Potassium in PDB 6j6t: Crystal Structure of HDA15 Hd Domain
Enzymatic activity of Crystal Structure of HDA15 Hd Domain
All present enzymatic activity of Crystal Structure of HDA15 Hd Domain:
3.5.1.98;
Protein crystallography data
The structure of Crystal Structure of HDA15 Hd Domain, PDB code: 6j6t
was solved by
Y.S.Cheng,
J.C.Hsu,
H.C.Hung,
T.C.Liu,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
29.52 /
2.36
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.809,
78.833,
176.794,
90.00,
94.22,
90.00
|
|
R / Rfree (%)
|
16.7 /
21.8
|
Other elements in 6j6t:
The structure of Crystal Structure of HDA15 Hd Domain also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Crystal Structure of HDA15 Hd Domain
(pdb code 6j6t). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the
Crystal Structure of HDA15 Hd Domain, PDB code: 6j6t:
Jump to Potassium binding site number:
1;
2;
3;
4;
Potassium binding site 1 out
of 4 in 6j6t
Go back to
Potassium Binding Sites List in 6j6t
Potassium binding site 1 out
of 4 in the Crystal Structure of HDA15 Hd Domain
 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 HDA15 Hd Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K602
b:17.5
occ:1.00
|
O
|
A:ASP313
|
2.6
|
11.6
|
1.0
|
|
O
|
A:HIS315
|
2.8
|
13.9
|
1.0
|
|
O
|
A:LEU335
|
2.8
|
13.0
|
1.0
|
|
O
|
A:ASP311
|
2.9
|
12.3
|
1.0
|
|
OD1
|
A:ASP311
|
2.9
|
15.3
|
1.0
|
|
OG
|
A:SER334
|
3.0
|
13.9
|
1.0
|
|
CG
|
A:ASP311
|
3.2
|
15.2
|
1.0
|
|
C
|
A:ASP311
|
3.6
|
11.2
|
1.0
|
|
C
|
A:ASP313
|
3.6
|
12.7
|
1.0
|
|
C
|
A:HIS315
|
3.7
|
12.8
|
1.0
|
|
C
|
A:LEU335
|
3.8
|
12.4
|
1.0
|
|
OD2
|
A:ASP311
|
3.8
|
18.5
|
1.0
|
|
CB
|
A:ASP311
|
3.8
|
14.3
|
1.0
|
|
N
|
A:ASP313
|
3.8
|
12.9
|
1.0
|
|
CB
|
A:HIS336
|
3.9
|
11.7
|
1.0
|
|
N
|
A:LEU335
|
4.0
|
13.1
|
1.0
|
|
CB
|
A:SER334
|
4.0
|
14.9
|
1.0
|
|
CA
|
A:ASP313
|
4.0
|
13.0
|
1.0
|
|
CB
|
A:ASP313
|
4.1
|
11.6
|
1.0
|
|
C
|
A:TRP312
|
4.2
|
14.9
|
1.0
|
|
N
|
A:TRP312
|
4.2
|
13.2
|
1.0
|
|
CA
|
A:HIS316
|
4.2
|
13.9
|
1.0
|
|
ND1
|
A:HIS336
|
4.2
|
12.6
|
1.0
|
|
N
|
A:HIS316
|
4.3
|
10.9
|
1.0
|
|
CA
|
A:ASP311
|
4.3
|
11.5
|
1.0
|
|
CA
