Potassium in PDB 5hdk: Crystal Structure of Heat Shock Factor 2-Dbd
Protein crystallography data
The structure of Crystal Structure of Heat Shock Factor 2-Dbd, PDB code: 5hdk
was solved by
H.Feng,
W.Liu,
D.C.Wang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
38.32 /
1.32
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
65.660,
67.260,
93.250,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15.3 /
17.4
|
Other elements in 5hdk:
The structure of Crystal Structure of Heat Shock Factor 2-Dbd also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Crystal Structure of Heat Shock Factor 2-Dbd
(pdb code 5hdk). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the
Crystal Structure of Heat Shock Factor 2-Dbd, PDB code: 5hdk:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
Potassium binding site 1 out
of 6 in 5hdk
Go back to
Potassium Binding Sites List in 5hdk
Potassium binding site 1 out
of 6 in the Crystal Structure of Heat Shock Factor 2-Dbd
![](/pictures/K/pdb/hd/5hdk-K-sphere_01.jpg) Mono view
![](/pictures/K/pdb/hd/5hdk-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 Heat Shock Factor 2-Dbd within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K201
b:17.4
occ:1.00
|
O
|
A:GLU20
|
2.6
|
24.4
|
1.0
|
O
|
A:ILE27
|
2.7
|
15.6
|
1.0
|
OG1
|
A:THR23
|
2.7
|
19.3
|
1.0
|
OD1
|
A:ASN24
|
2.7
|
22.9
|
1.0
|
O
|
A:VAL18
|
2.7
|
16.3
|
1.0
|
O
|
A:LEU17
|
3.0
|
16.5
|
1.0
|
C
|
A:VAL18
|
3.4
|
16.2
|
1.0
|
N
|
A:ASN24
|
3.5
|
17.1
|
1.0
|
C
|
A:THR23
|
3.6
|
17.5
|
1.0
|
C
|
A:GLU20
|
3.7
|
22.1
|
1.0
|
CA
|
A:VAL18
|
3.8
|
14.3
|
1.0
|
CG
|
A:ASN24
|
3.8
|
21.4
|
1.0
|
CA
|
A:ASN24
|
3.8
|
19.4
|
1.0
|
C
|
A:ILE27
|
3.9
|
14.3
|
1.0
|
CB
|
A:THR23
|
3.9
|
19.5
|
1.0
|
O
|
A:HOH347
|
3.9
|
22.4
|
1.0
|
O
|
A:THR23
|
3.9
|
17.6
|
1.0
|
N
|
A:GLU20
|
4.0
|
18.3
|
1.0
|
C
|
A:LEU17
|
4.1
|
15.1
|
1.0
|
CA
|
A:THR23
|
4.1
|
18.6
|
1.0
|
CG2
|
A:ILE27
|
4.3
|
15.5
|
1.0
|
N
|
A:THR23
|
4.3
|
19.9
|
1.0
|
CA
|
A:GLU20
|
4.3
|
21.6
|
1.0
|
C
|
A:GLU19
|
4.4
|
19.0
|
1.0
|
N
|
A:GLU19
|
4.4
|
16.0
|
1.0
|
CA
|
A:THR28
|
4.5
|
15.5
|
1.0
|
N
|
A:VAL18
|
4.5
|
13.6
|
1.0
|
CB
|
A:ASN24
|
4.5
|
20.9
|
1.0
|
N
|
A:THR28
|
4.6
|
15.1
|
1.0
|
CB
|
A:GLU20
|
4.6
|
24.6
|
1.0
|
N
|
A:THR21
|
4.7
|
24.0
|
1.0
|
O
|
A:GLU19
|
4.8
|
23.6
|
1.0
|
CA
|
A:THR21
|
4.9
|
23.6
|
1.0
|
ND2
|
