Potassium in PDB 8qa7: Crystal Structure of HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component.
Protein crystallography data
The structure of Crystal Structure of HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component., PDB code: 8qa7
was solved by
J.Sandmark,
M.Ek,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
66.63 /
1.47
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
75.39,
92.373,
96.19,
90,
90,
90
|
R / Rfree (%)
|
21.7 /
24
|
Other elements in 8qa7:
The structure of Crystal Structure of HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component. also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Crystal Structure of HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component.
(pdb code 8qa7). 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 HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component., PDB code: 8qa7:
Jump to Potassium binding site number:
1;
2;
3;
4;
Potassium binding site 1 out
of 4 in 8qa7
Go back to
Potassium Binding Sites List in 8qa7
Potassium binding site 1 out
of 4 in the Crystal Structure of HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component.
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 HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K801
b:21.1
occ:1.00
|
O
|
A:ASP612
|
2.6
|
16.2
|
1.0
|
OD1
|
A:ASP610
|
2.7
|
16.0
|
1.0
|
O
|
A:HIS614
|
2.8
|
16.3
|
1.0
|
O
|
A:LEU634
|
2.8
|
18.4
|
1.0
|
OG
|
A:SER633
|
2.8
|
17.8
|
1.0
|
O
|
A:ASP610
|
2.8
|
16.6
|
1.0
|
CG
|
A:ASP610
|
3.3
|
16.9
|
1.0
|
C
|
A:ASP610
|
3.5
|
16.7
|
1.0
|
C
|
A:ASP612
|
3.7
|
16.1
|
1.0
|
C
|
A:HIS614
|
3.7
|
16.6
|
1.0
|
C
|
A:LEU634
|
3.8
|
18.4
|
1.0
|
N
|
A:ASP612
|
3.9
|
16.9
|
1.0
|
CB
|
A:ASP610
|
3.9
|
16.4
|
1.0
|
OD2
|
A:ASP610
|
4.0
|
17.1
|
1.0
|
N
|
A:LEU634
|
4.0
|
17.8
|
1.0
|
CB
|
A:SER633
|
4.0
|
17.0
|
1.0
|
CB
|
A:HIS635
|
4.1
|
17.8
|
1.0
|
CA
|
A:ASP612
|
4.2
|
16.2
|
1.0
|
N
|
A:TRP611
|
4.2
|
16.0
|
1.0
|
C
|
A:TRP611
|
4.2
|
16.4
|
1.0
|
CA
|
A:HIS615
|
4.3
|
16.4
|
1.0
|
CA
|
A:ASP610
|
4.3
|
16.1
|
1.0
|
CB
|
A:ASP612
|
4.3
|
16.5
|
1.0
|
CA
|
A:SER633
|
4.3
|
17.6
|
1.0
|
CA
|
A:TRP611
|
4.3
|
16.5
|
1.0
|
ND1
|
A:HIS635
|
4.4
|
18.5
|
1.0
|
N
|
A:HIS615
|
4.4
|
15.9
|
1.0
|
N
|
A:GLY616
|
4.4
|
16.2
|
1.0
|
C
|
A:SER633
|
4.5
|
17.9
|
1.0
|
N
|
A:HIS614
|
4.5
|
16.4
|
1.0
|
CA
|
A:HIS635
|
4.5
|
17.5
|
1.0
|
CA
|
A:LEU634
|
4.6
|
18.8
|
1.0
|
N
|
A:HIS635
|
4.6
|
17.6
|
1.0
|
CG
|
A:HIS635
|
4.7
|
18.5
|
1.0
|
O
|
A:HOH909
|
4.7
|
18.7
|
1.0
|
C
|
A:HIS615
|
4.7
|
16.1
|
1.0
|
C
|
A:VAL613
|
4.7
|
16.6
|
1.0
|
CE1
|
A:HIS573
|
4.7
|
16.6
|
1.0
|
N
|
A:VAL613
|
4.7
|
15.7
|
1.0
|
CA
|
A:HIS614
|
4.7
|
16.1
|
1.0
|
OH
|
A:TYR631
|
4.8
|
18.4
|
1.0
|
ND1
|
A:HIS573
|
4.9
|
16.4
|
1.0
|
O
|
A:TRP611
|
5.0
|
17.3
|
1.0
|
|
Potassium binding site 2 out
of 4 in 8qa7
Go back to
Potassium Binding Sites List in 8qa7
Potassium binding site 2 out
of 4 in the Crystal Structure of HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component.
