Potassium in PDB 5eei: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha
Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha
All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha:
3.5.1.98;
Protein crystallography data
The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha, PDB code: 5eei
was solved by
Y.Hai,
D.W.Christianson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
36.26 /
1.32
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.790,
83.551,
86.806,
90.00,
98.09,
90.00
|
|
R / Rfree (%)
|
12.5 /
14.8
|
Other elements in 5eei:
The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha
(pdb code 5eei). 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 Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha, PDB code: 5eei:
Jump to Potassium binding site number:
1;
2;
3;
4;
Potassium binding site 1 out
of 4 in 5eei
Go back to
Potassium Binding Sites List in 5eei
Potassium binding site 1 out
of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with 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 Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K2002
b:13.5
occ:0.89
|
O
|
A:ASP612
|
2.5
|
12.2
|
1.0
|
|
O
|
A:LEU634
|
2.7
|
12.3
|
1.0
|
|
OD1
|
A:ASP610
|
2.7
|
12.2
|
1.0
|
|
O
|
A:HIS614
|
2.7
|
12.7
|
1.0
|
|
OG
|
A:SER633
|
2.7
|
12.6
|
1.0
|
|
HG
|
A:SER633
|
2.8
|
15.1
|
1.0
|
|
O
|
A:ASP610
|
2.8
|
11.7
|
1.0
|
|
HB3
|
A:HIS635
|
3.0
|
14.1
|
1.0
|
|
CG
|
A:ASP610
|
3.2
|
12.6
|
1.0
|
|
HB3
|
A:ASP610
|
3.5
|
14.8
|
1.0
|
|
C
|
A:ASP610
|
3.5
|
11.3
|
1.0
|
|
HA
|
A:HIS615
|
3.5
|
13.5
|
1.0
|
|
HB3
|
A:ASP612
|
3.5
|
13.3
|
1.0
|
|
H
|
A:LEU634
|
3.6
|
14.2
|
1.0
|
|
C
|
A:ASP612
|
3.6
|
11.5
|
1.0
|
|
C
|
A:HIS614
|
3.7
|
11.1
|
1.0
|
|
C
|
A:LEU634
|
3.7
|
11.9
|
1.0
|
|
CB
|
A:ASP610
|
3.8
|
12.4
|
1.0
|
|
HA
|
A:SER633
|
3.9
|
13.3
|
1.0
|
|
N
|
A:ASP612
|
3.9
|
11.5
|
1.0
|
|
N
|
A:LEU634
|
3.9
|
11.8
|
1.0
|
|
CB
|
A:SER633
|
3.9
|
12.5
|
1.0
|
|
H
|
A:ASP612
|
3.9
|
13.8
|
1.0
|
|
CB
|
A:HIS635
|
4.0
|
11.8
|
1.0
|
|
OD2
|
A:ASP610
|
4.0
|
13.2
|
1.0
|
|
HE1
|
A:HIS573
|
4.0
|
16.9
|
1.0
|
|
H
|
A:GLY616
|
4.0
|
14.6
|
1.0
|
|
HA
|
A:TRP611
|
4.0
|
14.4
|
1.0
|
|
CA
|
A:ASP612
|
4.1
|
10.9
|
1.0
|
|
N
|
A:TRP611
|
4.2
