
|
4.4
|
14.6
|
1.0
|
CE1
|
B:HIS142
|
4.4
|
16.2
|
1.0
|
CD2
|
B:HIS182
|
4.5
|
13.2
|
1.0
|
CB
|
B:ASP268
|
4.5
|
11.6
|
1.0
|
OH
|
B:TYR312
|
4.5
|
20.3
|
1.0
|
CA
|
B:HIS182
|
4.5
|
12.4
|
1.0
|
NE2
|
B:HIS143
|
4.7
|
15.7
|
1.0
|
C
|
B:ASP180
|
4.8
|
14.5
|
1.0
|
C
|
B:GLY310
|
4.8
|
15.9
|
1.0
|
CA
|
B:ASP180
|
4.9
|
13.8
|
1.0
|
CZ
|
B:TYR312
|
4.9
|
20.3
|
1.0
|
C
|
B:VAL181
|
4.9
|
13.9
|
1.0
|
N
|
B:GLY311
|
4.9
|
15.2
|
1.0
|
|
Zinc binding site 3 out
of 4 in 9gkx
Go back to
Zinc Binding Sites List in 9gkx
Zinc binding site 3 out
of 4 in the Crystal Structure of Rhizorhabdus Wittichii Dimethoate Hydrolase (Dmha) in Complex with Saha
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 Rhizorhabdus Wittichii Dimethoate Hydrolase (Dmha) in Complex with Saha within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn402
b:23.7
occ:0.60
|
O1
|
C:SHH401
|
2.1
|
18.6
|
0.6
|
OD2
|
C:ASP268
|
2.2
|
16.0
|
1.0
|
OD1
|
C:ASP180
|
2.2
|
14.4
|
1.0
|
ND1
|
C:HIS182
|
2.3
|
15.6
|
1.0
|
OD2
|
C:ASP180
|
2.5
|
15.3
|
1.0
|
O2
|
C:SHH401
|
2.6
|
16.2
|
0.6
|
N1
|
C:SHH401
|
2.7
|
15.7
|
0.6
|
CG
|
C:ASP180
|
2.7
|
17.9
|
1.0
|
C1
|
C:SHH401
|
2.8
|
18.8
|
0.6
|
CG
|
C:ASP268
|
3.1
|
15.9
|
1.0
|
CE1
|
C:HIS182
|
3.2
|
15.5
|
1.0
|
CG
|
C:HIS182
|
3.4
|
15.8
|
1.0
|
OD1
|
C:ASP268
|
3.5
|
14.6
|
1.0
|
CB
|
C:HIS182
|
3.7
|
17.3
|
1.0
|
N
|
C:HIS182
|
4.0
|
14.6
|
1.0
|
CA
|
C:GLY310
|
4.0
|
15.6
|
1.0
|
NE2
|
C:HIS142
|
4.0
|
16.7
|
1.0
|
C2
|
C:SHH401
|
4.2
|
19.6
|
0.6
|
CB
|
C:ASP180
|
4.2
|
14.5
|
1.0
|
N
|
C:VAL181
|
4.3
|
14.4
|
1.0
|
CG1
|
C:VAL181
|
4.3
|
12.7
|
1.0
|
NE2
|
C:HIS182
|
4.4
|
18.1
|
1.0
|
CE2
|
C:TYR312
|
4.4
|
16.8
|
1.0
|
N
|
C:GLY310
|
4.4
|
17.2
|
1.0
|
CE1
|
C:HIS142
|
4.4
|
16.4
|
1.0
|
C3
|
C:SHH401
|
4.5
|
20.4
|
0.6
|
OH
|
C:TYR312
|
4.5
|
19.5
|
1.0
|
CB
|
C:ASP268
|
4.5
|
14.1
|
1.0
|
CD2
|
C:HIS182
|
4.5
|
17.6
|
1.0
|
CA
|
C:HIS182
|
4.5
|
17.4
|
1.0
|
NE2
|
C:HIS143
|
4.7
|
20.0
|
1.0
|
C
|
C:ASP180