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 HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K802
b:43.0
occ:1.00
|
O
|
A:HOH920
|
2.7
|
23.0
|
1.0
|
O
|
A:PHE623
|
2.9
|
20.2
|
1.0
|
O
|
A:TYR662
|
2.9
|
22.6
|
1.0
|
O
|
A:HOH931
|
2.9
|
21.7
|
1.0
|
O
|
A:VAL629
|
2.9
|
22.6
|
1.0
|
O
|
A:ASP626
|
3.2
|
27.1
|
1.0
|
C
|
A:TYR662
|
3.6
|
22.0
|
1.0
|
C
|
A:PHE623
|
3.7
|
20.5
|
1.0
|
CB
|
A:PHE623
|
3.8
|
20.3
|
1.0
|
CB
|
A:TYR662
|
3.9
|
23.8
|
1.0
|
C
|
A:VAL629
|
4.1
|
21.1
|
1.0
|
N
|
A:ASN663
|
4.2
|
21.6
|
1.0
|
N
|
A:TYR631
|
4.3
|
17.8
|
1.0
|
CA
|
A:TYR662
|
4.3
|
23.2
|
1.0
|
C
|
A:ASP626
|
4.3
|
27.2
|
1.0
|
CA
|
A:PHE623
|
4.4
|
19.9
|
1.0
|
N
|
A:GLU624
|
4.5
|
21.8
|
1.0
|
CB
|
A:TYR631
|
4.5
|
17.4
|
1.0
|
CA
|
A:ASN663
|
4.5
|
21.4
|
1.0
|
CA
|
A:GLU624
|
4.5
|
24.8
|
1.0
|
CB
|
A:ASN663
|
4.6
|
21.3
|
1.0
|
CA
|
A:LEU630
|
4.7
|
19.7
|
1.0
|
O
|
A:GLU624
|
4.7
|
23.0
|
1.0
|
OD1
|
A:ASN663
|
4.7
|
21.3
|
1.0
|
N
|
A:ASP626
|
4.7
|
25.2
|
1.0
|
C
|
A:GLU624
|
4.7
|
24.4
|
1.0
|
O
|
A:GLY659
|
4.9
|
26.3
|
1.0
|
N
|
A:LEU630
|
4.9
|
20.2
|
1.0
|
C
|
A:LEU630
|
4.9
|
18.7
|
1.0
|
CA
|
A:ASP626
|
4.9
|
25.9
|
1.0
|
CB
|
A:ASP626
|
4.9
|
27.6
|
1.0
|
|
Potassium binding site 3 out
of 4 in 8qa7
Go back to
Potassium Binding Sites List in 8qa7
Potassium binding site 3 out
of 4 in the Crystal Structure of HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component.
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 HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K801
b:24.0
occ:1.00
|
O
|
B:ASP612
|
2.6
|
18.8
|
1.0
|
O
|
B:LEU634
|
2.7
|
19.7
|
1.0
|
OD1
|
B:ASP610
|
2.8
|
17.9
|
1.0
|
O
|
B:HIS614
|
2.8
|
18.9
|
1.0
|
O
|
B:ASP610
|
2.8
|
18.4
|
1.0
|
OG
|
B:SER633
|
2.9
|
19.2
|
1.0
|
CG
|
B:ASP610
|
3.3
|
18.6
|
1.0
|
C
|
B:ASP610
|
3.5
|
18.6
|
1.0
|
C
|
B:ASP612
|
3.6
|
18.4
|
1.0
|
C
|
B:HIS614
|
3.7
|
18.4
|
1.0
|
C
|
B:LEU634
|
3.7
|
19.8
|
1.0
|
CB
|
B:ASP610
|
3.8
|
18.5
|
1.0
|
N
|
B:ASP612
|
3.9
|
18.0
|
1.0
|
N
|
B:LEU634
|
4.0
|
18.8
|
1.0
|
OD2
|
B:ASP610
|
4.0
|
18.7
|
1.0
|
CB
|
B:SER633
|
4.0
|
19.1
|
1.0
|
CB
|
B:HIS635
|
4.1
|
20.2
|
1.0
|
CA
|
B:ASP612
|
4.2
|
17.6
|
1.0
|
N
|
B:TRP611
|
4.2
|
18.1
|
1.0
|
CA
|
B:HIS615
|
4.2
|
17.6
|
1.0
|
CA
|
B:ASP610
|
4.3
|
18.4
|
1.0
|
C
|
B:TRP611
|
4.3
|
18.5
|
1.0
|
CB
|
B:ASP612
