Potassium in PDB 9gky: Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid
Protein crystallography data
The structure of Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid, PDB code: 9gky
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)
|
46.14 /
1.13
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
51.11,
51.15,
108.82,
90,
102.22,
90
|
|
R / Rfree (%)
|
15.8 /
17.9
|
Other elements in 9gky:
The structure of Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid
(pdb code 9gky). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 9 binding sites of Potassium where determined in the
Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid, PDB code: 9gky:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Potassium binding site 1 out
of 9 in 9gky
Go back to
Potassium Binding Sites List in 9gky
Potassium binding site 1 out
of 9 in the Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic 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 Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K405
b:17.5
occ:1.00
|
O
|
A:ILE191
|
2.6
|
16.6
|
1.0
|
|
O
|
A:HOH599
|
2.6
|
36.6
|
1.0
|
|
O
|
A:ARG188
|
2.6
|
21.4
|
1.0
|
|
O
|
A:CYS185
|
2.7
|
17.8
|
1.0
|
|
O
|
A:HOH687
|
2.9
|
32.0
|
1.0
|
|
O
|
A:HOH529
|
3.1
|
31.5
|
1.0
|
|
C
|
A:ARG188
|
3.6
|
24.0
|
1.0
|
|
HA
|
A:ASP189
|
3.7
|
21.9
|
1.0
|
|
H
|
A:ARG188
|
3.7
|
23.6
|
0.6
|
|
H
|
A:ARG188
|
3.7
|
24.0
|
0.4
|
|
HA
|
A:ALA186
|
3.8
|
17.6
|
1.0
|
|
C
|
A:CYS185
|
3.8
|
16.6
|
1.0
|
|
C
|
A:ILE191
|
3.8
|
14.3
|
1.0
|
|
HB3
|
A:CYS185
|
3.9
|
16.4
|
1.0
|
|
HA
|
A:ILE192
|
3.9
|
13.2
|
1.0
|
|
HB2
|
A:ARG188
|
4.0
|
23.1
|
0.6
|
|
HD13
|
A:ILE192
|
4.0
|
17.4
|
1.0
|
|
H
|
A:ILE191
|
4.1
|
14.9
|
1.0
|
|
O
|
A:ALA186
|
4.1
|
22.8
|
1.0
|
|
HG
|
A:SER210
|
4.1
|
10.2
|
0.0
|
|
OG
|
A:SER210
|
4.2
|
14.6
|
1.0
|
|
C
|
A:ALA186
|
4.2
|
18.6
|
1.0
|
|
HB2
|
A:ARG188
|
4.2
|
26.7
|
0.4
|
|
N
|
A:ARG188
|
4.2
|
24.3
|
1.0
|
|
O
|
A:HOH639
|
4.3
|
21.3
|
1.0
|
|
HB
|
A:ILE191
|
4.3
|
14.8
|
1.0
|
|
CA
|
A:ALA186
|
4.3
|
17.3
|
1.0
|
|
N
|
A:ASP189
|
4.4
|
20.8
|
1.0
|
|
CA
|
A:ASP189
|
4.4
|
21.1
|
1.0
|
|
CA
|
A:ARG188
|
4.4
|
23.0
|
0.6
|
|
CA
|
A:ARG188
|
4.5
|
24.7
|
0.4
|
|
N
|
A:ALA186
|
4.5
|
16.3
|
1.0
|
|
CB
|
A:CYS185
|
4.6
|
16.1
|
1.0
|
|
HG1
|
A:THR193
|
4.6
|
7.6
|
0.0
|
|
HB2
|
A:CYS185
|
4.7
|
16.1
|
1.0
|
|
N
|
A:ILE191
|
4.7
|
14.2
|
1.0
|
|
CB
|
A:ARG188
|
4.7
|
23.1
|
0.6
|
|
H
|
A:THR193
|
4.7
|
11.7
|
1.0
|
|
N
|
A:ILE192
|
4.7
|
13.1
|
