Potassium in PDB 9gn7: Crystal Structure of Deacetylase (Hdah) From Klebsiella Pneumoniae Subsp. Ozaenae in Complex with the Inhibitor Tsa
Protein crystallography data
The structure of Crystal Structure of Deacetylase (Hdah) From Klebsiella Pneumoniae Subsp. Ozaenae in Complex with the Inhibitor Tsa, PDB code: 9gn7
was solved by
C.Qin,
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)
|
46.39 /
2.18
|
Space group
|
I 2 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
146.57,
146.57,
146.57,
90,
90,
90
|
R / Rfree (%)
|
14.8 /
18.6
|
Other elements in 9gn7:
The structure of Crystal Structure of Deacetylase (Hdah) From Klebsiella Pneumoniae Subsp. Ozaenae in Complex with the Inhibitor Tsa also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Crystal Structure of Deacetylase (Hdah) From Klebsiella Pneumoniae Subsp. Ozaenae in Complex with the Inhibitor Tsa
(pdb code 9gn7). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the
Crystal Structure of Deacetylase (Hdah) From Klebsiella Pneumoniae Subsp. Ozaenae in Complex with the Inhibitor Tsa, PDB code: 9gn7:
Jump to Potassium binding site number:
1;
2;
Potassium binding site 1 out
of 2 in 9gn7
Go back to
Potassium Binding Sites List in 9gn7
Potassium binding site 1 out
of 2 in the Crystal Structure of Deacetylase (Hdah) From Klebsiella Pneumoniae Subsp. Ozaenae in Complex with the Inhibitor Tsa
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 Deacetylase (Hdah) From Klebsiella Pneumoniae Subsp. Ozaenae in Complex with the Inhibitor Tsa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K401
b:37.4
occ:1.00
|
O
|
A:LEU203
|
2.5
|
38.8
|
1.0
|
O
|
A:ASP181
|
2.6
|
35.4
|
1.0
|
OD1
|
A:ASP179
|
2.6
|
43.3
|
1.0
|
O
|
A:HIS183
|
2.6
|
32.4
|
1.0
|
O
|
A:ASP179
|
2.8
|
34.5
|
1.0
|
OG
|
A:SER202
|
2.9
|
39.9
|
1.0
|
HB3
|
A:HIS204
|
3.0
|
35.3
|
1.0
|
CG
|
A:ASP179
|
3.2
|
49.5
|
1.0
|
HG
|
A:SER202
|
3.2
|
39.8
|
0.0
|
C
|
A:ASP179
|
3.5
|
34.9
|
1.0
|
C
|
A:LEU203
|
3.6
|
34.0
|
1.0
|
HB3
|
A:ASP181
|
3.6
|
33.4
|
1.0
|
HB3
|
A:ASP179
|
3.6
|
39.1
|
1.0
|
HA
|
A:HIS184
|
3.6
|
36.3
|
1.0
|
C
|
A:ASP181
|
3.6
|
33.8
|
1.0
|
H
|
A:GLY185
|
3.7
