Potassium in PDB 9gn6: Crystal Structure of Deacetylase (Hdah) From Klebsiella Pneumoniae Subsp. Ozaenae in Complex with the Inhibitor Saha
Protein crystallography data
The structure of Crystal Structure of Deacetylase (Hdah) From Klebsiella Pneumoniae Subsp. Ozaenae in Complex with the Inhibitor Saha, PDB code: 9gn6
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)
|
46.28 /
1.95
|
Space group
|
I 2 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
146.206,
146.206,
146.206,
90,
90,
90
|
R / Rfree (%)
|
13.7 /
17.6
|
Other elements in 9gn6:
The structure of Crystal Structure of Deacetylase (Hdah) From Klebsiella Pneumoniae Subsp. Ozaenae in Complex with the Inhibitor Saha 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 Saha
(pdb code 9gn6). 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 Saha, PDB code: 9gn6:
Jump to Potassium binding site number:
1;
2;
Potassium binding site 1 out
of 2 in 9gn6
Go back to
Potassium Binding Sites List in 9gn6
Potassium binding site 1 out
of 2 in the Crystal Structure of Deacetylase (Hdah) From Klebsiella Pneumoniae Subsp. Ozaenae in Complex with the Inhibitor Saha
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 Saha within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K401
b:42.8
occ:1.00
|
O
|
A:LEU203
|
2.5
|
43.4
|
1.0
|
O
|
A:ASP181
|
2.5
|
38.9
|
1.0
|
OD1
|
A:ASP179
|
2.6
|
42.8
|
1.0
|
O
|
A:HIS183
|
2.7
|
38.8
|
1.0
|
O
|
A:ASP179
|
2.8
|
41.6
|
1.0
|
OG
|
A:SER202
|
2.9
|
44.5
|
1.0
|
HB3
|
A:HIS204
|
3.1
|
38.5
|
1.0
|
CG
|
A:ASP179
|
3.2
|
45.8
|
1.0
|
HG
|
A:SER202
|
3.2
|
30.0
|
0.0
|
C
|
A:ASP179
|
3.5
|
41.0
|
1.0
|
C
|
A:LEU203
|
3.6
|
40.5
|
1.0
|
HB3
|
A:ASP179
|
3.6
|
42.6
|
1.0
|
C
|
A:ASP181
|
3.6
|
36.9
|
1.0
|
HA
|
A:HIS184
|
3.7
|
42.1
|
1.0
|
H
|
A:LEU203
|
3.7
|
39.1
|
1.0
|
HB3
|
A:ASP181
|
3.7
|
40.8
|
1.0
|
H
|
A:GLY185
|
3.8
|
41.5
|
1.0
|
HA
|
A:SER202
|
3.8
|
44.8
|
1.0
|
C
|
A:HIS183
|
3.8
|
39.3
|
1.0
|
CB
|
A:ASP179
|
3.8
|
40.6
|
1.0
|
OD2
|
A:ASP179
|
3.8
|
41.8
|
1.0
|
HA
|
A:TRP180
