Potassium in PDB 8tq0: Crystal Structure of Danio Reroof Histone Deacetylase 6 Catalytic Domain 2 Complexed with (R)-Lipoic Acid
Protein crystallography data
The structure of Crystal Structure of Danio Reroof Histone Deacetylase 6 Catalytic Domain 2 Complexed with (R)-Lipoic Acid, PDB code: 8tq0
was solved by
P.R.Watson,
D.W.Christianson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.60 /
2.40
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
74.894,
92.156,
96.666,
90,
90,
90
|
R / Rfree (%)
|
20.7 /
24.8
|
Other elements in 8tq0:
The structure of Crystal Structure of Danio Reroof Histone Deacetylase 6 Catalytic Domain 2 Complexed with (R)-Lipoic Acid also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Crystal Structure of Danio Reroof Histone Deacetylase 6 Catalytic Domain 2 Complexed with (R)-Lipoic Acid
(pdb code 8tq0). 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 Danio Reroof Histone Deacetylase 6 Catalytic Domain 2 Complexed with (R)-Lipoic Acid, PDB code: 8tq0:
Jump to Potassium binding site number:
1;
2;
3;
4;
Potassium binding site 1 out
of 4 in 8tq0
Go back to
Potassium Binding Sites List in 8tq0
Potassium binding site 1 out
of 4 in the Crystal Structure of Danio Reroof Histone Deacetylase 6 Catalytic Domain 2 Complexed with (R)-Lipoic 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 Danio Reroof Histone Deacetylase 6 Catalytic Domain 2 Complexed with (R)-Lipoic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K803
b:12.6
occ:1.00
|
O
|
A:PHE623
|
2.6
|
16.7
|
1.0
|
O
|
A:HOH914
|
2.6
|
17.0
|
1.0
|
O
|
A:TYR662
|
2.7
|
12.6
|
1.0
|
O
|
A:VAL629
|
2.8
|
14.0
|
1.0
|
O
|
A:ASP626
|
2.9
|
15.5
|
1.0
|
O
|
A:HOH936
|
3.1
|
19.1
|
1.0
|
C
|
A:TYR662
|
3.5
|
15.4
|
1.0
|
C
|
A:PHE623
|
3.6
|
16.0
|
1.0
|
CB
|
A:TYR662
|
3.6
|
20.1
|
1.0
|
CB
|
A:PHE623
|
3.8
|
15.4
|
1.0
|
C
|
A:VAL629
|
4.0
|
12.8
|
1.0
|
C
|
A:ASP626
|
4.0
|
19.1
|
1.0
|
CA
|
A:TYR662
|
4.2
|
17.3
|
1.0
|
N
|
A:TYR631
|
4.3
|
12.6
|
1.0
|
CA
|
A:PHE623
|
4.3
|
15.5
|
1.0
|
N
|
A:ASN663
|
4.4
|
14.8
|
1.0
|
N
|
A:ASP626
|
4.4
|
19.3
|
1.0
|
N
|
A:GLU624
|
4.5
|
15.4
|
1.0
|
CB
|
A:ASP626
|
4.6
|
20.7
|
1.0
|
CA
|
A:ASP626
|
4.6
|
20.6
|
1.0
|
CA
|
A:LEU630
|
4.6
|
12.6
|
1.0
|
O
|
A:GLU624
|
4.6
|
20.0
|
1.0
|
CA
|
A:GLU624
|
4.6
|
17.3
|
1.0
|
CB
|
A:ASN663
|
4.6
|
12.9
|
1.0
|
C
|
A:GLU624
|
4.7
|
21.4
|
1.0
|
CA
|
A:ASN663
|
4.7
|
15.3
|
1.0
|
CB
|
A:TYR631
|
4.7
|
15.1
|
1.0
|
N
|
A:LEU630
|
4.8
|
11.4
|
1.0
|
O
|
A:GLY659
|
4.8
|
18.2
|
1.0
|
C
|
A:LEU630
|
4.9
|
14.8
|
1.0
|
CG
|
A:TYR662
|
4.9
|
19.6
|
1.0
|
OD1
|
A:ASN663
|
4.9
|
12.3
|
1.0
|
|
Potassium binding site 2 out
of 4 in 8tq0
Go back to
Potassium Binding Sites List in 8tq0
Potassium binding site 2 out