1.0
|
|
CA
|
A:ILE192
|
4.7
|
12.6
|
1.0
|
|
CA
|
A:ILE191
|
4.7
|
14.3
|
1.0
|
|
C
|
A:ASP189
|
4.8
|
20.8
|
1.0
|
|
CA
|
A:CYS185
|
4.8
|
15.4
|
1.0
|
|
N
|
A:GLU187
|
4.9
|
19.1
|
1.0
|
|
CB
|
A:ARG188
|
4.9
|
27.0
|
0.4
|
|
CD1
|
A:ILE192
|
4.9
|
17.9
|
1.0
|
|
HD11
|
A:ILE192
|
5.0
|
17.6
|
1.0
|
|
CB
|
A:ILE191
|
5.0
|
14.6
|
1.0
|
|
Potassium binding site 2 out
of 9 in 9gky
Go back to
Potassium Binding Sites List in 9gky
Potassium binding site 2 out
of 9 in the Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic 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 Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K406
b:9.6
occ:0.90
|
O
|
A:PHE196
|
2.6
|
10.5
|
1.0
|
|
O
|
A:ASP174
|
2.6
|
10.2
|
1.0
|
|
O
|
A:HIS176
|
2.7
|
10.6
|
1.0
|
|
OD1
|
A:ASP172
|
2.8
|
10.6
|
1.0
|
|
OG
|
A:SER195
|
2.8
|
10.7
|
1.0
|
|
O
|
A:ASP172
|
2.9
|
10.2
|
1.0
|
|
HG
|
A:SER195
|
3.2
|
8.5
|
0.0
|
|
CG
|
A:ASP172
|
3.2
|
10.6
|
1.0
|
|
HB3
|
A:HIS197
|
3.2
|
10.2
|
1.0
|
|
HD1
|
A:HIS197
|
3.5
|
7.8
|
0.0
|
|
HA
|
A:HIS177
|
3.5
|
10.3
|
1.0
|
|
H
|
A:PHE196
|
3.5
|
9.8
|
1.0
|
|
C
|
A:ASP172
|
3.6
|
9.9
|
1.0
|
|
HB3
|
A:ASP174
|
3.6
|
10.2
|
1.0
|
|
C
|
A:HIS176
|
3.6
|
10.6
|
1.0
|
|
C
|
A:ASP174
|
3.7
|
10.2
|
1.0
|
|
OD2
|
A:ASP172
|
3.7
|
12.9
|
1.0
|
|
HB3
|
A:ASP172
|
3.7
|
10.2
|
1.0
|
|
C
|
A:PHE196
|
3.7
|
10.9
|
1.0
|
|
H
|
A:ASP174
|
3.7
|
9.8
|
1.0
|
|
N
|
A:ASP174
|
3.8
|
9.8
|
1.0
|
|
H
|
A:GLY178
|
3.8
|
10.6
|
1.0
|
|
CB
|
A:ASP172
|
3.9
|
10.1
|
1.0
|
|
HE1
|
A:HIS136
|
3.9
|
11.4
|
1.0
|
|
HA
|
A:SER195
|
3.9
|
9.8
|
1.0
|
|
N
|
A:PHE196
|
3.9
|
10.1
|
1.0
|
|
CB
|
A:SER195
|
4.0
|
10.6
|
1.0
|
|
HA
|
A:SER173
|
4.0
|
10.4
|
0.5
|
|
HD1
|
A:HIS136
|
4.1
|
9.8
|
0.0
|
|
CB
|
A:HIS197
|
4.1
|
10.4
|
1.0
|
|
HA
|
A:SER173
|
4.2
|
10.3
|
0.5
|
|
CA
|
A:ASP174
|
4.2
|
9.7
|
1.0
|
|
CA
|
A:HIS177
|
4.2
|
10.0
|
1.0
|
|
N
|
A:GLY178
|
4.2
|
10.5
|
1.0
|
|
C
|
A:SER173
|
4.2
|
9.9
|
1.0
|
|
ND1
|
A:HIS197
|
4.3
|
10.4
|
1.0
|
|
N
|
A:SER173
|
4.3
|
10.0
|
1.0
|
|
HA
|
A:HIS197
|
4.3
|
10.4
|
1.0
|
|
N
|
A:HIS177
|
4.3
|
10.4
|
1.0
|
|
CA
|
A:ASP172
|
4.3
|
9.5
|
1.0
|
|
CA
|
A:SER195
|
4.4
|
9.9
|
1.0
|
|
HB2
|
A:SER195
|
4.4
|
10.4
|
1.0
|
|
CB
|
A:ASP174
|
4.4
|
10.0
|
1.0
|
|
N
|
A:HIS176
|
4.4
|
10.1
|
1.0
|
|
H
|
A:HIS176
|
4.4
|
10.1
|
1.0
|
|
CA
|
A:SER173
|
4.4
|
10.1
|
0.5
|
|
CA
|
A:SER173
|
4.5
|
10.1
|
0.5
|
|
C
|
A:HIS177
|
4.5
|
10.4
|
1.0
|
|
CA
|
A:PHE196
|
4.5
|
9.6
|
1.0
|
|
C
|
A:SER195
|
4.5
|
10.0