|
3.8
|
40.8
|
1.0
|
N
|
A:LEU203
|
3.9
|
39.0
|
1.0
|
N
|
A:ASP181
|
3.9
|
40.8
|
1.0
|
HD1
|
A:HIS204
|
3.9
|
30.0
|
0.0
|
H
|
A:ASP181
|
3.9
|
41.0
|
1.0
|
CB
|
A:SER202
|
4.0
|
48.7
|
1.0
|
CB
|
A:HIS204
|
4.1
|
38.1
|
1.0
|
HA
|
A:HIS204
|
4.1
|
37.9
|
1.0
|
N
|
A:TRP180
|
4.2
|
38.6
|
1.0
|
HE1
|
A:HIS143
|
4.2
|
43.7
|
1.0
|
C
|
A:TRP180
|
4.2
|
40.4
|
1.0
|
CA
|
A:ASP181
|
4.2
|
41.1
|
1.0
|
CA
|
A:SER202
|
4.2
|
44.9
|
1.0
|
CA
|
A:ASP179
|
4.2
|
41.6
|
1.0
|
HB2
|
A:SER202
|
4.2
|
47.0
|
1.0
|
CA
|
A:TRP180
|
4.3
|
41.8
|
1.0
|
N
|
A:GLY185
|
4.3
|
40.6
|
1.0
|
HD1
|
A:HIS143
|
4.3
|
30.0
|
0.0
|
C
|
A:SER202
|
4.4
|
44.1
|
1.0
|
N
|
A:HIS183
|
4.4
|
38.5
|
1.0
|
H
|
A:HIS183
|
4.4
|
36.4
|
1.0
|
CA
|
A:LEU203
|
4.4
|
35.2
|
1.0
|
CA
|
A:HIS184
|
4.4
|
42.0
|
1.0
|
CA
|
A:HIS204
|
4.4
|
37.3
|
1.0
|
CB
|
A:ASP181
|
4.4
|
39.9
|
1.0
|
N
|
A:HIS204
|
4.4
|
40.0
|
1.0
|
N
|
A:HIS184
|
4.6
|
39.7
|
1.0
|
HB2
|
A:HIS204
|
4.6
|
38.4
|
1.0
|
HB2
|
A:LEU203
|
4.6
|
40.1
|
1.0
|
ND1
|
A:HIS204
|
4.6
|
45.0
|
1.0
|
C
|
A:VAL182
|
4.6
|
36.2
|
1.0
|
C
|
A:HIS184
|
4.6
|
44.4
|
1.0
|
N
|
A:VAL182
|
4.7
|
39.2
|
1.0
|
HA
|
A:VAL182
|
4.7
|
37.8
|
1.0
|
CA
|
A:HIS183
|
4.7
|
33.7
|
1.0
|
HB2
|
A:ASP179
|
4.7
|
42.4
|
1.0
|
HB3
|
A:SER202
|
4.8
|
47.5
|
1.0
|
HA
|
A:ASP179
|
4.8
|
41.3
|
1.0
|
CE1
|
A:HIS143
|
4.8
|
44.5
|
1.0
|
CG
|
A:HIS204
|
4.8
|
42.5
|
1.0
|
H
|
A:TRP180
|
4.9
|
39.7
|
1.0
|
ND1
|
A:HIS143
|
4.9
|
41.7
|
1.0
|
CA
|
A:VAL182
|
4.9
|
37.1
|
1.0
|
OD1
|
A:ASP181
|
4.9
|
36.9
|
1.0
|
O
|
A:TRP180
|
5.0
|
36.1
|
1.0
|
HA3
|
A:GLY185
|
5.0
|
39.8
|
1.0
|
|
Potassium binding site 2 out
of 2 in 9gn6
Go back to
Potassium Binding Sites List in 9gn6
Potassium binding site 2 out
of 2 in the Crystal Structure of Deacetylase (Hdah) From Klebsiella Pneumoniae Subsp. Ozaenae in Complex with the Inhibitor Saha
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 Saha within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K402
b:71.4
occ:1.00
|
O
|
A:HOH505
|
2.2
|
75.2
|
1.0