|
11.4
|
1.0
|
|
HB2
|
A:SER633
|
4.2
|
15.0
|
1.0
|
|
HA
|
A:HIS635
|
4.2
|
13.4
|
1.0
|
|
C
|
A:TRP611
|
4.2
|
11.4
|
1.0
|
|
CA
|
A:HIS615
|
4.3
|
11.2
|
1.0
|
|
CA
|
A:ASP610
|
4.3
|
11.8
|
1.0
|
|
CB
|
A:ASP612
|
4.3
|
11.1
|
1.0
|
|
CA
|
A:SER633
|
4.3
|
11.1
|
1.0
|
|
ND1
|
A:HIS635
|
4.3
|
13.0
|
1.0
|
|
N
|
A:HIS615
|
4.3
|
11.0
|
1.0
|
|
CA
|
A:TRP611
|
4.4
|
12.0
|
1.0
|
|
N
|
A:HIS614
|
4.5
|
11.3
|
1.0
|
|
CA
|
A:HIS635
|
4.5
|
11.1
|
1.0
|
|
C
|
A:SER633
|
4.5
|
12.3
|
1.0
|
|
N
|
A:HIS635
|
4.5
|
11.0
|
1.0
|
|
H
|
A:HIS614
|
4.5
|
13.6
|
1.0
|
|
N
|
A:GLY616
|
4.5
|
12.2
|
1.0
|
|
CA
|
A:LEU634
|
4.5
|
12.1
|
1.0
|
|
HB2
|
A:HIS635
|
4.5
|
14.1
|
1.0
|
|
HH
|
A:TYR631
|
4.5
|
15.9
|
1.0
|
|
CG
|
A:HIS635
|
4.6
|
11.3
|
1.0
|
|
O
|
A:HOH2131
|
4.6
|
14.4
|
1.0
|
|
HB3
|
A:SER633
|
4.7
|
15.0
|
1.0
|
|
N
|
A:VAL613
|
4.7
|
10.9
|
1.0
|
|
C
|
A:VAL613
|
4.7
|
11.7
|
1.0
|
|
CE1
|
A:HIS573
|
4.7
|
14.1
|
1.0
|
|
HB2
|
A:ASP610
|
4.7
|
14.8
|
1.0
|
|
CA
|
A:HIS614
|
4.7
|
10.9
|
1.0
|
|
C
|
A:HIS615
|
4.7
|
12.0
|
1.0
|
|
OH
|
A:TYR631
|
4.7
|
13.2
|
1.0
|
|
HA
|
A:ASP610
|
4.8
|
14.2
|
1.0
|
|
HA
|
A:VAL613
|
4.9
|
14.6
|
1.0
|
|
H
|
A:TRP611
|
4.9
|
13.6
|
1.0
|
|
ND1
|
A:HIS573
|
4.9
|
12.6
|
1.0
|
|
HB2
|
A:ASP612
|
4.9
|
13.3
|
1.0
|
|
HB2
|
A:LEU634
|
4.9
|
16.5
|
1.0
|
|
O
|
A:TRP611
|
4.9
|
12.0
|
1.0
|
|
Potassium binding site 2 out
of 4 in 5eei
Go back to
Potassium Binding Sites List in 5eei
Potassium binding site 2 out
of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with 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 Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K2003
b:14.0
occ:0.93
|
O
|
A:VAL629
|
2.7
|
14.8
|
1.0
|
|
O
|
A:HOH2239
|
2.7
|
13.4
|
1.0
|
|
O
|
A:PHE623
|
2.7
|
13.1
|
1.0
|
|
O
|
A:TYR662
|
2.8
|
13.2
|
1.0
|
|
O
|
A:ASP626
|
2.9
|
17.3
|
1.0
|
|
O
|
A:HOH2244
|
3.0
|
12.8
|
1.0
|
|
HB3
|
A:PHE623
|
3.0
|
15.1
|
1.0
|
|
HB3
|
A:TYR662
|
3.1
|
16.7
|
1.0
|
|
HB2
|
A:TYR662
|
3.3
|
16.7
|
1.0
|
|
C
|
A:TYR662
|
3.5
|
13.2
|
1.0
|
|
HB2
|
A:PHE623
|
3.6
|
15.1
|
1.0
|
|
CB
|
A:TYR662
|
3.6
|
13.9
|
1.0
|
|
C
|
A:PHE623
|
3.6
|
13.7
|
1.0
|
|
H
|
A:TYR631
|
3.7
|
13.7
|
1.0
|
|
CB
|
A:PHE623
|
3.7
|
12.6
|
1.0
|
|
H
|
