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Sodium 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 (K) 6 atoms
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 9 binding sites of Sodium where determined in the Crystal Structure of Heat Shock Factor 2-Dbd, PDB code: 5hdk:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 5hdk

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Sodium binding site 1 out of 9 in the Crystal Structure of Heat Shock Factor 2-Dbd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na202

b:22.7
occ:1.00
 O A:TYR95 2.8 15.3 1.0
O A:GLN100 2.8 18.4 1.0
N A:LYS97 2.9 15.2 1.0
CA A:PHE96 3.3 13.5 1.0
O A:LYS97 3.5 17.6 1.0
CD2 A:LEU104 3.6 17.4 1.0
C A:PHE96 3.6 13.0 1.0
C A:GLN100 3.6 18.2 1.0
C A:TYR95 3.6 14.3 1.0
NE1 A:TRP15 3.7 15.9 1.0
CD1 A:TRP15 3.8 15.9 1.0
CG A:LEU104 3.8 16.8 1.0
N A:PHE96 3.8 13.6 1.0
CB A:LEU103 4.0 19.1 1.0
CA A:LYS97 4.0 15.1 1.0
CA A:ASP101 4.1 19.2 1.0
C A:LYS97 4.2 14.9 1.0
N A:ASP101 4.2 18.9 1.0
N A:LEU104 4.2 16.8 1.0
CB A:LYS97 4.5 17.1 1.0
CB A:GLN100 4.5 23.2 1.0
C A:LEU103 4.5 16.8 1.0
CA A:GLN100 4.6 20.7 1.0
CB A:PHE96 4.6 13.0 1.0
CA A:LEU103 4.6 18.8 1.0
N A:LEU103 4.6 18.8 1.0
CA A:LEU104 4.7 16.6 1.0
CD1 A:LEU103 4.7 22.2 1.0
C A:ASP101 4.8 18.2 1.0
CE2 A:TRP15 4.8 16.6 1.0
CG A:LEU103 4.8 19.5 1.0
CD1 A:PHE96 4.8 14.5 1.0
O A:PHE96 4.8 14.2 1.0
CG A:PHE96 4.8 13.2 1.0
CB A:LEU104 4.8 16.3 1.0
CG A:TRP15 4.9 15.6 1.0
CA A:TYR95 4.9 14.0 1.0
CD1 A:LEU104 4.9 17.0 1.0
N A:GLN100 5.0 20.4 1.0

Sodium binding site 2 out of 9 in 5hdk

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Sodium binding site 2 out of 9 in the Crystal Structure of Heat Shock Factor 2-Dbd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Heat Shock Factor 2-Dbd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:19.6
occ:1.00
 O A:PHE70 2.7 12.7 1.0
OD1 A:ASN66 2.8 17.0 1.0
O B:HOH316 3.5 26.5 1.0
CG A:ARG71 3.7 13.1 1.0
C A:PHE70 3.8 10.6 1.0
CG A:ASN66 3.9 16.6 1.0
CA A:ARG71 4.0 11.4 1.0
N A:ARG71 4.4 11.0 1.0
NZ A:LYS110 4.4 25.9 1.0
CA A:ASN66 4.4 13.4 1.0
CB A:ASN66 4.4 14.3 1.0
CB A:ARG71 4.5 12.1 1.0
CD A:ARG71 4.7 12.7 1.0
O A:HOH361 4.8 17.5 1.0
O A:ASN66 4.9 14.7 1.0
C A:GLY69 4.9 11.7 1.0