of 4 in the Crystal Structure of Danio Reroof Histone Deacetylase 6 Catalytic Domain 2 Complexed with (R)-Lipoic 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 Danio Reroof Histone Deacetylase 6 Catalytic Domain 2 Complexed with (R)-Lipoic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K804
b:13.7
occ:1.00
|
O
|
A:ASP612
|
2.5
|
13.2
|
1.0
|
O
|
A:LEU634
|
2.7
|
12.3
|
1.0
|
OG
|
A:SER633
|
2.7
|
13.7
|
1.0
|
O
|
A:ASP610
|
2.8
|
12.5
|
1.0
|
O
|
A:HIS614
|
2.8
|
12.8
|
1.0
|
OD1
|
A:ASP610
|
3.0
|
13.6
|
1.0
|
CG
|
A:ASP610
|
3.3
|
13.2
|
1.0
|
C
|
A:ASP610
|
3.5
|
11.2
|
1.0
|
C
|
A:ASP612
|
3.6
|
14.1
|
1.0
|
C
|
A:LEU634
|
3.6
|
13.4
|
1.0
|
C
|
A:HIS614
|
3.7
|
17.1
|
1.0
|
CB
|
A:ASP610
|
3.8
|
10.0
|
1.0
|
CB
|
A:HIS635
|
3.9
|
14.5
|
1.0
|
N
|
A:LEU634
|
3.9
|
11.5
|
1.0
|
N
|
A:ASP612
|
3.9
|
13.1
|
1.0
|
CB
|
A:SER633
|
3.9
|
13.9
|
1.0
|
OD2
|
A:ASP610
|
4.0
|
15.1
|
1.0
|
CA
|
A:HIS615
|
4.1
|
16.3
|
1.0
|
CA
|
A:ASP612
|
4.1
|
12.7
|
1.0
|
N
|
A:HIS615
|
4.2
|
16.5
|
1.0
|
C
|
A:TRP611
|
4.3
|
12.2
|
1.0
|
CA
|
A:ASP610
|
4.3
|
10.5
|
1.0
|
N
|
A:TRP611
|
4.3
|
11.4
|
1.0
|
ND1
|
A:HIS635
|
4.3
|
14.2
|
1.0
|
CB
|
A:ASP612
|
4.3
|
12.5
|
1.0
|
N
|
A:GLY616
|
4.3
|
14.5
|
1.0
|
CA
|
A:SER633
|
4.3
|
11.9
|
1.0
|
CA
|
A:HIS635
|
4.4
|
13.9
|
1.0
|
N
|
A:HIS614
|
4.4
|
12.8
|
1.0
|
C
|
A:SER633
|
4.4
|
11.3
|
1.0
|
CA
|
A:TRP611
|
4.4
|
11.2
|
1.0
|
CA
|
A:LEU634
|
4.4
|
11.6
|
1.0
|
N
|
A:HIS635
|
4.4
|
11.6
|
1.0
|
CG
|
A:HIS635
|
4.5
|
15.1
|
1.0
|
C
|
A:HIS615
|
4.6
|
13.4
|
1.0
|
C
|
A:VAL613
|
4.6
|
14.0
|
1.0
|
CA
|
A:HIS614
|
4.7
|
14.4
|
1.0
|
O
|
A:HOH901
|
4.7
|
9.6
|
1.0
|
N
|
A:VAL613
|
4.7
|
13.6
|
1.0
|
OH
|
A:TYR631
|
4.7
|
14.9
|
1.0
|
O
|
A:TRP611
|
5.0
|
13.1
|
1.0
|
|
Potassium binding site 3 out
of 4 in 8tq0
Go back to
Potassium Binding Sites List in 8tq0
Potassium binding site 3 out
of 4 in the Crystal Structure of Danio Reroof Histone Deacetylase 6 Catalytic Domain 2 Complexed with (R)-Lipoic 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 Danio Reroof Histone Deacetylase 6 Catalytic Domain 2 Complexed with (R)-Lipoic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K803
b:12.4
occ:1.00
|
O
|
B:PHE623
|
2.5
|
13.5
|
1.0
|
O
|
B:HOH917
|
2.7
|
14.2
|
1.0
|
O
|
B:VAL629
|
2.7
|
15.9
|
1.0
|
O
|
B:ASP626
|
2.9
|
19.4
|
1.0
|
O
|
B:TYR662
|
2.9
|
16.3
|
1.0
|
O
|
B:HOH929
|
3.0
|
15.3
|
1.0
|
C
|
B:PHE623
|
3.5
|
11.7
|
1.0
|
C
|
B:TYR662
|
3.7
|
18.1
|
1.0
|
CB
|
B:PHE623
|
3.7
|
14.9
|
1.0
|
CB
|
B:TYR662
|
3.8
|
17.6
|
1.0
|
C
|
B:VAL629
|
4.0
|
18.1
|
1.0
|
C
|
B:ASP626
|
4.0
|
19.8
|
1.0
|
CA
|
B:PHE623
|
4.3
|
10.1
|
1.0
|
N
|
B:ASP626
|
4.4
|
15.9
|
1.0
|
CA
|
B:TYR662
|
4.4
|
16.7
|
1.0
|
N