A:ASP626
|
3.8
|
18.5
|
1.0
|
|
HA
|
A:LEU630
|
3.9
|
14.3
|
1.0
|
|
C
|
A:VAL629
|
3.9
|
13.1
|
1.0
|
|
HB3
|
A:ASP626
|
3.9
|
21.3
|
1.0
|
|
HB2
|
A:ASN663
|
4.0
|
15.6
|
1.0
|
|
HA
|
A:GLU624
|
4.0
|
17.2
|
1.0
|
|
C
|
A:ASP626
|
4.0
|
15.9
|
1.0
|
|
CA
|
A:TYR662
|
4.2
|
13.6
|
1.0
|
|
HB3
|
A:TYR631
|
4.2
|
15.3
|
1.0
|
|
CA
|
A:PHE623
|
4.3
|
13.3
|
1.0
|
|
N
|
A:TYR631
|
4.4
|
11.4
|
1.0
|
|
HB
|
A:VAL629
|
4.4
|
14.9
|
1.0
|
|
N
|
A:ASN663
|
4.4
|
12.3
|
1.0
|
|
HB2
|
A:TYR631
|
4.4
|
15.3
|
1.0
|
|
HA
|
A:ASN663
|
4.4
|
14.0
|
1.0
|
|
N
|
A:ASP626
|
4.5
|
15.4
|
1.0
|
|
N
|
A:GLU624
|
4.5
|
13.8
|
1.0
|
|
H
|
A:VAL629
|
4.6
|
15.5
|
1.0
|
|
CA
|
A:LEU630
|
4.6
|
12.0
|
1.0
|
|
CA
|
A:GLU624
|
4.6
|
14.3
|
1.0
|
|
CA
|
A:ASP626
|
4.7
|
16.3
|
1.0
|
|
N
|
A:LEU630
|
4.7
|
12.5
|
1.0
|
|
O
|
A:GLU624
|
4.7
|
14.6
|
1.0
|
|
HA
|
A:ASP627
|
4.7
|
19.6
|
1.0
|
|
CB
|
A:ASP626
|
4.7
|
17.7
|
1.0
|
|
C
|
A:GLU624
|
4.7
|
14.0
|
1.0
|
|
HA
|
A:PHE623
|
4.7
|
15.9
|
1.0
|
|
CB
|
A:TYR631
|
4.7
|
12.7
|
1.0
|
|
CA
|
A:ASN663
|
4.8
|
11.7
|
1.0
|
|
CB
|
A:ASN663
|
4.8
|
13.0
|
1.0
|
|
HA3
|
A:GLY659
|
4.8
|
20.6
|
1.0
|
|
HA
|
A:TYR662
|
4.8
|
16.3
|
1.0
|
|
HA2
|
A:GLY659
|
4.9
|
20.6
|
1.0
|
|
O
|
A:GLY659
|
4.9
|
15.2
|
1.0
|
|
CA
|
A:VAL629
|
4.9
|
12.3
|
1.0
|
|
CG
|
A:TYR662
|
4.9
|
14.8
|
1.0
|
|
C
|
A:LEU630
|
4.9
|
11.5
|
1.0
|
|
CG
|
A:PHE623
|
5.0
|
12.2
|
1.0
|
|
Potassium binding site 3 out
of 4 in 5eei
Go back to
Potassium Binding Sites List in 5eei
Potassium binding site 3 out
of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha
 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 Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K803
b:15.4
occ:0.90
|
O
|
B:ASP612
|
2.6
|
14.0
|
1.0
|
|
OD1
|
B:ASP610
|
2.7
|
14.0
|
1.0
|
|
O
|
B:LEU634
|
2.7
|
14.4
|
1.0
|
|
OG
|
B:SER633
|
2.7
|
15.6
|
1.0
|
|
O
|
B:HIS614
|
2.7
|
13.2
|
1.0
|
|
HG
|
B:SER633
|
2.8
|
18.7
|
1.0
|
|
O
|
B:ASP610
|
2.8
|
13.7
|
1.0
|
|
HB3
|
B:HIS635
|
3.0
|
17.4
|
1.0
|
|
CG
|
B:ASP610
|
3.3
|
14.1
|
1.0
|
|
HB3
|
B:ASP610
|
3.5
|
17.0
|
1.0
|
|
C
|
B:ASP610
|
3.5
|
12.9
|
1.0
|
|
HA
|
B:HIS615
|
3.5
|
16.1
|
1.0
|
|
HB3
|
B:ASP612
|
3.5
|
16.0
|
1.0
|
|
H
|
B:LEU634
|
3.5
|
17.0
|
1.0
|
|