|
38.1
|
1.0
|
H
|
A:LEU203
|
3.7
|
34.7
|
1.0
|
HA
|
A:SER202
|
3.7
|
38.6
|
1.0
|
C
|
A:HIS183
|
3.7
|
30.7
|
1.0
|
OD2
|
A:ASP179
|
3.8
|
39.6
|
1.0
|
HA
|
A:TRP180
|
3.8
|
32.0
|
1.0
|
CB
|
A:ASP179
|
3.8
|
37.1
|
1.0
|
HD1
|
A:HIS204
|
3.9
|
34.6
|
0.0
|
N
|
A:LEU203
|
3.9
|
35.9
|
1.0
|
H
|
A:ASP181
|
3.9
|
32.9
|
1.0
|
N
|
A:ASP181
|
3.9
|
33.1
|
1.0
|
CB
|
A:HIS204
|
4.0
|
35.2
|
1.0
|
CB
|
A:SER202
|
4.0
|
47.5
|
1.0
|
HA
|
A:HIS204
|
4.1
|
33.0
|
1.0
|
CA
|
A:SER202
|
4.2
|
36.2
|
1.0
|
HE1
|
A:HIS143
|
4.2
|
44.2
|
1.0
|
N
|
A:GLY185
|
4.2
|
41.1
|
1.0
|
N
|
A:TRP180
|
4.2
|
31.8
|
1.0
|
HB2
|
A:SER202
|
4.2
|
42.9
|
1.0
|
CA
|
A:ASP181
|
4.3
|
34.3
|
1.0
|
CA
|
A:ASP179
|
4.3
|
35.2
|
1.0
|
C
|
A:TRP180
|
4.3
|
31.1
|
1.0
|
H
|
A:HIS183
|
4.3
|
33.8
|
1.0
|
N
|
A:HIS183
|
4.3
|
34.1
|
1.0
|
CA
|
A:TRP180
|
4.3
|
31.2
|
1.0
|
HD1
|
A:HIS143
|
4.3
|
41.3
|
0.0
|
C
|
A:SER202
|
4.3
|
36.7
|
1.0
|
CB
|
A:ASP181
|
4.4
|
34.6
|
1.0
|
CA
|
A:HIS184
|
4.4
|
33.8
|
1.0
|
CA
|
A:HIS204
|
4.4
|
31.3
|
1.0
|
CA
|
A:LEU203
|
4.4
|
30.2
|
1.0
|
N
|
A:HIS204
|
4.4
|
32.1
|
1.0
|
HB2
|
A:HIS204
|
4.4
|
35.2
|
1.0
|
N
|
A:HIS184
|
4.5
|
35.1
|
1.0
|
ND1
|
A:HIS204
|
4.5
|
34.6
|
1.0
|
C
|
A:VAL182
|
4.6
|
36.1
|
1.0
|
C
|
A:HIS184
|
4.6
|
37.5
|
1.0
|
N
|
A:VAL182
|
4.7
|
33.1
|
1.0
|
CA
|
A:HIS183
|
4.7
|
31.0
|
1.0
|
HB2
|
A:LEU203
|
4.7
|
35.5
|
1.0
|
HB2
|
A:ASP179
|
4.7
|
39.2
|
1.0
|
HA
|
A:VAL182
|
4.7
|
34.7
|
1.0
|
CG
|
A:HIS204
|
4.8
|
39.5
|
1.0
|
HB3
|
A:SER202
|
4.8
|
42.9
|
1.0
|
HA3
|
A:GLY185
|
4.8
|
35.6
|
1.0
|
CE1
|
A:HIS143
|
4.8
|
46.6
|
1.0
|
HA
|
A:ASP179
|
4.8
|
35.8
|
1.0
|
ND1
|
A:HIS143
|
4.9
|
41.1
|
1.0
|
CA
|
A:VAL182
|
4.9
|
37.1
|
1.0
|
H
|
A:TRP180
|
4.9
|
32.4
|
1.0
|
HB2
|
A:ASP181
|
5.0
|
33.3
|
1.0
|
O
|
A:TRP180
|
5.0
|
30.1
|
1.0
|
|
Potassium binding site 2 out
of 2 in 9gn7
Go back to
Potassium Binding Sites List in 9gn7
Potassium binding site 2 out
of 2 in the Crystal Structure of Deacetylase (Hdah) From Klebsiella Pneumoniae Subsp. Ozaenae in Complex with the Inhibitor Tsa