Sodium binding site 3 out of 9 in 5hdk

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Sodium binding site 3 out of 9 in the Crystal Structure of Heat Shock Factor 2-Dbd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Heat Shock Factor 2-Dbd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:18.8
occ:1.00
 O A:PHE96 2.7 14.2 1.0
O A:GLN34 2.8 16.2 1.0
N A:HIS93 2.9 12.6 1.0
CA A:GLN92 3.2 12.8 1.0
O A:HIS93 3.2 13.0 1.0
C A:GLN92 3.5 12.5 1.0
C A:GLN34 3.6 13.8 1.0
CG A:GLN92 3.6 17.7 0.5
O A:HOH334 3.7 20.3 1.0
CA A:SER35 3.7 12.7 1.0
CB A:GLN92 3.7 16.2 1.0
C A:PHE96 3.8 13.0 1.0
CB A:PHE96 3.9 13.0 1.0
CD2 A:PHE96 3.9 14.1 1.0
CA A:HIS93 3.9 11.8 1.0
C A:HIS93 3.9 13.4 1.0
N A:SER35 4.0 13.9 1.0
O A:PHE91 4.2 13.5 1.0
C A:SER35 4.3 12.9 1.0
N A:GLN92 4.3 12.0 1.0
CA A:PHE96 4.4 13.5 1.0
CG A:PHE96 4.4 13.2 1.0
CB A:HIS93 4.4 12.4 1.0
N A:PHE36 4.7 12.8 1.0
C A:PHE91 4.7 12.9 1.0
N A:PHE96 4.7 13.6 1.0
CZ3 A:TRP29 4.7 15.1 1.0
O A:GLN92 4.8 12.9 1.0
CA A:GLN34 4.8 18.9 1.0
CB A:SER35 4.8 14.2 1.0
CD2 A:PHE36 4.9 15.9 1.0
CE2 A:PHE70 5.0 12.9 1.0
N A:LYS97 5.0 15.2 1.0
CG A:GLN92 5.0 16.4 0.5
CD A:GLN92 5.0 19.0 0.5

Sodium binding site 4 out of 9 in 5hdk

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Sodium binding site 4 out of 9 in the Crystal Structure of Heat Shock Factor 2-Dbd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Heat Shock Factor 2-Dbd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:36.7
occ:1.00
 O B:HOH409 2.6 51.4 1.0
O B:HOH402 2.8 46.3 1.0
O B:ARG63 2.9 16.9 1.0
ND2 B:ASN66 3.0 24.5 1.0
CG B:MET67 3.4 39.5 1.0
CG B:ARG63 3.5 29.5 1.0
CB B:ASN66 3.6 16.7 1.0
CG B:ASN66 3.8 19.7 1.0
C B:ARG63 3.8 17.3 1.0
N B:MET67 3.8 17.4 1.0
CA B:ARG63 3.9 18.3 1.0
C B:ASN66 4.2 16.9 1.0
CB B:ARG63 4.3 23.7 1.0
CA B:MET67 4.3 19.8 1.0
CB B:MET67 4.4 28.0 1.0
CA B:ASN66 4.4 16.4 1.0
O B:HOH404 4.6 35.9 1.0
SD B:MET67 4.7 50.7 1.0
CD B:ARG63 4.8 37.3 1.0
N B:ASN66 4.9 14.9 1.0
O B:ASN66 4.9 17.6 1.0
NE B:ARG63 4.9 44.5 1.0
OD1 B:ASN66 5.0 24.1 1.0
N B:GLN64 5.0 16.8 1.0

Sodium binding site 5 out of 9 in 5hdk

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Sodium binding site 5 out of 9 in the Crystal Structure of Heat Shock Factor 2-Dbd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Heat Shock Factor 2-Dbd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na204

b:18.6
occ:1.00
 O B:PHE96 2.7 13.7 1.0
O B:GLN34 2.8 12.9 1.0
N B:HIS93 2.9 12.5 1.0
CA B:GLN92 3.2 12.2 1.0
O B:HIS93 3.2 13.7 1.0
CB B:GLN92 3.5 14.7 0.5
C B:GLN92 3.6 12.7 1.0
CG B:GLN92 3.6 13.6 0.5
NZ B:LYS97 3.6 19.0 1.0
CA B:SER35 3.7 11.8 1.0
C B:GLN34 3.7 11.2 1.0
CB B:GLN92 3.7 14.7 0.5
C B:PHE96 3.8 13.4 1.0
CB B:PHE96 3.9 13.2 1.0
C B:HIS93 4.0 12.9 1.0
CA B:HIS93 4.0 12.7 1.0
CD2 B:PHE96 4.0 13.8 1.0
N B:SER35 4.0 11.9 1.0
O B:PHE91 4.2 12.2 1.0
N B:GLN92 4.4 11.5 1.0
CA B:PHE96 4.4 13.6 1.0
CE B:LYS97 4.4 24.8 1.0
CD B:LYS97 4.5 23.5 1.0
CG B:PHE96 4.5 13.2 1.0
C B:SER35 4.5 11.4 1.0
CZ3 B:TRP29 4.6 13.9 1.0
CB B:HIS93 4.6 13.9 1.0
CB B:SER35 4.7 13.8 1.0
C B:PHE91 4.7 11.6 1.0
N B:PHE96 4.7 14.7 1.0
CG B:GLN92 4.7 13.0 0.5
CD1 B:PHE36 4.7 17.7 1.0
N B:PHE36 4.8 11.7 1.0
O B:GLN92 4.8 14.1 1.0
CA B:GLN34 4.9 13.5 1.0
N B:LYS97 4.9 15.0 1.0
CD B:GLN92 4.9 15.0 0.5
O B:HOH333 5.0 42.4 1.0