A:ASN24
|
4.9
|
22.4
|
1.0
|
CA
|
A:GLU19
|
4.9
|
17.5
|
1.0
|
O
|
A:THR21
|
4.9
|
24.9
|
1.0
|
CA
|
A:ILE27
|
4.9
|
13.9
|
1.0
|
C
|
A:THR21
|
4.9
|
22.9
|
1.0
|
|
Potassium binding site 2 out
of 6 in 5hdk
Go back to
Potassium Binding Sites List in 5hdk
Potassium binding site 2 out
of 6 in the Crystal Structure of Heat Shock Factor 2-Dbd
![](/pictures/K/pdb/hd/5hdk-K-sphere_02.jpg) Mono view
![](/pictures/K/pdb/hd/5hdk-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 Heat Shock Factor 2-Dbd within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K201
b:11.6
occ:1.00
|
O
|
B:GLU20
|
2.6
|
15.9
|
1.0
|
OG1
|
B:THR23
|
2.7
|
11.9
|
0.7
|
OD1
|
B:ASN24
|
2.7
|
12.6
|
1.0
|
O
|
B:ILE27
|
2.7
|
11.4
|
1.0
|
O
|
B:VAL18
|
2.7
|
12.4
|
1.0
|
O
|
B:LEU17
|
2.8
|
12.5
|
1.0
|
OG1
|
B:THR23
|
2.9
|
15.0
|
0.3
|
C
|
B:VAL18
|
3.4
|
12.5
|
1.0
|
N
|
B:ASN24
|
3.6
|
11.2
|
1.0
|
C
|
B:THR23
|
3.6
|
11.0
|
1.0
|
CG
|
B:ASN24
|
3.6
|
12.0
|
1.0
|
C
|
B:GLU20
|
3.7
|
15.8
|
1.0
|
CA
|
B:VAL18
|
3.8
|
12.7
|
1.0
|
CA
|
B:ASN24
|
3.8
|
11.6
|
1.0
|
N
|
B:GLU20
|
3.9
|
15.8
|
1.0
|
C
|
B:ILE27
|
3.9
|
10.1
|
1.0
|
C
|
B:LEU17
|
3.9
|
12.2
|
1.0
|
CB
|
B:THR23
|
3.9
|
12.6
|
1.0
|
O
|
B:THR23
|
3.9
|
11.7
|
1.0
|
NA
|
B:NA205
|
4.0
|
18.4
|
1.0
|
CA
|
B:THR23
|
4.2
|
11.7
|
1.0
|
C
|
B:GLU19
|
4.2
|
16.6
|
1.0
|
CA
|
B:GLU20
|
4.2
|
18.1
|
1.0
|
N
|
B:GLU19
|
4.3
|
12.8
|
1.0
|
CG2
|
B:ILE27
|
4.3
|
13.1
|
1.0
|
CB
|
B:ASN24
|
4.3
|
11.6
|
1.0
|
N
|
B:THR23
|
4.4
|
12.7
|
1.0
|
N
|
B:VAL18
|
4.4
|
11.2
|
1.0
|
CA
|
B:THR28
|
4.5
|
10.8
|
1.0
|
CB
|
B:GLU20
|
4.5
|
20.9
|
1.0
|
ND2
|
B:ASN24
|
4.6
|
14.5
|
1.0
|
N
|
B:THR28
|
4.6
|
10.7
|
1.0
|
O
|
B:GLU19
|
4.7
|
18.5
|
1.0
|
CA
|
B:GLU19
|
4.8
|
15.1
|
1.0
|
N
|
B:THR21
|
4.8
|
16.0
|
1.0
|
CA
|
B:ILE27
|
4.9
|
10.4
|
1.0
|
|
Potassium binding site 3 out
of 6 in 5hdk
Go back to
Potassium Binding Sites List in 5hdk
Potassium binding site 3 out
of 6 in the Crystal Structure of Heat Shock Factor 2-Dbd
![](/pictures/K/pdb/hd/5hdk-K-sphere_03.jpg) Mono view
![](/pictures/K/pdb/hd/5hdk-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 Heat Shock Factor 2-Dbd within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K201
b:16.0
occ:1.00
|
O
|
C:GLU20
|
2.6
|
23.6
|
1.0
|
O
|
C:ILE27
|
2.7
|
14.0
|
1.0
|
OD1
|
C:ASN24
|
2.7
|
19.8
|
1.0
|
OG1
|
C:THR23
|