|
B:TYR631
|
4.4
|
13.2
|
1.0
|
N
|
B:GLU624
|
4.5
|
12.2
|
1.0
|
CB
|
B:ASP626
|
4.5
|
23.9
|
1.0
|
N
|
B:ASN663
|
4.5
|
15.5
|
1.0
|
CA
|
B:ASP626
|
4.5
|
20.9
|
1.0
|
CA
|
B:GLU624
|
4.6
|
15.9
|
1.0
|
O
|
B:GLU624
|
4.6
|
17.9
|
1.0
|
C
|
B:GLU624
|
4.6
|
20.3
|
1.0
|
CA
|
B:LEU630
|
4.7
|
15.8
|
1.0
|
CB
|
B:ASN663
|
4.7
|
12.3
|
1.0
|
O
|
B:GLY659
|
4.7
|
19.6
|
1.0
|
CA
|
B:ASN663
|
4.8
|
14.0
|
1.0
|
N
|
B:LEU630
|
4.8
|
14.8
|
1.0
|
CB
|
B:TYR631
|
4.8
|
16.1
|
1.0
|
CA
|
B:VAL629
|
5.0
|
13.4
|
1.0
|
OD1
|
B:ASN663
|
5.0
|
11.1
|
1.0
|
C
|
B:LEU630
|
5.0
|
17.4
|
1.0
|
CG
|
B:PHE623
|
5.0
|
11.7
|
1.0
|
|
Potassium binding site 4 out
of 4 in 8tq0
Go back to
Potassium Binding Sites List in 8tq0
Potassium binding site 4 out
of 4 in the Crystal Structure of Danio Reroof Histone Deacetylase 6 Catalytic Domain 2 Complexed with (R)-Lipoic 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 Danio Reroof Histone Deacetylase 6 Catalytic Domain 2 Complexed with (R)-Lipoic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K804
b:15.2
occ:1.00
|
O
|
B:ASP612
|
2.5
|
14.9
|
1.0
|
O
|
B:LEU634
|
2.8
|
17.1
|
1.0
|
OD1
|
B:ASP610
|
2.8
|
15.8
|
1.0
|
OG
|
B:SER633
|
2.8
|
14.6
|
1.0
|
O
|
B:ASP610
|
2.9
|
12.8
|
1.0
|
O
|
B:HIS614
|
2.9
|
14.4
|
1.0
|
CG
|
B:ASP610
|
3.3
|
16.2
|
1.0
|
C
|
B:ASP610
|
3.5
|
14.9
|
1.0
|
C
|
B:ASP612
|
3.6
|
13.9
|
1.0
|
CB
|
B:ASP610
|
3.7
|
12.7
|
1.0
|
C
|
B:HIS614
|
3.7
|
14.9
|
1.0
|
C
|
B:LEU634
|
3.8
|
16.5
|
1.0
|
N
|
B:ASP612
|
3.8
|
12.5
|
1.0
|
CB
|
B:HIS635
|
3.9
|
15.6
|
1.0
|
OD2
|
B:ASP610
|
3.9
|
15.0
|
1.0
|
N
|
B:LEU634
|
4.0
|
13.8
|
1.0
|
CA
|
B:ASP612
|
4.1
|
13.3
|
1.0
|
CB
|
B:SER633
|
4.1
|
17.0
|
1.0
|
CA
|
B:HIS615
|
4.1
|
15.6
|
1.0
|
CB
|
B:ASP612
|
4.2
|
13.4
|
1.0
|
N
|
B:GLY616
|
4.2
|
13.5
|
1.0
|
CA
|
B:ASP610
|
4.2
|
14.6
|
1.0
|
C
|
B:TRP611
|
4.2
|
13.5
|
1.0
|
N
|
B:TRP611
|
4.3
|
13.1
|
1.0
|
N
|
B:HIS615
|
4.3
|
13.1
|
1.0
|
ND1
|
B:HIS635
|
4.3
|
14.8
|
1.0
|
CA
|
B:TRP611
|
4.4
|
15.8
|
1.0
|
CA
|
B:SER633
|
4.4
|
14.5
|
1.0
|
CA
|
B:HIS635
|
4.5
|
14.2
|
1.0
|
N
|
B:HIS614
|
4.5
|
15.3
|
1.0
|
N
|
B:HIS635
|
4.5
|
15.5
|
1.0
|
OH
|
B:TYR631
|
4.6
|
15.2
|
1.0
|
CA
|
B:LEU634
|
4.6
|
12.2
|
1.0
|
C
|
B:SER633
|
4.6
|
13.8
|
1.0
|
C
|
B:HIS615
|
4.6
|
13.6
|
1.0
|
CG
|
B:HIS635
|
4.6
|
16.4
|
1.0
|
N
|
B:VAL613
|
4.7
|
15.8
|
1.0
|
C
|
B:VAL613
|
4.7
|
14.6
|
1.0
|
CA
|
B:HIS614
|
4.8
|
13.4
|
1.0
|
O
|
B:HOH903
|
4.8
|
14.0
|
1.0
|
O
|
B:TRP611
|
5.0
|
13.7
|
1.0
|
|
Reference:
P.R.Watson,
J.Goulart Stollmaier,
D.W.Christianson.
Crystal Structure of Danio Reroof Histone Deacetylase 6 Catalytic Domain 2 Complexed with (R)-Lipoic Acid To Be Published.
Page generated: Tue Aug 13 01:00:46 2024
|