|
1.0
|
|
CE1
|
A:HIS136
|
4.6
|
11.4
|
1.0
|
|
CA
|
A:HIS197
|
4.6
|
10.6
|
1.0
|
|
N
|
A:HIS197
|
4.6
|
10.5
|
1.0
|
|
ND1
|
A:HIS136
|
4.6
|
11.5
|
1.0
|
|
CA
|
A:HIS176
|
4.7
|
10.4
|
1.0
|
|
CG
|
A:HIS197
|
4.7
|
10.0
|
1.0
|
|
C
|
A:VAL175
|
4.7
|
10.2
|
1.0
|
|
O
|
A:HOH704
|
4.7
|
14.8
|
1.0
|
|
HB2
|
A:PHE196
|
4.7
|
10.0
|
1.0
|
|
N
|
A:VAL175
|
4.7
|
9.6
|
1.0
|
|
HB2
|
A:HIS197
|
4.8
|
10.3
|
1.0
|
|
HB3
|
A:SER195
|
4.8
|
10.7
|
1.0
|
|
HB2
|
A:ASP172
|
4.8
|
10.1
|
1.0
|
|
HA3
|
A:GLY178
|
4.9
|
10.5
|
1.0
|
|
HA
|
A:ASP172
|
4.9
|
9.4
|
1.0
|
|
H
|
A:SER173
|
4.9
|
9.9
|
0.5
|
|
H
|
A:SER173
|
4.9
|
9.9
|
0.5
|
|
O
|
A:SER173
|
5.0
|
12.4
|
1.0
|
|
HA
|
A:VAL175
|
5.0
|
10.1
|
1.0
|
|
Potassium binding site 3 out
of 9 in 9gky
Go back to
Potassium Binding Sites List in 9gky
Potassium binding site 3 out
of 9 in the Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic 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 Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K407
b:24.9
occ:0.70
|
O
|
A:HOH794
|
2.4
|
36.5
|
1.0
|
|
O
|
A:LEU162
|
2.5
|
26.1
|
1.0
|
|
O
|
A:LEU160
|
2.5
|
19.3
|
1.0
|
|
O
|
A:VAL165
|
2.5
|
19.2
|
1.0
|
|
O
|
A:HOH538
|
2.6
|
42.4
|
1.0
|
|
O
|
A:HOH782
|
2.9
|
34.8
|
1.0
|
|
OD1
|
A:ASP166
|
3.5
|
30.0
|
1.0
|
|
C
|
A:LEU160
|
3.5
|
19.2
|
1.0
|
|
H
|
A:VAL165
|
3.6
|
21.1
|
1.0
|
|
C
|
A:VAL165
|
3.6
|
17.5
|
1.0
|
|
C
|
A:LEU162
|
3.7
|
27.7
|
1.0
|
|
HA
|
A:LEU160
|
3.7
|
16.1
|
1.0
|
|
HA
|
A:ASP166
|
3.8
|
17.8
|
1.0
|
|
HA
|
A:PRO163
|
4.0
|
30.4
|
1.0
|
|
N
|
A:LEU162
|
4.1
|
22.6
|
1.0
|
|
H
|
A:LEU162
|
4.1
|
22.7
|
1.0
|
|
N
|
A:VAL165
|
4.2
|
21.0
|
1.0
|
|
CA
|
A:LEU160
|
4.2
|
15.7
|
1.0
|
|
O
|
A:PRO163
|
4.3
|
30.3
|
1.0
|
|
HB
|
A:VAL165
|
4.3
|
17.6
|
1.0
|
|
C
|
A:SER161
|
4.3
|
24.0
|
1.0
|
|
HA
|
A:SER161
|
4.4
|
22.8
|
1.0
|
|
CA
|
A:VAL165
|
4.4
|
17.5
|
1.0
|
|
C
|
A:PRO163
|
4.4
|
27.5
|
1.0
|
|
N
|
A:ASP166
|
4.5
|
16.4
|
1.0
|
|
N
|
A:SER161
|
4.5
|
20.9
|
1.0
|
|
CA
|
A:PRO163
|
4.5
|
30.6
|
1.0
|
|
CG
|
A:ASP166
|
4.5
|
26.5
|
1.0
|
|
N
|
A:PRO163
|
4.5
|
28.9
|
1.0
|
|
CA
|
A:LEU162
|
4.6
|
23.8
|
1.0
|
|
O
|
A:HOH815
|
4.6
|
46.0
|
1.0
|
|
CA
|
A:ASP166
|
4.6
|
17.8
|
1.0
|
|
HD21
|
A:LEU160
|
4.6
|
17.5
|
1.0
|
|
HB3
|
A:LEU160
|
4.6
|
16.7
|
1.0
|
|
CA
|
A:SER161
|
4.6
|
21.9
|
1.0
|
|
O
|
A:SER161
|
4.8
|
25.7
|
1.0
|
|
O
|
A:ALA159
|
4.8
|
15.6
|
1.0
|
|
CB
|
A:VAL165
|
4.9
|
17.4
|
1.0
|
|
Potassium binding site 4 out
of 9 in 9gky
Go back to