|
4.8
|
17.1
|
1.0
|
C
|
C:GLY310
|
4.8
|
16.6
|
1.0
|
CA
|
C:ASP180
|
4.9
|
13.4
|
1.0
|
C
|
C:VAL181
|
4.9
|
13.4
|
1.0
|
CZ
|
C:TYR312
|
4.9
|
19.2
|
1.0
|
N
|
C:GLY311
|
4.9
|
17.9
|
1.0
|
CA
|
C:VAL181
|
5.0
|
14.9
|
1.0
|
|
Zinc binding site 4 out
of 4 in 9gkx
Go back to
Zinc Binding Sites List in 9gkx
Zinc binding site 4 out
of 4 in the Crystal Structure of Rhizorhabdus Wittichii Dimethoate Hydrolase (Dmha) in Complex with Saha
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 Rhizorhabdus Wittichii Dimethoate Hydrolase (Dmha) in Complex with Saha within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn402
b:18.9
occ:0.50
|
OD1
|
D:ASP180
|
2.2
|
16.1
|
1.0
|
OD2
|
D:ASP268
|
2.2
|
16.1
|
1.0
|
O1
|
D:OCA401
|
2.3
|
15.1
|
0.5
|
O2
|
D:OCA401
|
2.3
|
11.9
|
0.5
|
ND1
|
D:HIS182
|
2.3
|
17.1
|
1.0
|
C1
|
D:OCA401
|
2.4
|
14.5
|
0.5
|
OD2
|
D:ASP180
|
2.5
|
16.8
|
1.0
|
CG
|
D:ASP180
|
2.7
|
16.0
|
1.0
|
CE1
|
D:HIS182
|
3.2
|
18.3
|
1.0
|
CG
|
D:ASP268
|
3.2
|
18.1
|
1.0
|
CG
|
D:HIS182
|
3.4
|
17.6
|
1.0
|
OD1
|
D:ASP268
|
3.5
|
15.6
|
1.0
|
CB
|
D:HIS182
|
3.7
|
12.5
|
1.0
|
C2
|
D:OCA401
|
3.8
|
17.0
|
0.5
|
CA
|
D:GLY310
|
4.0
|
17.0
|
1.0
|
N
|
D:HIS182
|
4.0
|
13.5
|
1.0
|
NE2
|
D:HIS142
|
4.1
|
18.4
|
1.0
|
CB
|
D:ASP180
|
4.2
|
15.8
|
1.0
|
N
|
D:VAL181
|
4.3
|
15.1
|
1.0
|
CE2
|
D:TYR312
|
4.3
|
15.9
|
1.0
|
C3
|
D:OCA401
|
4.3
|
15.0
|
0.5
|
CG1
|
D:VAL181
|
4.3
|
14.8
|
1.0
|
NE2
|
D:HIS182
|
4.4
|
14.6
|
1.0
|
N
|
D:GLY310
|
4.4
|
16.1
|
1.0
|
OH
|
D:TYR312
|
4.4
|
19.3
|
1.0
|
CE1
|
D:HIS142
|
4.4
|
14.6
|
1.0
|
CD2
|
D:HIS182
|
4.5
|
16.4
|
1.0
|
CA
|
D:HIS182
|
4.5
|
13.7
|
1.0
|
CB
|
D:ASP268
|
4.5
|
10.2
|
1.0
|
NE2
|
D:HIS143
|
4.7
|
18.0
|
1.0
|
C
|
D:ASP180
|
4.8
|
17.1
|
1.0
|
C
|
D:GLY310
|
4.9
|
17.2
|
1.0
|
CZ
|
D:TYR312
|
4.9
|
22.4
|
1.0
|
CA
|
D:ASP180
|
4.9
|
15.5
|
1.0
|
C
|
D:VAL181
|
4.9
|
14.6
|
1.0
|
N
|
D:GLY311
|
5.0
|
18.0
|
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
|