|
O
|
A:HOH597
|
2.5
|
51.2
|
1.0
|
O
|
A:TYR192
|
2.6
|
51.6
|
1.0
|
O
|
A:VAL198
|
2.7
|
53.7
|
1.0
|
O
|
A:ARG195
|
2.7
|
55.5
|
1.0
|
HB3
|
A:TYR192
|
3.1
|
48.8
|
1.0
|
HB2
|
A:TYR227
|
3.1
|
55.3
|
1.0
|
O
|
A:TYR227
|
3.2
|
47.4
|
1.0
|
HB3
|
A:TYR227
|
3.2
|
54.4
|
1.0
|
O
|
A:HOH615
|
3.5
|
54.7
|
1.0
|
H
|
A:ARG195
|
3.5
|
57.0
|
1.0
|
CB
|
A:TYR227
|
3.6
|
56.0
|
1.0
|
C
|
A:TYR192
|
3.6
|
50.9
|
1.0
|
HG1
|
A:THR200
|
3.8
|
30.0
|
0.0
|
C
|
A:TYR227
|
3.8
|
50.5
|
1.0
|
C
|
A:VAL198
|
3.8
|
51.3
|
1.0
|
C
|
A:ARG195
|
3.8
|
60.5
|
1.0
|
CB
|
A:TYR192
|
3.9
|
46.8
|
1.0
|
HA
|
A:LEU199
|
3.9
|
51.4
|
1.0
|
HB2
|
A:TYR192
|
4.0
|
47.4
|
1.0
|
HB
|
A:VAL198
|
4.0
|
51.8
|
1.0
|
HB2
|
A:ARG195
|
4.0
|
58.5
|
1.0
|
HG22
|
A:THR200
|
4.1
|
52.9
|
1.0
|
H
|
A:THR200
|
4.1
|
49.1
|
1.0
|
HA
|
A:LEU193
|
4.1
|
51.1
|
1.0
|
N
|
A:ARG195
|
4.2
|
57.4
|
1.0
|
HB2
|
A:ASN228
|
4.3
|
48.8
|
1.0
|
H
|
A:VAL198
|
4.3
|
53.6
|
1.0
|
CA
|
A:TYR192
|
4.3
|
49.2
|
1.0
|
CA
|
A:TYR227
|
4.3
|
51.3
|
1.0
|
HA3
|
A:GLY224
|
4.4
|
54.9
|
1.0
|
CA
|
A:ARG195
|
4.5
|
56.1
|
1.0
|
HA2
|
A:GLY224
|
4.5
|
55.6
|
1.0
|
HA
|
A:ASP196
|
4.5
|
63.6
|
1.0
|
OG1
|
A:THR200
|
4.5
|
65.6
|
1.0
|
N
|
A:LEU193
|
4.6
|
51.2
|
1.0
|
CB
|
A:ARG195
|
4.6
|
59.7
|
1.0
|
O
|
A:LEU193
|
4.6
|
54.9
|
1.0
|
C
|
A:LEU193
|
4.6
|
53.5
|
1.0
|
HG21
|
A:THR200
|
4.6
|
52.1
|
1.0
|
CA
|
A:LEU193
|
4.6
|
50.3
|
1.0
|
HG12
|
A:VAL198
|
4.6
|
50.7
|
1.0
|
O
|
A:GLY224
|
4.6
|
50.4
|
1.0
|
N
|
A:ASN228
|
4.7
|
48.1
|
1.0
|
CA
|
A:LEU199
|
4.7
|
51.6
|
1.0
|
N
|
A:LEU199
|
4.7
|
49.1
|
1.0
|
HB3
|
A:ARG195
|
4.7
|
59.5
|
1.0
|
N
|
A:THR200
|
4.7
|
48.4
|
1.0
|
HA
|
A:TYR192
|
4.7
|
49.8
|
1.0
|
CG2
|
A:THR200
|
4.8
|
51.8
|
1.0
|
CA
|
A:VAL198
|
4.8
|
51.0
|
1.0
|
CB
|
A:VAL198
|
4.8
|
51.7
|
1.0
|
HA
|
A:ASN228
|
4.9
|
45.8
|
1.0
|
CG
|
A:TYR227
|
4.9
|
57.6
|
1.0
|
N
|
A:VAL198
|
4.9
|
51.4
|
1.0
|
CA
|
A:GLY224
|
4.9
|
55.5
|
1.0
|
N
|
A:ASP196
|
4.9
|
64.4
|
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 11:17:42 2024
|