Potassium Binding Sites List in 9gky
Potassium binding site 4 out
of 9 in the Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic 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 Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K408
b:15.6
occ:0.80
|
O
|
A:HOH798
|
2.7
|
26.6
|
1.0
|
|
O
|
A:GLY259
|
2.7
|
12.1
|
1.0
|
|
O
|
A:LEU261
|
2.8
|
13.3
|
1.0
|
|
O
|
A:ASN254
|
2.8
|
12.4
|
1.0
|
|
O
|
A:HOH640
|
2.9
|
11.9
|
1.0
|
|
O
|
A:HIS253
|
2.9
|
10.9
|
1.0
|
|
C
|
A:ASN254
|
3.4
|
12.5
|
1.0
|
|
HA
|
A:ASN254
|
3.4
|
13.1
|
1.0
|
|
O
|
A:HOH759
|
3.5
|
30.4
|
1.0
|
|
HB3
|
A:ASP256
|
3.5
|
11.1
|
1.0
|
|
H
|
A:ASP256
|
3.5
|
11.4
|
1.0
|
|
O
|
A:ASP256
|
3.6
|
12.2
|
1.0
|
|
C
|
A:GLY259
|
3.6
|
11.2
|
1.0
|
|
HA
|
A:TYR260
|
3.7
|
13.1
|
1.0
|
|
H
|
A:LEU261
|
3.8
|
12.4
|
1.0
|
|
CA
|
A:ASN254
|
3.8
|
13.1
|
1.0
|
|
O
|
A:HOH517
|
3.9
|
14.6
|
1.0
|
|
N
|
A:ASP256
|
3.9
|
11.2
|
1.0
|
|
C
|
A:LEU261
|
3.9
|
12.8
|
1.0
|
|
N
|
A:LEU261
|
3.9
|
12.6
|
1.0
|
|
C
|
A:HIS253
|
4.0
|
10.4
|
1.0
|
|
O
|
A:HOH605
|
4.0
|
18.1
|
1.0
|
|
C
|
A:TYR260
|
4.2
|
13.7
|
1.0
|
|
CB
|
A:ASP256
|
4.2
|
10.7
|
1.0
|
|
N
|
A:TYR260
|
4.2
|
11.8
|
1.0
|
|
CA
|
A:TYR260
|
4.2
|
12.7
|
1.0
|
|
N
|
A:ASP255
|
4.2
|
11.8
|
1.0
|
|
HB2
|
A:ASP256
|
4.3
|
10.9
|
1.0
|
|
N
|
A:ASN254
|
4.3
|
11.7
|
1.0
|
|
C
|
A:ASP256
|
4.4
|
12.2
|
1.0
|
|
CA
|
A:ASP256
|
4.4
|
11.4
|
1.0
|
|
HA3
|
A:GLY259
|
4.4
|
11.0
|
1.0
|
|
O
|
A:HOH722
|
4.4
|
22.1
|
1.0
|
|
HA
|
A:SER262
|
4.5
|
13.1
|
1.0
|
|
CA
|
A:GLY259
|
4.5
|
11.1
|
1.0
|
|
O
|
A:HOH725
|
4.6
|
27.3
|
1.0
|
|
CA
|
A:LEU261
|
4.6
|
11.9
|
1.0
|
|
C
|
A:ASP255
|
4.6
|
12.2
|
1.0
|
|
HA
|
A:ASP255
|
4.6
|
12.4
|
1.0
|
|
CA
|
A:ASP255
|
4.8
|
11.9
|
1.0
|
|
H
|
A:ASP255
|
4.8
|
11.8
|
1.0
|
|
N
|
A:GLY259
|
4.9
|
11.3
|
1.0
|
|
H
|
A:GLY259
|
4.9
|
11.4
|
1.0
|
|
O
|
A:TYR260
|
4.9
|
15.3
|
1.0
|
|
O
|
A:ILE252
|
4.9
|
11.0
|
1.0
|
|
H
|
A:TYR260
|
5.0
|
11.7
|
1.0
|
|
N
|
A:SER262
|
5.0
|
13.2
|
1.0
|
|
Potassium binding site 5 out
of 9 in 9gky
Go back to
Potassium Binding Sites List in 9gky
Potassium binding site 5 out
of 9 in the Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic 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 Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K409
b:22.0
occ:0.80
|
O
|
A:SER22
|
2.7
|
15.1
|
1.0
|
|
O
|
A:LEU24
|
2.8
|
22.5
|
1.0
|
|
O
|
A:HOH786
|
2.8
|
39.5
|
1.0
|
|
OD1
|
A:ASN35
|
2.9
|
17.0
|
1.0
|
|
HG22
|
A:ILE34
|
3.3
|
14.0
|
1.0
|
|
HG21
