Potassium in PDB 8eqi: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Cyclopeptide DES4.2.0
Protein crystallography data
The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Cyclopeptide DES4.2.0, PDB code: 8eqi
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)
|
78.89 /
2.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.45,
92.03,
153.2,
90,
90,
90
|
R / Rfree (%)
|
23.6 /
27.2
|
Other elements in 8eqi:
The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Cyclopeptide DES4.2.0 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 Complexed with Cyclopeptide DES4.2.0
(pdb code 8eqi). 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 Complexed with Cyclopeptide DES4.2.0, PDB code: 8eqi:
Jump to Potassium binding site number:
1;
2;
3;
4;
Potassium binding site 1 out
of 4 in 8eqi
Go back to
Potassium Binding Sites List in 8eqi
Potassium binding site 1 out
of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Cyclopeptide DES4.2.0
![](/pictures/K/pdb/eq/8eqi-K-sphere_01.jpg) Mono view
![](/pictures/K/pdb/eq/8eqi-K-sphere_01_stereo.jpg) 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 Complexed with Cyclopeptide DES4.2.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K802
b:10.8
occ:1.00
|
O
|
A:ASP612
|
2.5
|
7.7
|
1.0
|
O
|
A:HIS614
|
2.7
|
6.8
|
1.0
|
OD1
|
A:ASP610
|
2.7
|
10.5
|
1.0
|
OG
|
A:SER633
|
2.8
|
11.8
|
1.0
|
O
|
A:LEU634
|
2.8
|
11.6
|
1.0
|
O
|
A:ASP610
|
2.8
|
11.2
|
1.0
|
CG
|
A:ASP610
|
3.2
|
8.9
|
1.0
|
C
|
A:ASP610
|
3.5
|
10.1
|
1.0
|
C
|
A:ASP612
|
3.6
|
7.8
|
1.0
|
C
|
A:LEU634
|
3.7
|
15.7
|
1.0
|
C
|
A:HIS614
|
3.7
|
10.9
|
1.0
|
N
|
A:ASP612
|
3.8
|
6.4
|
1.0
|
CB
|
A:ASP610
|
3.8
|
9.7
|
1.0
|
OD2
|
A:ASP610
|
3.8
|
9.2
|
1.0
|
CB
|
A:SER633
|
3.9
|
12.1
|
1.0
|
N
|
A:LEU634
|
3.9
|
13.0
|
1.0
|
CB
|
A:HIS635
|
4.0
|
11.4
|
1.0
|
CA
|
A:ASP612
|
4.1
|
7.6
|
1.0
|
C
|
A:TRP611
|
4.2
|
10.2
|
1.0
|
N
|
A:TRP611
|
4.2
|
8.7
|
1.0
|
CB
|
A:ASP612
|
4.2
|
6.8
|
1.0
|
CA
|
A:HIS615
|
4.3
|
11.5
|
1.0
|
CA
|
A:ASP610
|
4.3
|
10.2
|
1.0
|
CA
|
A:SER633
|
4.3
|
12.1
|
1.0
|
CA
|
A:TRP611
|
4.3
|
11.4
|
1.0
|
ND1
|
A:HIS635
|
4.3
|
11.3
|
1.0
|
O
|
A:HOH901
|
4.3
|
9.9
|
1.0
|
N
|
A:HIS615
|
4.4
|
8.4
|
1.0
|
N
|
A:GLY616
|
4.4
|
11.8
|
1.0
|
C
|
A:SER633
|
4.5
|
11.1
|
1.0
|
N
|
A:HIS614
|
4.5
|
9.2
|
1.0
|
CA
|
A:HIS635
|
4.5
|
9.0
|
1.0
|
CA
|
A:LEU634
|
4.5
|
12.6
|
1.0
|
N
|
A:HIS635
|
4.5
|
11.8
|
1.0
|
CG
|
A:HIS635
|
4.6
|
12.3
|
1.0
|
C
|
A:VAL613
|
4.7
|
9.2
|
1.0
|
N
|
A:VAL613
|
4.7
|
10.5
|
1.0
|
CA
|
A:HIS614
|
4.8
|
8.5
|
1.0
|
C
|
A:HIS615
|
4.8
|
10.5
|
1.0
|
OH
|
A:TYR631
|
4.8
|
10.4
|
1.0
|
O
|
A:TRP611
|
4.9
|
9.1
|
1.0
|
ND1
|
A:HIS573
|
4.9
|
7.8
|
1.0
|
CE1
|