C
|
B:ASP612
|
3.6
|
13.0
|
1.0
|
|
C
|
B:LEU634
|
3.7
|
13.8
|
1.0
|
|
C
|
B:HIS614
|
3.7
|
13.2
|
1.0
|
|
CB
|
B:ASP610
|
3.8
|
14.2
|
1.0
|
|
HA
|
B:SER633
|
3.8
|
16.9
|
1.0
|
|
H
|
B:ASP612
|
3.8
|
15.9
|
1.0
|
|
N
|
B:ASP612
|
3.9
|
13.3
|
1.0
|
|
N
|
B:LEU634
|
3.9
|
14.2
|
1.0
|
|
H
|
B:GLY616
|
3.9
|
17.3
|
1.0
|
|
CB
|
B:SER633
|
3.9
|
14.5
|
1.0
|
|
CB
|
B:HIS635
|
3.9
|
14.5
|
1.0
|
|
HA
|
B:TRP611
|
4.0
|
16.0
|
1.0
|
|
OD2
|
B:ASP610
|
4.0
|
15.0
|
1.0
|
|
HE1
|
B:HIS573
|
4.0
|
15.4
|
1.0
|
|
CA
|
B:ASP612
|
4.1
|
12.6
|
1.0
|
|
N
|
B:TRP611
|
4.2
|
12.4
|
1.0
|
|
C
|
B:TRP611
|
4.2
|
12.9
|
1.0
|
|
HB2
|
B:SER633
|
4.2
|
17.4
|
1.0
|
|
HA
|
B:HIS635
|
4.2
|
16.9
|
1.0
|
|
CA
|
B:ASP610
|
4.2
|
12.6
|
1.0
|
|
CA
|
B:SER633
|
4.3
|
14.1
|
1.0
|
|
CA
|
B:HIS615
|
4.3
|
13.4
|
1.0
|
|
CB
|
B:ASP612
|
4.3
|
13.4
|
1.0
|
|
ND1
|
B:HIS635
|
4.3
|
15.5
|
1.0
|
|
N
|
B:HIS615
|
4.3
|
13.4
|
1.0
|
|
CA
|
B:TRP611
|
4.4
|
13.3
|
1.0
|
|
C
|
B:SER633
|
4.4
|
14.6
|
1.0
|
|
N
|
B:HIS614
|
4.5
|
13.4
|
1.0
|
|
CA
|
B:HIS635
|
4.5
|
14.1
|
1.0
|
|
N
|
B:GLY616
|
4.5
|
14.4
|
1.0
|
|
H
|
B:HIS614
|
4.5
|
16.1
|
1.0
|
|
HH
|
B:TYR631
|
4.5
|
18.0
|
1.0
|
|
CA
|
B:LEU634
|
4.5
|
14.8
|
1.0
|
|
N
|
B:HIS635
|
4.5
|
14.1
|
1.0
|
|
HB2
|
B:HIS635
|
4.5
|
17.4
|
1.0
|
|
CG
|
B:HIS635
|
4.6
|
14.7
|
1.0
|
|
O
|
B:HOH918
|
4.6
|
16.5
|
1.0
|
|
HB3
|
B:SER633
|
4.6
|
17.4
|
1.0
|
|
C
|
B:VAL613
|
4.7
|
13.5
|
1.0
|
|
N
|
B:VAL613
|
4.7
|
13.4
|
1.0
|
|
HB2
|
B:ASP610
|
4.7
|
17.0
|
1.0
|
|
CA
|
B:HIS614
|
4.7
|
13.1
|
1.0
|
|
OH
|
B:TYR631
|
4.7
|
15.0
|
1.0
|
|
CE1
|
B:HIS573
|
4.7
|
12.9
|
1.0
|
|
C
|
B:HIS615
|
4.8
|
13.4
|
1.0
|
|
HA
|
B:ASP610
|
4.8
|
15.2
|
1.0
|
|
H
|
B:TRP611
|
4.9
|
14.9
|
1.0
|
|
HA
|
B:VAL613
|
4.9
|
16.2
|
1.0
|
|
HB2
|
B:ASP612
|
4.9
|
16.0
|
1.0
|
|
O
|
B:TRP611
|
4.9
|
13.1
|
1.0
|
|
ND1
|
B:HIS573
|
4.9
|
13.7
|
1.0
|
|
HB2
|
B:LEU634
|
5.0
|
19.8
|
1.0
|
|
Potassium binding site 4 out
of 4 in 5eei
Go back to
Potassium Binding Sites List in 5eei
Potassium binding site 4 out
of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha
 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 Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K804
b:17.0