|
A:ILE34
|
3.4
|
14.1
|
1.0
|
|
HA
|
A:ASP25
|
3.8
|
28.1
|
1.0
|
|
CG2
|
A:ILE34
|
3.8
|
14.1
|
1.0
|
|
C
|
A:LEU24
|
3.8
|
22.6
|
1.0
|
|
C
|
A:SER22
|
3.9
|
14.8
|
1.0
|
|
CG
|
A:ASN35
|
3.9
|
14.9
|
1.0
|
|
HD21
|
A:ASN35
|
3.9
|
17.5
|
1.0
|
|
HG13
|
A:ILE34
|
3.9
|
15.4
|
1.0
|
|
O
|
A:HOH582
|
3.9
|
19.4
|
0.5
|
|
HB3
|
A:SER22
|
4.1
|
12.0
|
1.0
|
|
HG12
|
A:ILE34
|
4.2
|
15.7
|
1.0
|
|
HH12
|
A:ARG38
|
4.2
|
18.9
|
0.5
|
|
ND2
|
A:ASN35
|
4.2
|
18.3
|
1.0
|
|
HA
|
A:GLN23
|
4.3
|
17.9
|
1.0
|
|
C
|
A:GLN23
|
4.3
|
21.1
|
1.0
|
|
N
|
A:LEU24
|
4.4
|
18.5
|
1.0
|
|
H
|
A:LEU26
|
4.4
|
24.1
|
1.0
|
|
CG1
|
A:ILE34
|
4.4
|
15.4
|
1.0
|
|
O
|
A:GLN23
|
4.5
|
24.2
|
1.0
|
|
HG23
|
A:ILE34
|
4.5
|
14.0
|
1.0
|
|
CA
|
A:ASP25
|
4.6
|
28.5
|
1.0
|
|
N
|
A:ASP25
|
4.6
|
24.6
|
1.0
|
|
H
|
A:LEU24
|
4.6
|
19.2
|
1.0
|
|
CA
|
A:GLN23
|
4.7
|
17.1
|
1.0
|
|
CB
|
A:ILE34
|
4.7
|
13.2
|
1.0
|
|
HA
|
A:SER22
|
4.7
|
12.1
|
1.0
|
|
HA
|
A:ASN35
|
4.7
|
11.6
|
1.0
|
|
N
|
A:GLN23
|
4.7
|
15.0
|
1.0
|
|
HH11
|
A:ARG38
|
4.7
|
18.9
|
0.5
|
|
CA
|
A:LEU24
|
4.8
|
20.8
|
1.0
|
|
CA
|
A:SER22
|
4.8
|
11.9
|
1.0
|
|
NH1
|
A:ARG38
|
4.8
|
18.4
|
0.5
|
|
O
|
A:HOH744
|
4.8
|
28.3
|
1.0
|
|
CB
|
A:SER22
|
4.9
|
11.8
|
1.0
|
|
HD22
|
A:ASN35
|
5.0
|
17.1
|
1.0
|
|
OD1
|
A:ASP25
|
5.0
|
42.2
|
1.0
|
|
Potassium binding site 6 out
of 9 in 9gky
Go back to
Potassium Binding Sites List in 9gky
Potassium binding site 6 out
of 9 in the Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic 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 Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K406
b:10.8
occ:0.90
|
O
|
B:PHE196
|
2.6
|
10.6
|
1.0
|
|
O
|
B:ASP174
|
2.6
|
11.5
|
1.0
|
|
O
|
B:HIS176
|
2.7
|
11.6
|
1.0
|
|
OD1
|
B:ASP172
|
2.8
|
12.1
|
1.0
|
|
OG
|
B:SER195
|
2.8
|
10.9
|
1.0
|
|
O
|
B:ASP172
|
2.9
|
11.1
|
1.0
|
|
HG
|
B:SER195
|
3.1
|
7.2
|
0.0
|
|
HB3
|
B:HIS197
|
3.2
|
10.8
|
1.0
|
|
CG
|
B:ASP172
|
3.2
|
12.2
|
1.0
|
|
HA
|
B:HIS177
|
3.5
|
11.3
|
1.0
|
|
HD1
|
B:HIS197
|
3.6
|
7.5
|
0.0
|
|
H
|
B:PHE196
|
3.6
|
10.1
|
1.0
|
|
C
|
B:ASP172
|
3.6
|
10.9
|
1.0
|
|
C
|
B:HIS176
|
3.6
|
10.4
|
1.0
|
|
OD2
|
B:ASP172
|
3.6
|
13.5
|
1.0
|
|
C
|
B:ASP174
|
3.7
|
11.2
|
1.0
|
|
HB3
|
B:ASP172
|
3.7
|
12.0
|
1.0
|
|
HB3
|
B:ASP174
|
3.7
|
11.4
|
1.0
|
|
C
|
B:PHE196
|
3.7
|
10.9
|
1.0
|
|
H
|
B:ASP174
|
3.7
|
10.9
|
1.0
|
|
H
|
B:GLY178
|
3.7
|
11.8
|
1.0
|
|
N
|
B:ASP174
|
3.8
|
10.9
|
1.0
|
|
HE1
|
B:HIS136
|
3.8
|
12.6
|
1.0
|
|
CB
|