|
A:SER334
|
4.3
|
13.4
|
1.0
|
|
CA
|
A:TRP312
|
4.4
|
17.5
|
1.0
|
|
N
|
A:HIS315
|
4.4
|
12.7
|
1.0
|
|
C
|
A:SER334
|
4.5
|
13.4
|
1.0
|
|
CG
|
A:HIS336
|
4.5
|
13.0
|
1.0
|
|
N
|
A:GLY317
|
4.6
|
12.8
|
1.0
|
|
CA
|
A:HIS336
|
4.6
|
14.9
|
1.0
|
|
CA
|
A:LEU335
|
4.6
|
12.8
|
1.0
|
|
N
|
A:HIS336
|
4.6
|
13.3
|
1.0
|
|
CE1
|
A:HIS276
|
4.7
|
13.8
|
1.0
|
|
N
|
A:VAL314
|
4.7
|
13.1
|
1.0
|
|
C
|
A:VAL314
|
4.7
|
14.3
|
1.0
|
|
CA
|
A:HIS315
|
4.7
|
13.1
|
1.0
|
|
O
|
A:HOH712
|
4.7
|
11.3
|
1.0
|
|
C
|
A:HIS316
|
4.8
|
13.6
|
1.0
|
|
ND1
|
A:HIS276
|
4.8
|
15.8
|
1.0
|
|
O
|
A:TRP312
|
4.9
|
13.0
|
1.0
|
|
OH
|
A:TYR332
|
5.0
|
15.6
|
1.0
|
|
Potassium binding site 2 out
of 4 in 6j6t
Go back to
Potassium Binding Sites List in 6j6t
Potassium binding site 2 out
of 4 in the Crystal Structure of HDA15 Hd Domain
 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 HDA15 Hd Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K602
b:17.1
occ:1.00
|
O
|
B:ASP313
|
2.5
|
11.5
|
1.0
|
|
O
|
B:HIS315
|
2.7
|
13.7
|
1.0
|
|
O
|
B:LEU335
|
2.8
|
12.3
|
1.0
|
|
OD1
|
B:ASP311
|
2.8
|
18.5
|
1.0
|
|
O
|
B:ASP311
|
2.8
|
14.8
|
1.0
|
|
OG
|
B:SER334
|
3.0
|
17.5
|
1.0
|
|
CG
|
B:ASP311
|
3.2
|
19.9
|
1.0
|
|
C
|
B:ASP313
|
3.5
|
13.7
|
1.0
|
|
C
|
B:ASP311
|
3.5
|
14.3
|
1.0
|
|
N
|
B:ASP313
|
3.7
|
16.3
|
1.0
|
|
C
|
B:LEU335
|
3.7
|
12.5
|
1.0
|
|
C
|
B:HIS315
|
3.8
|
14.0
|
1.0
|
|
OD2
|
B:ASP311
|
3.8
|
21.9
|
1.0
|
|
CB
|
B:ASP311
|
3.9
|
14.0
|
1.0
|
|
CB
|
B:HIS336
|
3.9
|
13.0
|
1.0
|
|
CA
|
B:ASP313
|
4.0
|
14.0
|
1.0
|
|
N
|
B:LEU335
|
4.0
|
11.5
|
1.0
|
|
CB
|
B:SER334
|
4.0
|
18.3
|
1.0
|
|
C
|
B:TRP312
|
4.1
|
14.2
|
1.0
|
|
CB
|
B:ASP313
|
4.1
|
12.8
|
1.0
|
|
N
|
B:TRP312
|
4.2
|
14.1
|
1.0
|
|
CA
|
B:TRP312
|
4.2
|
13.5
|
1.0
|
|
CA
|
B:HIS316
|
4.3
|
15.8
|
1.0
|
|
CA
|
B:ASP311
|
4.3
|
17.2
|
1.0
|
|
CA
|
B:SER334
|
4.4
|
12.9
|
1.0
|
|
ND1
|
B:HIS336
|
4.4
|
15.1
|
1.0
|
|
N
|
B:HIS316
|
4.4
|
12.9
|
1.0
|
|
C
|
B:SER334
|
4.5
|
15.8
|
1.0
|
|
CA
|
B:HIS336
|
4.5
|
16.1
|
1.0
|
|
N
|
B:HIS336
|
4.5
|
13.6
|
1.0
|
|
N
|
B:HIS315
|
4.5
|
13.5
|
1.0
|
|
CA
|
B:LEU335
|
4.5
|
12.6