2.7
|
20.3
|
1.0
|
O
|
C:VAL18
|
2.7
|
16.1
|
1.0
|
O
|
C:LEU17
|
2.8
|
15.7
|
1.0
|
C
|
C:VAL18
|
3.4
|
14.3
|
1.0
|
N
|
C:ASN24
|
3.6
|
19.2
|
1.0
|
C
|
C:THR23
|
3.6
|
18.2
|
1.0
|
C
|
C:GLU20
|
3.7
|
24.1
|
1.0
|
CA
|
C:VAL18
|
3.7
|
13.8
|
1.0
|
CG
|
C:ASN24
|
3.8
|
19.1
|
1.0
|
CA
|
C:ASN24
|
3.8
|
16.8
|
1.0
|
N
|
C:GLU20
|
3.9
|
21.0
|
1.0
|
C
|
C:LEU17
|
3.9
|
16.0
|
1.0
|
CB
|
C:THR23
|
3.9
|
19.3
|
1.0
|
C
|
C:ILE27
|
3.9
|
13.2
|
1.0
|
O
|
C:THR23
|
3.9
|
16.5
|
1.0
|
O
|
C:HOH340
|
4.1
|
17.9
|
1.0
|
CA
|
C:THR23
|
4.2
|
19.0
|
1.0
|
CA
|
C:GLU20
|
4.2
|
24.1
|
1.0
|
CG2
|
C:ILE27
|
4.3
|
13.3
|
1.0
|
C
|
C:GLU19
|
4.3
|
20.1
|
1.0
|
N
|
C:VAL18
|
4.3
|
14.9
|
1.0
|
N
|
C:GLU19
|
4.3
|
15.8
|
1.0
|
N
|
C:THR23
|
4.4
|
20.6
|
1.0
|
CB
|
C:ASN24
|
4.4
|
16.9
|
1.0
|
CB
|
C:GLU20
|
4.4
|
31.3
|
1.0
|
CA
|
C:THR28
|
4.5
|
12.9
|
1.0
|
N
|
C:THR28
|
4.6
|
12.9
|
1.0
|
N
|
C:THR21
|
4.7
|
26.5
|
1.0
|
ND2
|
C:ASN24
|
4.8
|
21.6
|
1.0
|
O
|
C:GLU19
|
4.8
|
25.2
|
1.0
|
CA
|
C:GLU19
|
4.9
|
17.8
|
1.0
|
CA
|
C:THR21
|
4.9
|
27.7
|
1.0
|
CA
|
C:ILE27
|
5.0
|
12.0
|
1.0
|
|
Potassium binding site 4 out
of 6 in 5hdk
Go back to
Potassium Binding Sites List in 5hdk
Potassium binding site 4 out
of 6 in the Crystal Structure of Heat Shock Factor 2-Dbd
![](/pictures/K/pdb/hd/5hdk-K-sphere_04.jpg) Mono view
![](/pictures/K/pdb/hd/5hdk-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 Heat Shock Factor 2-Dbd within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K201
b:20.6
occ:0.47
|
O
|
B:HOH370
|
2.8
|
17.4
|
1.0
|
O
|
B:HOH375
|
2.8
|
14.7
|
1.0
|
O
|
B:HOH315
|
2.8
|
21.4
|
1.0
|
OD1
|
B:ASN32
|
3.6
|
14.7
|
0.2
|
ND2
|
B:ASN32
|
3.8
|
15.5
|
0.8
|
CB
|
B:SER30
|
3.9
|
12.8
|
1.0
|
OE2
|
B:GLU90
|
4.1
|
17.7
|
1.0
|
OG
|
B:SER30
|
4.2
|
15.6
|
1.0
|
CG
|
B:ASN32
|
4.3
|
13.2
|
1.0
|
OD1
|
B:ASN32
|
4.3
|
13.3
|
0.8
|
O
|
B:HOH369
|
4.4
|
33.6
|
1.0
|
ND2
|
B:ASN32
|
4.5
|
12.4
|
0.2
|
CL
|
B:CL202
|
4.5
|
18.7
|
0.5
|
OG
|
B:SER35
|
4.5
|
15.1
|
1.0
|
CD
|
B:GLU90
|
5.0
|
15.2
|
1.0
|
|
Potassium binding site 5 out
of 6 in 5hdk
Go back to
Potassium Binding Sites List in 5hdk
Potassium binding site 5 out
of 6 in the Crystal Structure of Heat Shock Factor 2-Dbd
![](/pictures/K/pdb/hd/5hdk-K-sphere_05.jpg) Mono view