B:ASP172
|
3.9
|
12.0
|
1.0
|
|
HA
|
B:SER195
|
3.9
|
10.6
|
1.0
|
|
N
|
B:PHE196
|
4.0
|
10.0
|
1.0
|
|
CB
|
B:SER195
|
4.0
|
11.7
|
1.0
|
|
HA
|
B:SER173
|
4.0
|
11.1
|
0.5
|
|
CB
|
B:HIS197
|
4.1
|
11.1
|
1.0
|
|
HD1
|
B:HIS136
|
4.1
|
9.5
|
0.0
|
|
HA
|
B:SER173
|
4.2
|
11.2
|
0.5
|
|
CA
|
B:ASP174
|
4.2
|
10.7
|
1.0
|
|
N
|
B:GLY178
|
4.2
|
12.0
|
1.0
|
|
CA
|
B:HIS177
|
4.2
|
11.2
|
1.0
|
|
HA
|
B:HIS197
|
4.2
|
10.6
|
1.0
|
|
C
|
B:SER173
|
4.2
|
11.0
|
1.0
|
|
N
|
B:SER173
|
4.3
|
10.0
|
1.0
|
|
N
|
B:HIS177
|
4.3
|
11.2
|
1.0
|
|
ND1
|
B:HIS197
|
4.3
|
11.5
|
1.0
|
|
HB2
|
B:SER195
|
4.3
|
11.4
|
1.0
|
|
CA
|
B:ASP172
|
4.4
|
10.9
|
1.0
|
|
CA
|
B:SER195
|
4.4
|
10.7
|
1.0
|
|
CB
|
B:ASP174
|
4.4
|
11.4
|
1.0
|
|
N
|
B:HIS176
|
4.4
|
10.2
|
1.0
|
|
CA
|
B:SER173
|
4.4
|
11.1
|
0.5
|
|
CA
|
B:SER173
|
4.5
|
11.2
|
0.5
|
|
H
|
B:HIS176
|
4.5
|
10.4
|
1.0
|
|
C
|
B:HIS177
|
4.5
|
11.6
|
1.0
|
|
CA
|
B:PHE196
|
4.5
|
10.4
|
1.0
|
|
CE1
|
B:HIS136
|
4.5
|
12.6
|
1.0
|
|
CA
|
B:HIS197
|
4.5
|
10.9
|
1.0
|
|
C
|
B:SER195
|
4.5
|
10.9
|
1.0
|
|
N
|
B:HIS197
|
4.6
|
10.5
|
1.0
|
|
ND1
|
B:HIS136
|
4.6
|
12.7
|
1.0
|
|
C
|
B:VAL175
|
4.6
|
10.9
|
1.0
|
|
CA
|
B:HIS176
|
4.7
|
11.3
|
1.0
|
|
HB2
|
B:PHE196
|
4.7
|
10.4
|
1.0
|
|
HB2
|
B:HIS197
|
4.7
|
11.0
|
1.0
|
|
CG
|
B:HIS197
|
4.7
|
10.7
|
1.0
|
|
O
|
B:HOH740
|
4.7
|
14.4
|
1.0
|
|
N
|
B:VAL175
|
4.7
|
10.8
|
1.0
|
|
HB2
|
B:ASP172
|
4.8
|
11.9
|
1.0
|
|
HB3
|
B:SER195
|
4.8
|
11.6
|
1.0
|
|
HA3
|
B:GLY178
|
4.9
|
11.7
|
1.0
|
|
HA
|
B:ASP172
|
4.9
|
10.9
|
1.0
|
|
H
|
B:SER173
|
4.9
|
10.3
|
0.5
|
|
H
|
B:SER173
|
4.9
|
10.3
|
0.5
|
|
O
|
B:SER173
|
5.0
|
12.4
|
1.0
|
|
HA
|
B:VAL175
|
5.0
|
10.8
|
1.0
|
|
Potassium binding site 7 out
of 9 in 9gky
Go back to
Potassium Binding Sites List in 9gky
Potassium binding site 7 out
of 9 in the Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic 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 Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K407
b:20.9
occ:0.80
|
O
|
B:CYS185
|
2.4
|
20.8
|
1.0
|
|
O
|
B:HOH818
|
2.5
|
26.9
|
1.0
|
|
O
|
B:ILE191
|
2.6
|
19.0
|
1.0
|
|
O
|
B:ARG188
|
2.6
|
29.2
|
1.0
|
|
O
|
B:HOH646
|
2.7
|
29.2
|
1.0
|
|
HB3
|
B:CYS185
|
3.5
|
17.9
|
1.0
|
|
C
|
B:CYS185
|
3.6
|
17.9
|
1.0
|
|
H
|
B:ARG188
|
3.7
|
30.7
|
1.0
|
|
C
|
B:ARG188
|
3.7
|
31.0
|
1.0
|
|
O
|
B:HOH575
|
3.8
|
22.9
|
1.0
|
|
HB2
|
B:ARG188
|
3.8
|
32.8
|
1.0
|
|
C
|
B:ILE191
|
3.8
|
16.5
|
1.0
|
|
HA
|
B:ASP189
|
3.8
|
28.2
|
