Potassium in PDB 5d1b: Crystal Structure of G117E HDAC8 in Complex with Tsa
Enzymatic activity of Crystal Structure of G117E HDAC8 in Complex with Tsa
All present enzymatic activity of Crystal Structure of G117E HDAC8 in Complex with Tsa:
3.5.1.98;
Protein crystallography data
The structure of Crystal Structure of G117E HDAC8 in Complex with Tsa, PDB code: 5d1b
was solved by
C.Decroos,
N.H.Christianson,
L.E.Gullett,
C.M.Bowman,
K.E.Christianson,
M.A.Deardorff,
D.W.Christianson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.80 /
2.90
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
52.197,
83.031,
98.460,
90.00,
102.77,
90.00
|
R / Rfree (%)
|
19.3 /
22.8
|
Other elements in 5d1b:
The structure of Crystal Structure of G117E HDAC8 in Complex with Tsa also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Crystal Structure of G117E HDAC8 in Complex with Tsa
(pdb code 5d1b). 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 G117E HDAC8 in Complex with Tsa, PDB code: 5d1b:
Jump to Potassium binding site number:
1;
2;
3;
4;
Potassium binding site 1 out
of 4 in 5d1b
Go back to
Potassium Binding Sites List in 5d1b
Potassium binding site 1 out
of 4 in the Crystal Structure of G117E HDAC8 in Complex with Tsa
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 G117E HDAC8 in Complex with Tsa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K402
b:21.2
occ:1.00
|
OD1
|
A:ASP176
|
2.7
|
23.2
|
1.0
|
O
|
A:LEU200
|
2.8
|
21.6
|
1.0
|
O
|
A:ASP178
|
2.8
|
24.6
|
1.0
|
O
|
A:HIS180
|
2.8
|
24.3
|
1.0
|
OG
|
A:SER199
|
2.9
|
21.8
|
1.0
|
O
|
A:ASP176
|
2.9
|
22.1
|
1.0
|
CG
|
A:ASP176
|
3.4
|
24.5
|
1.0
|
C
|
A:LEU200
|
3.5
|
22.5
|
1.0
|
C
|
A:ASP176
|
3.5
|
22.7
|
1.0
|
CB
|
A:HIS201
|
3.6
|
23.0
|
1.0
|
N
|
A:ASP178
|
3.6
|
23.5
|
1.0
|
CB
|
A:ASP176
|
3.7
|
22.8
|
1.0
|
C
|
A:ASP178
|
3.7
|
21.9
|
1.0
|
C
|
A:HIS180
|
3.8
|
24.0
|
1.0
|
N
|
A:LEU200
|
3.9
|
24.1
|
1.0
|
CA
|
A:ASP178
|
4.0
|
22.1
|
1.0
|
CB
|
A:SER199
|
4.1
|
23.5
|
1.0
|
CA
|
A:HIS201
|
4.1
|
24.2
|
1.0
|
ND1
|
A:HIS201
|
4.1
|
26.9
|
1.0
|
N
|
A:HIS201
|
4.2
|
23.2
|
1.0
|
C
|
A:LEU177
|
4.2
|
23.6
|
1.0
|
CB
|
A:ASP178
|
4.2
|
21.5
|
1.0
|
N
|
A:LEU177
|
4.2
|
23.1
|
1.0
|
CA
|
A:ASP176
|
4.2
|
23.0
|
1.0
|
CA
|
A:HIS181
|
4.3
|
24.6
|
1.0
|
N
|
A:GLY182
|
4.3
|
24.7
|
1.0
|
C
|
A:SER199
|
4.3
|
25.2
|
1.0
|
CG
|
A:HIS201
|
4.3
|
26.1
|
1.0
|
CA
|
A:SER199
|
4.3
|
25.2
|
1.0
|
CA
|
A:LEU200
|
4.4
|
23.2
|
1.0
|
CA
|
A:LEU177
|
4.4
|
23.5
|
1.0
|
N
|
A:HIS181
|
4.4
|
24.4
|
1.0
|
OD2
|
A:ASP176
|
4.5
|
24.8
|
1.0
|
N
|
A:HIS180
|
4.6
|
21.5