Sodium binding site 6 out of 9 in 5hdk

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Sodium binding site 6 out of 9 in the Crystal Structure of Heat Shock Factor 2-Dbd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Heat Shock Factor 2-Dbd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na205

b:18.4
occ:1.00
 OD1 B:ASN24 2.7 12.6 1.0
O B:VAL18 2.8 12.4 1.0
N B:TRP29 2.9 10.9 1.0
CD1 B:TRP29 3.2 12.7 1.0
CG B:ASN24 3.6 12.0 1.0
OG1 B:THR28 3.6 12.4 1.0
CA B:THR28 3.6 10.8 1.0
CB B:TRP29 3.7 12.8 1.0
CG B:TRP29 3.7 12.4 1.0
C B:THR28 3.7 10.8 1.0
ND2 B:ASN24 3.8 14.5 1.0
CA B:TRP29 3.9 11.7 1.0
C B:VAL18 3.9 12.5 1.0
K B:K201 4.0 11.6 1.0
CB B:THR28 4.2 11.0 1.0
NE1 B:TRP29 4.2 13.8 1.0
O B:GLU19 4.5 18.5 1.0
CG1 B:VAL18 4.5 14.6 1.0
CA B:GLU19 4.6 15.1 1.0
O B:TRP29 4.6 11.4 1.0
C B:GLU19 4.6 16.6 1.0
O B:ILE27 4.7 11.4 1.0
N B:GLU19 4.7 12.8 1.0
C B:TRP29 4.8 10.7 1.0
N B:THR28 4.9 10.7 1.0
CD2 B:TRP29 4.9 12.0 1.0
CB B:ASN24 4.9 11.6 1.0
CA B:VAL18 4.9 12.7 1.0
O B:THR28 4.9 11.3 1.0
O B:GLU20 5.0 15.9 1.0

Sodium binding site 7 out of 9 in 5hdk

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Sodium binding site 7 out of 9 in the Crystal Structure of Heat Shock Factor 2-Dbd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Heat Shock Factor 2-Dbd within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na202

b:17.5
occ:1.00
 O C:PHE96 2.7 13.3 1.0
O C:GLN34 2.8 14.5 1.0
N C:HIS93 2.9 11.0 1.0
CA C:GLN92 3.2 12.2 1.0
O C:HIS93 3.2 12.2 1.0
C C:GLN92 3.5 11.4 1.0
C C:GLN34 3.6 13.9 1.0
CB C:GLN92 3.6 14.4 0.7
CA C:SER35 3.7 13.1 1.0
O C:HOH334 3.7 21.0 1.0
CB C:GLN92 3.8 14.9 0.3
CD2 C:PHE96 3.8 12.8 1.0
CB C:PHE96 3.8 12.2 1.0
C C:PHE96 3.8 12.7 1.0
CG C:GLN92 3.9 14.4 0.3
C C:HIS93 3.9 12.0 1.0
CA C:HIS93 4.0 11.2 1.0
N C:SER35 4.0 13.2 1.0
O C:PHE91 4.1 11.6 1.0
CG C:PHE96 4.3 12.8 1.0
CA C:PHE96 4.3 11.9 1.0
N C:GLN92 4.4 10.6 1.0
C C:SER35 4.4 12.2 1.0
CB C:HIS93 4.5 11.3 1.0
CZ3 C:TRP29 4.6 13.2 1.0
N C:PHE36 4.7 12.5 1.0
N C:PHE96 4.7 12.6 1.0
C C:PHE91 4.7 10.4 1.0
CA C:GLN34 4.7 15.1 1.0
CB C:SER35 4.7 14.8 1.0
CE2 C:PHE70 4.8 11.7 1.0
O C:GLN92 4.8 12.3 1.0
CG C:GLN92 4.9 14.9 0.7
CD2 C:PHE36 4.9 13.8 1.0
CE2 C:PHE96 4.9 15.1 1.0
CD C:GLN92 5.0 21.2 0.3
N C:LYS97 5.0 13.0 1.0
OG C:SER35 5.0 15.7 0.3