1.0
|
|
HA
|
B:ILE192
|
3.9
|
14.8
|
1.0
|
|
O
|
B:HOH791
|
3.9
|
45.9
|
1.0
|
|
HA
|
B:ALA186
|
3.9
|
21.4
|
1.0
|
|
HD13
|
B:ILE192
|
4.0
|
19.9
|
1.0
|
|
H
|
B:ILE191
|
4.1
|
18.2
|
1.0
|
|
HG
|
B:SER210
|
4.2
|
8.8
|
0.0
|
|
O
|
B:HOH577
|
4.2
|
19.6
|
0.5
|
|
O
|
B:ALA186
|
4.2
|
26.9
|
1.0
|
|
N
|
B:ARG188
|
4.2
|
31.5
|
1.0
|
|
OG
|
B:SER210
|
4.2
|
15.2
|
1.0
|
|
C
|
B:ALA186
|
4.3
|
24.8
|
1.0
|
|
CB
|
B:CYS185
|
4.3
|
17.7
|
1.0
|
|
HB
|
B:ILE191
|
4.4
|
16.7
|
1.0
|
|
CA
|
B:ALA186
|
4.4
|
21.0
|
1.0
|
|
CA
|
B:ARG188
|
4.4
|
31.1
|
1.0
|
|
HB2
|
B:CYS185
|
4.5
|
17.6
|
1.0
|
|
N
|
B:ALA186
|
4.5
|
20.0
|
1.0
|
|
CA
|
B:CYS185
|
4.5
|
17.5
|
1.0
|
|
N
|
B:ASP189
|
4.5
|
28.1
|
1.0
|
|
CA
|
B:ASP189
|
4.6
|
27.4
|
1.0
|
|
CB
|
B:ARG188
|
4.6
|
33.4
|
1.0
|
|
HG1
|
B:THR193
|
4.6
|
7.6
|
0.0
|
|
CA
|
B:ILE192
|
4.7
|
14.3
|
1.0
|
|
N
|
B:ILE192
|
4.7
|
14.7
|
1.0
|
|
H
|
B:THR193
|
4.7
|
13.1
|
1.0
|
|
N
|
B:ILE191
|
4.7
|
17.5
|
1.0
|
|
HA
|
B:CYS185
|
4.8
|
17.7
|
1.0
|
|
CA
|
B:ILE191
|
4.8
|
16.6
|
1.0
|
|
N
|
B:GLU187
|
4.8
|
25.0
|
1.0
|
|
HG22
|
B:THR193
|
4.9
|
13.5
|
1.0
|
|
CD1
|
B:ILE192
|
4.9
|
20.7
|
1.0
|
|
HB3
|
B:ARG188
|
4.9
|
33.3
|
1.0
|
|
C
|
B:ASP189
|
5.0
|
26.4
|
1.0
|
|
O
|
B:HOH537
|
5.0
|
18.8
|
0.5
|
|
O
|
A:HOH671
|
5.0
|
21.9
|
1.0
|
|
Potassium binding site 8 out
of 9 in 9gky
Go back to
Potassium Binding Sites List in 9gky
Potassium binding site 8 out
of 9 in the Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic 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 Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K408
b:16.4
occ:0.90
|
O
|
B:HOH797
|
2.5
|
31.3
|
1.0
|
|
O
|
B:GLY259
|
2.7
|
13.0
|
1.0
|
|
O
|
B:ASN254
|
2.8
|
13.1
|
1.0
|
|
O
|
B:LEU261
|
2.9
|
13.8
|
1.0
|
|
O
|
B:HOH663
|
2.9
|
11.9
|
1.0
|
|
O
|
B:HIS253
|
3.0
|
11.1
|
1.0
|
|
O
|
B:HOH678
|
3.2
|
41.4
|
1.0
|
|
O
|
B:ASP256
|
3.3
|
13.1
|
1.0
|
|
HB3
|
B:ASP256
|
3.3
|
11.5
|
1.0
|
|
H
|
B:ASP256
|
3.4
|
11.1
|
1.0
|
|
C
|
B:ASN254
|
3.4
|
11.9
|
1.0
|
|
HA
|
B:ASN254
|
3.6
|
12.8
|
1.0
|
|
C
|
B:GLY259
|
3.6
|
11.7
|
1.0
|
|
HA
|
B:TYR260
|
3.7
|
13.6
|
1.0
|
|
N
|
B:ASP256
|
3.8
|
10.9
|
1.0
|
|
H
|
B:LEU261
|
3.8
|
12.3
|
1.0
|
|
O
|
B:HOH517
|
3.9
|
21.2
|
1.0
|
|
CA
|
B:ASN254
|
4.0
|
12.8
|
1.0
|
|
C
|
B:HIS253
|
4.0
|
10.4
|
1.0
|
|
C
|
B:LEU261
|
4.0
|
13.4
|
1.0
|
|
O
|
B:HOH554
|
4.0
|
30.9
|
1.0
|
|
CB
|
B:ASP256
|
4.0
|
11.3
|
1.0
|
|
N
|
B:LEU261
|
4.1
|
12.3
|
1.0
|
|
C
|
B:ASP256
|
4.1
|
12.3