|
1.0
|
C
|
A:HIS181
|
4.7
|
24.9
|
1.0
|
C
|
A:LEU179
|
4.7
|
21.6
|
1.0
|
N
|
A:LEU179
|
4.8
|
21.6
|
1.0
|
CE1
|
A:HIS142
|
4.8
|
23.8
|
1.0
|
CA
|
A:HIS180
|
4.8
|
23.2
|
1.0
|
O
|
A:LEU177
|
5.0
|
26.0
|
1.0
|
O
|
A:LEU179
|
5.0
|
21.9
|
1.0
|
|
Potassium binding site 2 out
of 4 in 5d1b
Go back to
Potassium Binding Sites List in 5d1b
Potassium binding site 2 out
of 4 in the Crystal Structure of G117E HDAC8 in Complex with Tsa
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 G117E HDAC8 in Complex with Tsa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K403
b:35.2
occ:1.00
|
O
|
A:PHE189
|
2.7
|
29.5
|
1.0
|
O
|
A:VAL195
|
2.7
|
30.6
|
1.0
|
O
|
A:TYR225
|
2.8
|
31.8
|
1.0
|
O
|
A:THR192
|
3.1
|
31.3
|
1.0
|
C
|
A:TYR225
|
3.5
|
32.1
|
1.0
|
CB
|
A:TYR225
|
3.6
|
33.0
|
1.0
|
C
|
A:PHE189
|
3.7
|
29.7
|
1.0
|
OG
|
A:SER226
|
3.8
|
28.6
|
1.0
|
C
|
A:VAL195
|
3.9
|
30.3
|
1.0
|
O
|
A:GLY222
|
4.1
|
34.5
|
1.0
|
CA
|
A:TYR225
|
4.2
|
33.2
|
1.0
|
N
|
A:SER226
|
4.3
|
29.5
|
1.0
|
CA
|
A:MET196
|
4.3
|
31.2
|
1.0
|
C
|
A:THR192
|
4.3
|
30.4
|
1.0
|
CA
|
A:SER190
|
4.3
|
30.6
|
1.0
|
CB
|
A:PHE189
|
4.4
|
27.1
|
1.0
|
N
|
A:SER190
|
4.5
|
27.8
|
1.0
|
N
|
A:THR197
|
4.5
|
28.4
|
1.0
|
N
|
A:MET196
|
4.6
|
30.7
|
1.0
|
C
|
A:SER190
|
4.6
|
30.6
|
1.0
|
N
|
A:THR192
|
4.7
|
29.3
|
1.0
|
CA
|
A:SER226
|
4.7
|
29.1
|
1.0
|
CA
|
A:PHE189
|
4.7
|
29.7
|
1.0
|
CG2
|
A:THR192
|
4.7
|
33.3
|
1.0
|
OG1
|
A:THR197
|
4.8
|
27.4
|
1.0
|
CA
|
A:GLY222
|
4.8
|
34.5
|
1.0
|
CB
|
A:SER226
|
4.8
|
29.3
|
1.0
|
CG
|
A:TYR225
|
4.9
|
33.6
|
1.0
|
O
|
A:SER190
|
4.9
|
30.9
|
1.0
|
C
|
A:GLY222
|
4.9
|
35.2
|
1.0
|
C
|
A:MET196
|
4.9
|
30.2
|
1.0
|
|
Potassium binding site 3 out
of 4 in 5d1b
Go back to
Potassium Binding Sites List in 5d1b
Potassium binding site 3 out
of 4 in the Crystal Structure of G117E HDAC8 in Complex with Tsa
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 G117E HDAC8 in Complex with Tsa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K402
b:20.5
occ:1.00
|
OD1
|
B:ASP176
|
2.6
|
21.8
|
1.0
|
O
|
B:ASP178
|
2.7
|
24.8
|
1.0
|
O
|
B:LEU200
|
2.8
|
21.1
|
1.0
|
O
|
B:ASP176
|
2.8
|
20.7
|
1.0
|
O
|
B:HIS180
|
3.1
|
23.0
|
1.0
|
OG
|
B:SER199
|
3.1
|
19.9
|
1.0
|
C
|
B:LEU200
|
3.3
|
21.9
|
1.0
|
C
|
B:ASP176
|
3.4
|
21.3
|
1.0
|
N
|
B:ASP178
|
3.4
|
23.7
|
1.0
|
CG
|
B:ASP176
|
3.5
|
23.1
|
1.0
|
CB
|
B:HIS201
|
3.6
|
20.3
|
1.0
|
C
|
B:ASP178
|
3.6
|
22.1
|
1.0
|
N
|
B:LEU200
|
3.6
|
23.5
|
1.0
|
CB
|
B:ASP176
|
3.7
|
21.4
|
1.0
|
CA
|
B:ASP178
|
3.9
|
22.3
|
1.0
|
C
|
B:LEU177
|
3.9
|
21.8
|
1.0
|