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 Deacetylase (Hdah) From Klebsiella Pneumoniae Subsp. Ozaenae in Complex with the Inhibitor Tsa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K402
b:63.7
occ:1.00
|
O
|
A:HOH584
|
2.5
|
41.2
|
1.0
|
O
|
A:VAL198
|
2.5
|
40.6
|
1.0
|
O
|
A:TYR192
|
2.6
|
37.7
|
1.0
|
O
|
A:ARG195
|
3.0
|
59.5
|
1.0
|
HB3
|
A:TYR192
|
3.0
|
37.6
|
1.0
|
O
|
A:TYR227
|
3.1
|
45.1
|
1.0
|
HG1
|
A:THR200
|
3.1
|
64.2
|
0.0
|
HB3
|
A:TYR227
|
3.2
|
52.0
|
1.0
|
O
|
A:HOH541
|
3.2
|
44.7
|
1.0
|
HB2
|
A:TYR227
|
3.5
|
52.0
|
1.0
|
C
|
A:TYR192
|
3.6
|
42.1
|
1.0
|
C
|
A:VAL198
|
3.7
|
37.8
|
1.0
|
CB
|
A:TYR227
|
3.7
|
53.1
|
1.0
|
H
|
A:ARG195
|
3.7
|
49.4
|
1.0
|
CB
|
A:TYR192
|
3.8
|
36.1
|
1.0
|
HG22
|
A:THR200
|
3.8
|
46.5
|
1.0
|
C
|
A:TYR227
|
3.8
|
43.6
|
1.0
|
HB2
|
A:TYR192
|
3.8
|
37.6
|
1.0
|
H
|
A:THR200
|
3.8
|
41.0
|
1.0
|
OG1
|
A:THR200
|
3.9
|
64.2
|
1.0
|
HA
|
A:LEU199
|
3.9
|
40.6
|
1.0
|
HB
|
A:VAL198
|
4.0
|
44.2
|
1.0
|
C
|
A:ARG195
|
4.0
|
49.6
|
1.0
|
HA
|
A:LEU193
|
4.2
|
39.5
|
1.0
|
HB2
|
A:ASN228
|
4.2
|
41.2
|
1.0
|
CA
|
A:TYR192
|
4.3
|
39.0
|
1.0
|
H
|
A:VAL198
|
4.3
|
46.2
|
1.0
|
HG12
|
A:VAL198
|
4.3
|
45.2
|
1.0
|
HB2
|
A:ARG195
|
4.3
|
55.9
|
1.0
|
CA
|
A:TYR227
|
4.4
|
47.6
|
1.0
|
HG21
|
A:THR200
|
4.4
|
46.5
|
1.0
|
N
|
A:THR200
|
4.4
|
39.9
|
1.0
|
CG2
|
A:THR200
|
4.5
|
46.7
|
1.0
|
N
|
A:ARG195
|
4.5
|
44.6
|
1.0
|
N
|
A:LEU199
|
4.6
|
39.2
|
1.0
|
N
|
A:LEU193
|
4.6
|
35.3
|
1.0
|
CA
|
A:LEU199
|
4.6
|
40.8
|
1.0
|
HA
|
A:ASP196
|
4.6
|
52.3
|
1.0
|
N
|
A:ASN228
|
4.6
|
43.5
|
1.0
|
HA
|
A:ASN228
|
4.6
|
41.1
|
1.0
|
CA
|
A:ARG195
|
4.7
|
51.3
|
1.0
|
CA
|
A:VAL198
|
4.7
|
42.7
|
1.0
|
CA
|
A:LEU193
|
4.7
|
39.1
|
1.0
|
CB
|
A:VAL198
|
4.7
|
46.2
|
1.0
|
HA
|
A:TYR192
|
4.7
|
39.8
|
1.0
|
HA2
|
A:GLY224
|
4.8
|
53.2
|
1.0
|
C
|
A:LEU193
|
4.8
|
45.4
|
1.0
|
CB
|
A:THR200
|
4.8
|
45.9
|
1.0
|
HA3
|
A:GLY224
|
4.8
|
53.1
|
1.0
|
CB
|
A:ARG195
|
4.8
|
57.5
|
1.0
|
HB3
|
A:ARG195
|
4.8
|
55.8
|
1.0
|
O
|
A:GLY224
|
4.9
|
45.7
|
1.0
|
N
|
A:VAL198
|
4.9
|
45.4
|
1.0
|
C
|
A:LEU199
|
4.9
|
44.6
|
1.0
|
O
|
A:LEU193
|
4.9
|
47.6
|
1.0
|
CA
|
A:ASN228
|
5.0
|
39.2
|
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 11:17:33 2024
|