|
4.3
|
18.3
|
1.0
|
CA
|
B:SER633
|
4.3
|
19.2
|
1.0
|
N
|
B:HIS615
|
4.3
|
17.8
|
1.0
|
ND1
|
B:HIS635
|
4.4
|
20.4
|
1.0
|
CA
|
B:TRP611
|
4.4
|
18.5
|
1.0
|
N
|
B:GLY616
|
4.4
|
17.6
|
1.0
|
C
|
B:SER633
|
4.5
|
20.2
|
1.0
|
CA
|
B:HIS635
|
4.5
|
19.8
|
1.0
|
N
|
B:HIS614
|
4.5
|
18.7
|
1.0
|
N
|
B:HIS635
|
4.5
|
19.6
|
1.0
|
CA
|
B:LEU634
|
4.5
|
20.1
|
1.0
|
O
|
B:HOH904
|
4.6
|
24.1
|
1.0
|
CG
|
B:HIS635
|
4.7
|
20.1
|
1.0
|
C
|
B:HIS615
|
4.7
|
17.5
|
1.0
|
C
|
B:VAL613
|
4.7
|
19.3
|
1.0
|
N
|
B:VAL613
|
4.7
|
18.6
|
1.0
|
OH
|
B:TYR631
|
4.8
|
18.1
|
1.0
|
CA
|
B:HIS614
|
4.8
|
19.0
|
1.0
|
CE1
|
B:HIS573
|
4.8
|
17.4
|
1.0
|
ND1
|
B:HIS573
|
4.9
|
17.3
|
1.0
|
O
|
B:TRP611
|
5.0
|
19.8
|
1.0
|
|
Potassium binding site 4 out
of 4 in 8qa7
Go back to
Potassium Binding Sites List in 8qa7
Potassium binding site 4 out
of 4 in the Crystal Structure of HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component.
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 HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K802
b:41.6
occ:1.00
|
O
|
B:HOH909
|
2.8
|
23.0
|
1.0
|
O
|
B:VAL629
|
2.8
|
22.9
|
1.0
|
O
|
B:PHE623
|
2.8
|
20.5
|
1.0
|
O
|
B:HOH962
|
2.9
|
21.1
|
1.0
|
O
|
B:TYR662
|
2.9
|
23.4
|
1.0
|
O
|
B:ASP626
|
3.1
|
27.3
|
1.0
|
C
|
B:TYR662
|
3.7
|
23.9
|
1.0
|
C
|
B:PHE623
|
3.7
|
20.4
|
1.0
|
CB
|
B:PHE623
|
3.8
|
20.3
|
1.0
|
CB
|
B:TYR662
|
3.9
|
25.0
|
1.0
|
C
|
B:VAL629
|
4.0
|
21.6
|
1.0
|
C
|
B:ASP626
|
4.3
|
26.7
|
1.0
|
N
|
B:TYR631
|
4.3
|
19.4
|
1.0
|
N
|
B:ASN663
|
4.3
|
22.0
|
1.0
|
CA
|
B:PHE623
|
4.4
|
20.2
|
1.0
|
CA
|
B:TYR662
|
4.4
|
24.2
|
1.0
|
N
|
B:GLU624
|
4.5
|
22.0
|
1.0
|
CB
|
B:TYR631
|
4.6
|
18.4
|
1.0
|
CA
|
B:GLU624
|
4.6
|
23.1
|
1.0
|
CA
|
B:LEU630
|
4.6
|
21.1
|
1.0
|
CA
|
B:ASN663
|
4.7
|
22.4
|
1.0
|
CB
|
B:ASN663
|
4.7
|
22.0
|
1.0
|
N
|
B:ASP626
|
4.7
|
25.2
|
1.0
|
O
|
B:GLU624
|
4.7
|
21.7
|
1.0
|
C
|
B:GLU624
|
4.8
|
23.3
|
1.0
|
N
|
B:LEU630
|
4.8
|
20.6
|
1.0
|
OD1
|
B:ASN663
|
4.8
|
22.2
|
1.0
|
CA
|
B:ASP626
|
4.9
|
26.5
|
1.0
|
C
|
B:LEU630
|
4.9
|
20.5
|
1.0
|
O
|
B:GLY659
|
4.9
|
27.6
|
1.0
|
CB
|
B:ASP626
|
4.9
|
28.8
|
1.0
|
|
Reference:
J.Sandmark,
M.Ek.
Crystal Structure of HDAC6 Catalytic Domain 2 From Zebrafish in Complex with Buffer Component. To Be Published.
Page generated: Sat Sep 28 22:14:29 2024
|