occ:0.92
|
O
|
B:VAL629
|
2.7
|
16.6
|
1.0
|
|
O
|
B:PHE623
|
2.7
|
16.9
|
1.0
|
|
O
|
B:HOH967
|
2.7
|
17.3
|
1.0
|
|
O
|
B:TYR662
|
2.8
|
16.5
|
1.0
|
|
O
|
B:ASP626
|
2.9
|
19.3
|
1.0
|
|
O
|
B:HOH1024
|
3.0
|
15.7
|
1.0
|
|
HB3
|
B:PHE623
|
3.1
|
18.3
|
1.0
|
|
HB3
|
B:TYR662
|
3.1
|
20.6
|
1.0
|
|
HB2
|
B:TYR662
|
3.3
|
20.6
|
1.0
|
|
C
|
B:TYR662
|
3.6
|
15.9
|
1.0
|
|
CB
|
B:TYR662
|
3.6
|
17.1
|
1.0
|
|
HB2
|
B:PHE623
|
3.6
|
18.3
|
1.0
|
|
C
|
B:PHE623
|
3.6
|
17.1
|
1.0
|
|
H
|
B:TYR631
|
3.7
|
17.4
|
1.0
|
|
CB
|
B:PHE623
|
3.7
|
15.2
|
1.0
|
|
H
|
B:ASP626
|
3.8
|
23.6
|
1.0
|
|
HA
|
B:LEU630
|
3.8
|
18.2
|
1.0
|
|
C
|
B:VAL629
|
3.9
|
15.0
|
1.0
|
|
HB3
|
B:ASP626
|
3.9
|
25.2
|
1.0
|
|
HB2
|
B:ASN663
|
4.0
|
19.1
|
1.0
|
|
HA
|
B:GLU624
|
4.0
|
21.5
|
1.0
|
|
C
|
B:ASP626
|
4.1
|
18.5
|
1.0
|
|
CA
|
B:TYR662
|
4.2
|
16.6
|
1.0
|
|
HB3
|
B:TYR631
|
4.3
|
17.2
|
1.0
|
|
CA
|
B:PHE623
|
4.3
|
15.9
|
1.0
|
|
N
|
B:TYR631
|
4.4
|
14.5
|
1.0
|
|
HB
|
B:VAL629
|
4.4
|
18.1
|
1.0
|
|
N
|
B:ASN663
|
4.4
|
15.9
|
1.0
|
|
HB2
|
B:TYR631
|
4.4
|
17.2
|
1.0
|
|
HA
|
B:ASN663
|
4.5
|
18.4
|
1.0
|
|
N
|
B:ASP626
|
4.5
|
19.7
|
1.0
|
|
N
|
B:GLU624
|
4.5
|
16.6
|
1.0
|
|
H
|
B:VAL629
|
4.5
|
18.7
|
1.0
|
|
CA
|
B:LEU630
|
4.6
|
15.1
|
1.0
|
|
CA
|
B:GLU624
|
4.6
|
17.9
|
1.0
|
|
CA
|
B:ASP626
|
4.7
|
18.8
|
1.0
|
|
N
|
B:LEU630
|
4.7
|
15.0
|
1.0
|
|
C
|
B:GLU624
|
4.7
|
17.8
|
1.0
|
|
O
|
B:GLU624
|
4.7
|
18.3
|
1.0
|
|
HA
|
B:ASP627
|
4.7
|
22.7
|
1.0
|
|
CB
|
B:ASP626
|
4.7
|
21.0
|
1.0
|
|
CB
|
B:TYR631
|
4.8
|
14.3
|
1.0
|
|
CA
|
B:ASN663
|
4.8
|
15.4
|
1.0
|
|
HA
|
B:PHE623
|
4.8
|
19.1
|
1.0
|
|
HA3
|
B:GLY659
|
4.8
|
25.4
|
1.0
|
|
CB
|
B:ASN663
|
4.8
|
15.9
|
1.0
|
|
HG12
|
B:VAL629
|
4.8
|
18.6
|
1.0
|
|
HA
|
B:TYR662
|
4.8
|
19.9
|
1.0
|
|
O
|
B:GLY659
|
4.9
|
18.7
|
1.0
|
|
CA
|
B:VAL629
|
4.9
|
14.5
|
1.0
|
|
C
|
B:LEU630
|
4.9
|
15.1
|
1.0
|
|
HA2
|
B:GLY659
|
4.9
|
25.4
|
1.0
|
|
CG
|
B:TYR662
|
4.9
|
18.6
|
1.0
|
|
Reference:
Y.Hai,
D.W.Christianson.
Histone Deacetylase 6 Structure and Molecular Basis of Catalysis and Inhibition. Nat.Chem.Biol. V. 12 741 2016.
ISSN: ESSN 1552-4469
PubMed: 27454933
DOI: 10.1038/NCHEMBIO.2134
Page generated: Sun Dec 13 23:56:54 2020
|