Sodium binding site 8 out of 9 in 5hdk

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Sodium binding site 8 out of 9 in the Crystal Structure of Heat Shock Factor 2-Dbd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Heat Shock Factor 2-Dbd within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na206

b:18.4
occ:1.00
 O D:PHE96 2.8 12.1 1.0
O D:GLN34 2.8 14.9 1.0
N D:HIS93 2.9 11.8 1.0
CA D:GLN92 3.2 12.1 1.0
O D:HIS93 3.2 11.7 1.0
CG D:GLN92 3.5 13.3 0.4
C D:GLN92 3.6 11.5 1.0
NZ D:LYS97 3.6 11.9 0.5
C D:GLN34 3.6 12.3 1.0
CA D:SER35 3.6 11.1 1.0
CB D:GLN92 3.7 14.7 0.2
CB D:GLN92 3.7 14.1 0.4
CB D:GLN92 3.7 15.9 0.4
C D:PHE96 3.9 11.6 1.0
CB D:PHE96 3.9 11.6 1.0
CD2 D:PHE96 4.0 12.9 1.0
C D:HIS93 4.0 11.5 1.0
N D:SER35 4.0 11.0 1.0
CA D:HIS93 4.0 11.6 1.0
O D:PHE91 4.1 11.3 1.0
CG D:GLN92 4.1 20.3 0.4
N D:GLN92 4.3 11.8 1.0
CA D:PHE96 4.4 11.8 1.0
CG D:PHE96 4.4 12.5 1.0
C D:SER35 4.5 10.3 1.0
CD D:GLN92 4.6 15.3 0.4
CB D:HIS93 4.6 12.3 1.0
CZ3 D:TRP29 4.6 12.5 1.0
CB D:SER35 4.6 13.3 1.0
C D:PHE91 4.7 10.3 1.0
CE D:LYS97 4.7 17.6 0.5
N D:PHE96 4.7 12.8 1.0
CD D:LYS97 4.7 19.5 0.5
N D:PHE36 4.8 10.7 1.0
O D:GLN92 4.8 12.9 1.0
CA D:GLN34 4.8 12.8 1.0
CD1 D:PHE36 4.8 16.2 1.0
CG D:GLN92 4.9 16.2 0.2
NE2 D:GLN92 5.0 16.1 0.4
N D:LYS97 5.0 13.7 1.0

Sodium binding site 9 out of 9 in 5hdk

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Sodium binding site 9 out of 9 in the Crystal Structure of Heat Shock Factor 2-Dbd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Heat Shock Factor 2-Dbd within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na207

b:18.1
occ:1.00
 OD1 D:ASN24 2.7 12.8 1.0
O D:VAL18 2.8 12.1 1.0
N D:TRP29 2.9 9.1 1.0
CD1 D:TRP29 3.2 11.6 1.0
OG1 D:THR28 3.6 12.2 1.0
CG D:ASN24 3.6 12.2 1.0
CA D:THR28 3.6 10.5 1.0
CG D:TRP29 3.6 10.4 1.0
CB D:TRP29 3.6 11.0 1.0
C D:THR28 3.7 9.5 1.0
ND2 D:ASN24 3.7 13.5 1.0
CA D:TRP29 3.8 9.8 1.0
K D:K202 4.0 11.7 1.0
C D:VAL18 4.0 11.5 1.0
CB D:THR28 4.2 11.3 1.0
NE1 D:TRP29 4.2 12.3 1.0
O D:HOH342 4.3 48.6 1.0
CG1 D:VAL18 4.5 13.1 1.0
O D:GLU19 4.5 16.7 1.0
O D:ILE27 4.6 10.7 1.0
CA D:GLU19 4.6 13.8 1.0
O D:TRP29 4.6 10.6 1.0
C D:GLU19 4.7 15.1 1.0
N D:GLU19 4.8 12.1 1.0
C D:TRP29 4.8 9.7 1.0
N D:THR28 4.8 9.7 1.0
CD2 D:TRP29 4.8 11.3 1.0
NE2 D:GLN98 4.9 18.5 1.0
CB D:ASN24 4.9 11.7 1.0
O D:THR28 4.9 10.2 1.0
CA D:VAL18 5.0 10.8 1.0

Reference:

H.Feng, W.Liu, D.C.Wang. HSF1-Dbd Crystal Structure To Be Published.
Page generated: Mon Aug 18 00:05:58 2025

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