|
1.0
|
|
N
|
B:GLY317
|
4.6
|
17.0
|
1.0
|
|
CG
|
B:HIS336
|
4.6
|
15.8
|
1.0
|
|
O
|
B:HOH704
|
4.6
|
13.1
|
1.0
|
|
N
|
B:VAL314
|
4.6
|
12.9
|
1.0
|
|
C
|
B:VAL314
|
4.7
|
14.9
|
1.0
|
|
O
|
B:TRP312
|
4.7
|
15.9
|
1.0
|
|
CE1
|
B:HIS276
|
4.8
|
20.1
|
1.0
|
|
OH
|
B:TYR332
|
4.8
|
18.4
|
1.0
|
|
CA
|
B:HIS315
|
4.8
|
14.1
|
1.0
|
|
C
|
B:HIS316
|
4.8
|
19.4
|
1.0
|
|
ND1
|
B:HIS276
|
4.9
|
17.2
|
1.0
|
|
Potassium binding site 3 out
of 4 in 6j6t
Go back to
Potassium Binding Sites List in 6j6t
Potassium binding site 3 out
of 4 in the Crystal Structure of HDA15 Hd Domain
 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 HDA15 Hd Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K602
b:33.2
occ:1.00
|
O
|
C:ASP313
|
2.7
|
29.7
|
1.0
|
|
OD1
|
C:ASP311
|
2.8
|
35.0
|
1.0
|
|
O
|
C:HIS315
|
2.8
|
28.2
|
1.0
|
|
O
|
C:ASP311
|
2.8
|
29.2
|
1.0
|
|
O
|
C:LEU335
|
2.9
|
33.2
|
1.0
|
|
OG
|
C:SER334
|
3.0
|
33.5
|
1.0
|
|
CG
|
C:ASP311
|
3.1
|
39.0
|
1.0
|
|
C
|
C:ASP311
|
3.5
|
27.7
|
1.0
|
|
OD2
|
C:ASP311
|
3.6
|
34.7
|
1.0
|
|
C
|
C:ASP313
|
3.7
|
28.7
|
1.0
|
|
C
|
C:LEU335
|
3.7
|
36.6
|
1.0
|
|
C
|
C:HIS315
|
3.7
|
28.4
|
1.0
|
|
N
|
C:ASP313
|
3.7
|
34.4
|
1.0
|
|
CB
|
C:ASP311
|
3.8
|
33.4
|
1.0
|
|
CB
|
C:HIS336
|
3.8
|
31.5
|
1.0
|
|
N
|
C:LEU335
|
3.9
|
30.1
|
1.0
|
|
CA
|
C:ASP313
|
4.1
|
31.0
|
1.0
|
|
C
|
C:TRP312
|
4.1
|
36.4
|
1.0
|
|
CB
|
C:SER334
|
4.1
|
33.4
|
1.0
|
|
N
|
C:TRP312
|
4.2
|
23.6
|
1.0
|
|
CA
|
C:HIS316
|
4.2
|
31.5
|
1.0
|
|
CB
|
C:ASP313
|
4.2
|
29.8
|
1.0
|
|
CA
|
C:TRP312
|
4.2
|
35.4
|
1.0
|
|
CA
|
C:ASP311
|
4.3
|
28.9
|
1.0
|
|
N
|
C:HIS316
|
4.3
|
23.6
|
1.0
|
|
ND1
|
C:HIS336
|
4.3
|
27.0
|
1.0
|
|
CA
|
C:SER334
|
4.4
|
33.9
|
1.0
|
|
CA
|
C:HIS336
|
4.4
|
38.1
|
1.0
|
|
N
|
C:GLY317
|
4.4
|
32.7
|
1.0
|
|
O
|
C:HOH701
|
4.4
|
30.4
|
1.0
|
|
N
|
C:HIS336
|
4.4
|
32.6
|
1.0
|
|
C
|
C:SER334
|
4.5
|
32.0
|
1.0
|
|
CA
|
C:LEU335
|
4.5
|
35.4
|
1.0
|
|
CG
|
C:HIS336
|
4.5
|
35.9
|
1.0
|
|
N
|
C:HIS315
|
4.6
|
28.8
|
1.0
|
|
C
|
C:HIS316
|
4.7
|
32.1
|
1.0
|
|
OH
|
C:TYR332
|
4.7
|
34.9
|
1.0
|
|
CA
|
C:HIS315
|
4.8
|
29.7
|
1.0
|
|
C
|
C:VAL314
|