|
1.0
|
|
CA
|
B:ASP256
|
4.2
|
11.5
|
1.0
|
|
HB2
|
B:ASP256
|
4.2
|
11.2
|
1.0
|
|
N
|
B:ASP255
|
4.3
|
11.3
|
1.0
|
|
N
|
B:TYR260
|
4.3
|
12.5
|
1.0
|
|
CA
|
B:TYR260
|
4.3
|
13.2
|
1.0
|
|
C
|
B:TYR260
|
4.3
|
13.7
|
1.0
|
|
HA3
|
B:GLY259
|
4.4
|
11.4
|
1.0
|
|
N
|
B:ASN254
|
4.4
|
11.0
|
1.0
|
|
C
|
B:ASP255
|
4.4
|
11.8
|
1.0
|
|
CA
|
B:GLY259
|
4.5
|
11.6
|
1.0
|
|
HA
|
B:ASP255
|
4.5
|
12.6
|
1.0
|
|
HA
|
B:SER262
|
4.6
|
13.2
|
1.0
|
|
CA
|
B:ASP255
|
4.7
|
12.3
|
1.0
|
|
CA
|
B:LEU261
|
4.7
|
11.9
|
1.0
|
|
H
|
B:GLY259
|
4.8
|
12.1
|
1.0
|
|
N
|
B:GLY259
|
4.8
|
12.1
|
1.0
|
|
H
|
B:ASP255
|
4.9
|
11.4
|
1.0
|
|
O
|
B:HOH755
|
4.9
|
29.7
|
1.0
|
|
O
|
B:ILE252
|
5.0
|
10.3
|
1.0
|
|
O
|
B:ASP251
|
5.0
|
10.6
|
1.0
|
|
Potassium binding site 9 out
of 9 in 9gky
Go back to
Potassium Binding Sites List in 9gky
Potassium binding site 9 out
of 9 in the Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic 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 Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K409
b:28.3
occ:0.80
|
O
|
B:LEU160
|
2.6
|
23.0
|
1.0
|
|
O
|
B:HOH525
|
2.6
|
38.1
|
1.0
|
|
O
|
B:VAL165
|
2.6
|
22.8
|
1.0
|
|
O
|
B:HOH796
|
2.6
|
38.4
|
1.0
|
|
O
|
B:LEU162
|
2.8
|
29.1
|
1.0
|
|
O
|
B:HOH808
|
3.0
|
42.6
|
1.0
|
|
C
|
B:LEU160
|
3.6
|
21.7
|
1.0
|
|
OD1
|
B:ASP166
|
3.6
|
33.4
|
1.0
|
|
C
|
B:VAL165
|
3.6
|
20.4
|
1.0
|
|
H
|
B:VAL165
|
3.6
|
25.9
|
1.0
|
|
C
|
B:LEU162
|
3.7
|
32.8
|
1.0
|
|
HA
|
B:PRO163
|
3.8
|
34.1
|
1.0
|
|
HA
|
B:LEU160
|
3.8
|
19.9
|
1.0
|
|
HA
|
B:ASP166
|
3.9
|
21.9
|
1.0
|
|
H
|
B:LEU162
|
4.1
|
25.9
|
1.0
|
|
N
|
B:LEU162
|
4.1
|
25.5
|
1.0
|
|
N
|
B:VAL165
|
4.2
|
25.6
|
1.0
|
|
CA
|
B:LEU160
|
4.3
|
19.8
|
1.0
|
|
O
|
B:PRO163
|
4.3
|
36.8
|
1.0
|
|
HB
|
B:VAL165
|
4.3
|
20.6
|
1.0
|
|
C
|
B:SER161
|
4.4
|
27.1
|
1.0
|
|
CA
|
B:PRO163
|
4.4
|
34.0
|
1.0
|
|
C
|
B:PRO163
|
4.4
|
32.6
|
1.0
|
|
HA
|
B:SER161
|
4.4
|
25.1
|
1.0
|
|
CA
|
B:VAL165
|
4.4
|
20.9
|
1.0
|
|
N
|
B:ASP166
|
4.5
|
20.3
|
1.0
|
|
N
|
B:PRO163
|
4.5
|
31.8
|
1.0
|
|
N
|
B:SER161
|
4.5
|
21.8
|
1.0
|
|
HB3
|
B:LEU160
|
4.5
|
20.6
|
1.0
|
|
CA
|
B:LEU162
|
4.5
|
28.2
|
1.0
|
|
CG
|
B:ASP166
|
4.5
|
29.8
|
1.0
|
|
CA
|
B:ASP166
|
4.6
|
21.5
|
1.0
|
|
CA
|
B:SER161
|
4.7
|
24.5
|
1.0
|
|
HD21
|
B:LEU160
|
4.7
|
20.1
|
1.0
|
|
O
|
B:SER161
|
4.9
|
29.0
|
1.0
|
|
O
|
B:ALA159
|
4.9
|
19.1
|
1.0
|
|
CB
|
B:VAL165
|
4.9
|
20.4
|
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 11:17:29 2024
|
