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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:

Chlorine (Cl) 3 atoms
Sodium (Na) 9 atoms

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


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 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

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Potassium binding site 2 out of 6 in the Crystal Structure of Heat Shock Factor 2-Dbd


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 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


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 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


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 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


Mono view


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


Mono view


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

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