4.8
|
29.7
|
1.0
|
|
N
|
C:VAL314
|
4.9
|
30.8
|
1.0
|
|
O
|
C:TRP312
|
4.9
|
35.0
|
1.0
|
|
ND1
|
C:HIS276
|
5.0
|
28.3
|
1.0
|
|
Potassium binding site 4 out
of 4 in 6j6t
Go back to
Potassium Binding Sites List in 6j6t
Potassium binding site 4 out
of 4 in the Crystal Structure of HDA15 Hd Domain
 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 HDA15 Hd Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K602
b:20.4
occ:1.00
|
O
|
D:ASP313
|
2.6
|
17.7
|
1.0
|
|
OD1
|
D:ASP311
|
2.8
|
20.0
|
1.0
|
|
O
|
D:ASP311
|
2.8
|
14.8
|
1.0
|
|
OG
|
D:SER334
|
2.8
|
18.0
|
1.0
|
|
O
|
D:LEU335
|
2.9
|
16.8
|
1.0
|
|
O
|
D:HIS315
|
3.0
|
19.0
|
1.0
|
|
CG
|
D:ASP311
|
3.3
|
20.7
|
1.0
|
|
C
|
D:ASP311
|
3.5
|
16.0
|
1.0
|
|
C
|
D:ASP313
|
3.6
|
16.6
|
1.0
|
|
N
|
D:ASP313
|
3.7
|
18.9
|
1.0
|
|
CB
|
D:ASP311
|
3.7
|
14.4
|
1.0
|
|
C
|
D:LEU335
|
3.8
|
21.7
|
1.0
|
|
CB
|
D:SER334
|
3.9
|
15.0
|
1.0
|
|
CB
|
D:HIS336
|
3.9
|
17.4
|
1.0
|
|
C
|
D:HIS315
|
3.9
|
18.6
|
1.0
|
|
N
|
D:LEU335
|
3.9
|
16.1
|
1.0
|
|
CA
|
D:ASP313
|
4.0
|
17.8
|
1.0
|
|
OD2
|
D:ASP311
|
4.0
|
20.2
|
1.0
|
|
CB
|
D:ASP313
|
4.1
|
16.3
|
1.0
|
|
C
|
D:TRP312
|
4.2
|
15.9
|
1.0
|
|
CA
|
D:ASP311
|
4.2
|
17.3
|
1.0
|
|
N
|
D:TRP312
|
4.2
|
15.7
|
1.0
|
|
CA
|
D:SER334
|
4.3
|
14.1
|
1.0
|
|
CA
|
D:TRP312
|
4.3
|
16.7
|
1.0
|
|
ND1
|
D:HIS336
|
4.4
|
18.5
|
1.0
|
|
CA
|
D:HIS316
|
4.4
|
19.2
|
1.0
|
|
C
|
D:SER334
|
4.4
|
19.1
|
1.0
|
|
N
|
D:GLY317
|
4.5
|
15.1
|
1.0
|
|
CA
|
D:LEU335
|
4.5
|
16.2
|
1.0
|
|
CA
|
D:HIS336
|
4.5
|
21.9
|
1.0
|
|
N
|
D:HIS316
|
4.5
|
17.3
|
1.0
|
|
N
|
D:HIS315
|
4.6
|
16.3
|
1.0
|
|
N
|
D:HIS336
|
4.6
|
18.3
|
1.0
|
|
CG
|
D:HIS336
|
4.6
|
20.0
|
1.0
|
|
CE1
|
D:HIS276
|
4.7
|
17.9
|
1.0
|
|
OH
|
D:TYR332
|
4.7
|
20.1
|
1.0
|
|
O
|
D:HOH719
|
4.8
|
19.6
|
1.0
|
|
N
|
D:VAL314
|
4.8
|
16.9
|
1.0
|
|
C
|
D:HIS316
|
4.8
|
17.8
|
1.0
|
|
C
|
D:VAL314
|
4.8
|
18.8
|
1.0
|
|
CA
|
D:HIS315
|
4.9
|
15.5
|
1.0
|
|
ND1
|
D:HIS276
|
4.9
|
18.4
|
1.0
|
|
O
|
D:TRP312
|
4.9
|
15.3
|
1.0
|
|
Reference:
Y.S.Cheng,
Y.S.Cheng,
J.C.Hsu,
H.C.Hung,
T.C.Liu.
N/A N/A.
Page generated: Mon Dec 14 00:43:38 2020
|