![](/pictures/K/pdb/hd/5hdk-K-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 5 of Crystal Structure of Heat Shock Factor 2-Dbd within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K202
b:11.7
occ:1.00
|
OD1
|
D:ASN24
|
2.7
|
12.8
|
1.0
|
O
|
D:GLU20
|
2.7
|
15.8
|
1.0
|
OG1
|
D:THR23
|
2.7
|
13.8
|
1.0
|
O
|
D:ILE27
|
2.7
|
10.7
|
1.0
|
O
|
D:VAL18
|
2.7
|
12.1
|
1.0
|
O
|
D:LEU17
|
2.9
|
12.9
|
1.0
|
C
|
D:VAL18
|
3.4
|
11.5
|
1.0
|
N
|
D:ASN24
|
3.6
|
11.9
|
1.0
|
C
|
D:THR23
|
3.7
|
12.0
|
1.0
|
CG
|
D:ASN24
|
3.7
|
12.2
|
1.0
|
C
|
D:GLU20
|
3.7
|
15.5
|
1.0
|
CA
|
D:VAL18
|
3.8
|
10.8
|
1.0
|
CA
|
D:ASN24
|
3.9
|
11.6
|
1.0
|
C
|
D:ILE27
|
3.9
|
9.8
|
1.0
|
CB
|
D:THR23
|
3.9
|
14.5
|
1.0
|
N
|
D:GLU20
|
3.9
|
14.2
|
1.0
|
NA
|
D:NA207
|
4.0
|
18.1
|
1.0
|
C
|
D:LEU17
|
4.0
|
12.3
|
1.0
|
O
|
D:THR23
|
4.0
|
11.0
|
1.0
|
CA
|
D:THR23
|
4.2
|
13.7
|
1.0
|
CA
|
D:GLU20
|
4.2
|
17.4
|
1.0
|
CG2
|
D:ILE27
|
4.2
|
12.0
|
1.0
|
C
|
D:GLU19
|
4.2
|
15.1
|
1.0
|
N
|
D:GLU19
|
4.3
|
12.1
|
1.0
|
N
|
D:THR23
|
4.4
|
13.8
|
1.0
|
CB
|
D:ASN24
|
4.4
|
11.7
|
1.0
|
N
|
D:VAL18
|
4.4
|
11.7
|
1.0
|
CB
|
D:GLU20
|
4.5
|
21.5
|
1.0
|
CA
|
D:THR28
|
4.5
|
10.5
|
1.0
|
N
|
D:THR28
|
4.6
|
9.7
|
1.0
|
ND2
|
D:ASN24
|
4.6
|
13.5
|
1.0
|
O
|
D:GLU19
|
4.7
|
16.7
|
1.0
|
CA
|
D:GLU19
|
4.8
|
13.8
|
1.0
|
N
|
D:THR21
|
4.8
|
15.3
|
1.0
|
CA
|
D:ILE27
|
4.9
|
9.7
|
1.0
|
CA
|
D:THR21
|
5.0
|
16.3
|
1.0
|
|
Potassium binding site 6 out
of 6 in 5hdk
Go back to
Potassium Binding Sites List in 5hdk
Potassium binding site 6 out
of 6 in the Crystal Structure of Heat Shock Factor 2-Dbd
![](/pictures/K/pdb/hd/5hdk-K-sphere_06.jpg) Mono view
![](/pictures/K/pdb/hd/5hdk-K-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 6 of Crystal Structure of Heat Shock Factor 2-Dbd within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:K203
b:18.1
occ:0.46
|
O
|
D:ASN24
|
2.8
|
12.6
|
1.0
|
CD1
|
D:LEU39
|
3.5
|
21.7
|
1.0
|
C
|
D:ASN24
|
3.8
|
12.1
|
1.0
|
CG2
|
D:THR28
|
3.9
|
12.7
|
1.0
|
CB
|
D:THR28
|
4.1
|
11.3
|
1.0
|
CA
|
D:GLU25
|
4.3
|
13.1
|
1.0
|
OG1
|
D:THR28
|
4.3
|
12.2
|
1.0
|
N
|
D:GLU25
|
4.4
|
12.1
|
1.0
|
CB
|
D:ASN24
|
4.6
|
11.7
|
1.0
|
CG
|
D:LEU39
|
4.7
|
15.8
|
1.0
|
CA
|
D:ASN24
|
4.7
|
11.6
|
1.0
|
C
|
D:GLU25
|
4.9
|
13.2
|
1.0
|
|
Reference:
H.Feng,
W.Liu,
D.C.Wang.
HSF1-Dbd Crystal Structure To Be Published.
Page generated: Mon Aug 12 13:48:19 2024
|