N
|
B:HIS201
|
4.0
|
20.5
|
1.0
|
N
|
B:LEU177
|
4.0
|
21.3
|
1.0
|
CA
|
B:HIS201
|
4.0
|
21.6
|
1.0
|
C
|
B:HIS180
|
4.1
|
22.7
|
1.0
|
CA
|
B:LEU177
|
4.1
|
21.8
|
1.0
|
CA
|
B:LEU200
|
4.1
|
22.6
|
1.0
|
CB
|
B:ASP178
|
4.2
|
21.7
|
1.0
|
CA
|
B:ASP176
|
4.2
|
21.6
|
1.0
|
ND1
|
B:HIS201
|
4.2
|
24.3
|
1.0
|
CB
|
B:SER199
|
4.2
|
21.7
|
1.0
|
C
|
B:SER199
|
4.2
|
23.4
|
1.0
|
CA
|
B:SER199
|
4.3
|
23.4
|
1.0
|
CG
|
B:HIS201
|
4.4
|
23.4
|
1.0
|
CA
|
B:HIS181
|
4.5
|
21.7
|
1.0
|
OD2
|
B:ASP176
|
4.6
|
23.4
|
1.0
|
N
|
B:GLY182
|
4.6
|
23.0
|
1.0
|
N
|
B:HIS181
|
4.7
|
21.5
|
1.0
|
N
|
B:LEU179
|
4.8
|
20.6
|
1.0
|
O
|
B:LEU177
|
4.8
|
24.2
|
1.0
|
C
|
B:LEU179
|
4.8
|
20.5
|
1.0
|
N
|
B:HIS180
|
4.8
|
20.2
|
1.0
|
O
|
B:LEU179
|
4.9
|
20.8
|
1.0
|
|
Potassium binding site 4 out
of 4 in 5d1b
Go back to
Potassium Binding Sites List in 5d1b
Potassium binding site 4 out
of 4 in the Crystal Structure of G117E HDAC8 in Complex with Tsa
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 G117E HDAC8 in Complex with Tsa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K403
b:29.7
occ:1.00
|
O
|
B:PHE189
|
2.6
|
25.2
|
1.0
|
O
|
B:VAL195
|
2.7
|
24.7
|
1.0
|
O
|
B:TYR225
|
2.8
|
27.4
|
1.0
|
O
|
B:HOH502
|
2.9
|
24.9
|
1.0
|
O
|
B:HOH501
|
3.0
|
27.4
|
1.0
|
O
|
B:THR192
|
3.3
|
28.3
|
1.0
|
C
|
B:TYR225
|
3.5
|
27.6
|
1.0
|
CB
|
B:TYR225
|
3.5
|
28.5
|
1.0
|
OG
|
B:SER226
|
3.6
|
26.4
|
1.0
|
C
|
B:PHE189
|
3.7
|
25.4
|
1.0
|
C
|
B:VAL195
|
3.9
|
24.4
|
1.0
|
CA
|
B:TYR225
|
4.1
|
28.8
|
1.0
|
N
|
B:SER226
|
4.2
|
27.3
|
1.0
|
CA
|
B:MET196
|
4.3
|
24.6
|
1.0
|
O
|
B:GLY222
|
4.3
|
29.6
|
1.0
|
CB
|
B:PHE189
|
4.3
|
22.8
|
1.0
|
CA
|
B:SER190
|
4.3
|
27.9
|
1.0
|
N
|
B:THR197
|
4.4
|
24.7
|
1.0
|
C
|
B:THR192
|
4.4
|
27.4
|
1.0
|
N
|
B:SER190
|
4.5
|
25.2
|
1.0
|
N
|
B:MET196
|
4.6
|
24.2
|
1.0
|
CA
|
B:SER226
|
4.7
|
26.9
|
1.0
|
CA
|
B:PHE189
|
4.7
|
25.4
|
1.0
|
CB
|
B:SER226
|
4.7
|
27.1
|
1.0
|
C
|
B:SER190
|
4.7
|
28.0
|
1.0
|
OG1
|
B:THR197
|
4.7
|
23.7
|
1.0
|
CG
|
B:TYR225
|
4.9
|
29.2
|
1.0
|
OG1
|
B:THR192
|
4.9
|
29.5
|
1.0
|
C
|
B:MET196
|
4.9
|
23.6
|
1.0
|
N
|
B:THR192
|
4.9
|
26.3
|
1.0
|
CG2
|
B:THR197
|
5.0
|
23.9
|
1.0
|
|
Reference:
C.Decroos,
N.H.Christianson,
L.E.Gullett,
C.M.Bowman,
K.E.Christianson,
M.A.Deardorff,
D.W.Christianson.
Biochemical and Structural Characterization of HDAC8 Mutants Associated with Cornelia De Lange Syndrome Spectrum Disorders. Biochemistry V. 54 6501 2015.
ISSN: ISSN 0006-2960
PubMed: 26463496
DOI: 10.1021/ACS.BIOCHEM.5B00881
Page generated: Mon Aug 12 13:09:20 2024
|