A:HIS573
|
5.0
|
6.8
|
1.0
|
|
Potassium binding site 2 out
of 4 in 8eqi
Go back to
Potassium Binding Sites List in 8eqi
Potassium binding site 2 out
of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Cyclopeptide DES4.2.0
![](/pictures/K/pdb/eq/8eqi-K-sphere_02.jpg) Mono view
![](/pictures/K/pdb/eq/8eqi-K-sphere_02_stereo.jpg) 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 Complexed with Cyclopeptide DES4.2.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K803
b:16.7
occ:1.00
|
O
|
A:PHE623
|
2.5
|
12.1
|
1.0
|
O
|
A:HOH996
|
2.7
|
12.4
|
1.0
|
O
|
A:VAL629
|
2.8
|
13.6
|
1.0
|
O
|
A:ASP626
|
2.9
|
14.9
|
1.0
|
O
|
A:TYR662
|
3.0
|
14.8
|
1.0
|
O
|
A:HOH983
|
3.0
|
13.5
|
1.0
|
C
|
A:PHE623
|
3.6
|
11.6
|
1.0
|
C
|
A:TYR662
|
3.6
|
13.9
|
1.0
|
CB
|
A:TYR662
|
3.7
|
9.6
|
1.0
|
CB
|
A:PHE623
|
3.7
|
11.8
|
1.0
|
C
|
A:VAL629
|
4.0
|
8.0
|
1.0
|
C
|
A:ASP626
|
4.0
|
16.5
|
1.0
|
CA
|
A:PHE623
|
4.3
|
14.7
|
1.0
|
N
|
A:TYR631
|
4.3
|
13.0
|
1.0
|
CA
|
A:TYR662
|
4.3
|
19.1
|
1.0
|
N
|
A:ASN663
|
4.4
|
16.1
|
1.0
|
CB
|
A:ASP626
|
4.5
|
12.4
|
1.0
|
N
|
A:ASP626
|
4.5
|
19.0
|
1.0
|
N
|
A:GLU624
|
4.5
|
11.5
|
1.0
|
CA
|
A:ASP626
|
4.5
|
16.0
|
1.0
|
CA
|
A:LEU630
|
4.6
|
16.9
|
1.0
|
CB
|
A:ASN663
|
4.6
|
13.9
|
1.0
|
CA
|
A:GLU624
|
4.6
|
13.4
|
1.0
|
CB
|
A:TYR631
|
4.6
|
10.1
|
1.0
|
CA
|
A:ASN663
|
4.6
|
13.5
|
1.0
|
O
|
A:GLU624
|
4.7
|
20.3
|
1.0
|
N
|
A:LEU630
|
4.7
|
12.6
|
1.0
|
C
|
A:GLU624
|
4.8
|
16.5
|
1.0
|
C
|
A:LEU630
|
4.9
|
12.1
|
1.0
|
O
|
A:GLY659
|
5.0
|
16.9
|
1.0
|
|
Potassium binding site 3 out
of 4 in 8eqi
Go back to
Potassium Binding Sites List in 8eqi
Potassium binding site 3 out
of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Cyclopeptide DES4.2.0
![](/pictures/K/pdb/eq/8eqi-K-sphere_03.jpg) Mono view
![](/pictures/K/pdb/eq/8eqi-K-sphere_03_stereo.jpg) 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 Complexed with Cyclopeptide DES4.2.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K802
b:11.8
occ:1.00
|
O
|
B:ASP612
|
2.5
|
10.3
|
1.0
|
O
|
B:ASP610
|
2.8
|
11.6
|
1.0
|
OD1
|
B:ASP610
|
2.8
|
11.1
|
1.0
|
O
|
B:HIS614
|
2.8
|
8.2
|
1.0
|
O
|
B:LEU634
|
2.8
|
11.2
|
1.0
|
OG
|
B:SER633
|
2.9
|
11.7
|
1.0
|
CG
|
B:ASP610
|
3.2
|
8.4
|
1.0
|
C
|
B:ASP610
|
3.5
|
11.5
|
1.0
|
C
|
B:ASP612
|
3.5
|
9.7
|
1.0
|
C
|
B:HIS614
|
3.7
|
10.9
|
1.0
|
CB
|
B:ASP610
|
3.8
|
9.6
|
1.0
|
C
|
B:LEU634
|
3.8
|
16.3
|
1.0
|
N
|
B:ASP612
|
3.8
|
8.1
|
1.0
|
OD2
|
B:ASP610
|
3.9
|
11.0
|
1.0
|
CB
|
B:HIS635
|
3.9
|
14.1
|
1.0
|
CB
|
B:SER633
|
4.0
|
14.2
|
1.0
|
N
|
B:LEU634
|
4.0
|
13.8
|
1.0
|
CA
|
B:ASP612
|
4.0
|
8.5
|
1.0
|
CB
|
B:ASP612
|
4.1
|
9.3
|
1.0
|
C
|
B:TRP611
|
4.1
|
10.3
|
1.0
|
N
|
B:TRP611
|
4.2
|
10.4
|
1.0
|
CA
|
B:HIS615
|
4.2
|
13.6
|
1.0
|
CA
|
B:ASP610
|
4.2
|
7.7
|
1.0
|
CA
|
B:TRP611
|
4.3
|
10.5
|
1.0
|
ND1
|
B:HIS635
|
4.3
|
13.3
|
1.0
|
CA
|
B:SER633
|
4.3
|
11.7
|
1.0
|
N
|
B:HIS615
|
4.3
|
9.5
|
1.0
|
N
|
B:GLY616
|
4.4
|
12.5
|
1.0
|
N
|
B:HIS614
|
4.4
|
9.5
|
1.0
|
O
|
B:HOH908
|
4.4
|
12.3
|
1.0
|
C
|
B:SER633
|
4.5
|
14.2
|
1.0
|
CA
|
B:HIS635
|
4.5
|
11.0
|
1.0
|
CA
|
B:LEU634
|
4.5
|
12.7
|
1.0
|
N
|
B:HIS635
|
4.6
|
13.1
|
1.0
|
CG
|
B:HIS635
|
4.6
|
13.8
|
1.0
|
C
|
B:VAL613
|
4.7
|
10.4
|
1.0
|
N
|
B:VAL613
|
4.7
|
11.0
|
1.0
|
CA
|
B:HIS614
|
4.7
|
9.7
|
1.0
|
C
|
B:HIS615
|
4.7
|
11.2
|
1.0
|
OH
|
B:TYR631
|
4.7
|
11.9
|
1.0
|
O
|
B:TRP611
|
4.9
|
10.3
|
1.0
|
CE1
|
B:HIS573
|
4.9
|
8.9
|
1.0
|
ND1
|
B:HIS573
|
4.9
|
8.0
|
1.0
|
|
Potassium binding site 4 out
of 4 in 8eqi
Go back to
Potassium Binding Sites List in 8eqi
Potassium binding site 4 out
of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Cyclopeptide DES4.2.0
![](/pictures/K/pdb/eq/8eqi-K-sphere_04.jpg) Mono view
![](/pictures/K/pdb/eq/8eqi-K-sphere_04_stereo.jpg) 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 Complexed with Cyclopeptide DES4.2.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K803
b:16.3
occ:1.00
|
O
|
B:PHE623
|
2.6
|
15.1
|
1.0
|
O
|
B:VAL629
|
2.7
|
13.9
|
1.0
|
O
|
B:HOH934
|
2.8
|
13.6
|
1.0
|
O
|
B:TYR662
|
2.8
|
16.2
|
1.0
|
O
|
B:ASP626
|
2.9
|
18.5
|
1.0
|
O
|
B:HOH926
|
3.2
|
12.9
|
1.0
|
C
|
B:TYR662
|
3.6
|
19.1
|
1.0
|
C
|
B:PHE623
|
3.6
|
12.6
|
1.0
|
CB
|
B:TYR662
|
3.7
|
9.9
|
1.0
|
CB
|
B:PHE623
|
3.7
|
8.6
|
1.0
|
C
|
B:VAL629
|
3.9
|
11.7
|
1.0
|
C
|
B:ASP626
|
4.0
|
19.0
|
1.0
|
CA
|
B:TYR662
|
4.2
|
14.8
|
1.0
|
N
|
B:TYR631
|
4.2
|
13.7
|
1.0
|
CA
|
B:PHE623
|
4.3
|
14.7
|
1.0
|
N
|
B:ASN663
|
4.4
|
15.6
|
1.0
|
N
|
B:ASP626
|
4.5
|
13.2
|
1.0
|
CA
|
B:LEU630
|
4.5
|
17.4
|
1.0
|
N
|
B:GLU624
|
4.5
|
11.4
|
1.0
|
CB
|
B:ASP626
|
4.5
|
16.3
|
1.0
|
CA
|
B:ASP626
|
4.6
|
14.7
|
1.0
|
CA
|
B:GLU624
|
4.6
|
15.1
|
1.0
|
CB
|
B:TYR631
|
4.6
|
12.0
|
1.0
|
N
|
B:LEU630
|
4.6
|
13.9
|
1.0
|
CB
|
B:ASN663
|
4.7
|
16.7
|
1.0
|
CA
|
B:ASN663
|
4.7
|
14.0
|
1.0
|
O
|
B:GLU624
|
4.7
|
18.3
|
1.0
|
C
|
B:GLU624
|
4.7
|
16.0
|
1.0
|
C
|
B:LEU630
|
4.8
|
13.8
|
1.0
|
CA
|
B:VAL629
|
5.0
|
12.1
|
1.0
|
O
|
B:GLY659
|
5.0
|
18.3
|
1.0
|
CG
|
B:PHE623
|
5.0
|
11.2
|
1.0
|
|
Reference:
P.R.Watson,
S.Gupta,
P.Hosseinzadeh,
B.P.Brown,
D.Baker,
D.W.Christianson.
Macrocyclic Octapeptide Binding and Inferences on Protein Substrate Binding to Histone Deacetylase 6. Acs Chem.Biol. 2023.
ISSN: ESSN 1554-8937
PubMed: 37027789
DOI: 10.1021/ACSCHEMBIO.3C00113
Page generated: Mon Aug 12 23:36:41 2024
|