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Sodium in PDB 7dcs: Crystal Structure of HSF1 Dna-Binding Domain in Complex with 3-Site Hse Dna (23 Bp)

Protein crystallography data

The structure of Crystal Structure of HSF1 Dna-Binding Domain in Complex with 3-Site Hse Dna (23 Bp), PDB code: 7dcs was solved by F.Na, L.Wei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.88 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.72, 93.72, 142.37, 90, 90, 90
R / Rfree (%) 19.5 / 22.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of HSF1 Dna-Binding Domain in Complex with 3-Site Hse Dna (23 Bp) (pdb code 7dcs). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of HSF1 Dna-Binding Domain in Complex with 3-Site Hse Dna (23 Bp), PDB code: 7dcs:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 7dcs

Go back to Sodium Binding Sites List in 7dcs
Sodium binding site 1 out of 5 in the Crystal Structure of HSF1 Dna-Binding Domain in Complex with 3-Site Hse Dna (23 Bp)


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 HSF1 Dna-Binding Domain in Complex with 3-Site Hse Dna (23 Bp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:49.8
occ:1.00
 O A:ILE35 2.4 51.1 1.0
OG1 A:THR31 2.5 47.7 1.0
O A:VAL26 2.5 50.1 1.0
O A:ASP28 2.6 45.6 1.0
O A:LEU25 2.8 38.4 1.0
OD1 A:ASP32 2.9 49.0 1.0
C A:VAL26 3.2 43.6 1.0
C A:ILE35 3.5 43.4 1.0
N A:ASP32 3.6 54.1 1.0
C A:THR31 3.6 54.5 1.0
C A:ASP28 3.6 52.9 1.0
CB A:THR31 3.7 54.6 1.0
CA A:VAL26 3.7 32.7 1.0
N A:ASP28 3.8 39.5 1.0
O A:THR31 3.9 56.3 1.0
CA A:ASP32 3.9 56.9 1.0
C A:LEU25 3.9 38.0 1.0
CG2 A:ILE35 3.9 36.5 1.0
CG A:ASP32 4.1 58.1 1.0
CA A:THR31 4.1 54.2 1.0
CA A:CYS36 4.1 44.4 1.0
CA A:ASP28 4.1 47.7 1.0
O A:HOH315 4.1 43.8 1.0
N A:SER27 4.2 41.8 1.0
C A:SER27 4.2 46.9 1.0
N A:CYS36 4.2 39.9 1.0
N A:VAL26 4.3 30.7 1.0
CB A:ASP28 4.3 52.0 1.0
N A:THR31 4.4 55.5 1.0
CB A:CYS36 4.6 56.9 1.0
CA A:ILE35 4.6 39.3 1.0
CB A:ASP32 4.6 58.7 1.0
CA A:SER27 4.6 42.0 1.0
CB A:ILE35 4.7 40.5 1.0
N A:PRO29 4.8 57.7 1.0
O A:SER27 4.8 55.1 1.0
N A:ILE35 4.9 40.5 1.0
CG2 A:THR31 4.9 61.6 1.0

Sodium binding site 2 out of 5 in 7dcs

Go back to Sodium Binding Sites List in 7dcs
Sodium binding site 2 out of 5 in the Crystal Structure of HSF1 Dna-Binding Domain in Complex with 3-Site Hse Dna (23 Bp)


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 HSF1 Dna-Binding Domain in Complex with 3-Site Hse Dna (23 Bp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:32.6
occ:0.73
 O B:ASP28 2.4 57.7 1.0
OG1 B:THR31 2.4 55.4 1.0
O B:ILE35 2.5 45.6 1.0
O B:VAL26 2.6 39.8 1.0
O B:LEU25 2.7 36.3 1.0
OD1 B:ASP32 2.9 56.7 1.0
C B:VAL26 3.3 41.5 1.0
C B:ASP28 3.4 57.1 1.0
N B:ASP32 3.5 39.6 1.0
C B:THR31 3.6 49.1 1.0
N B:ASP28 3.6 47.0 1.0
CB B:THR31 3.6 48.7 1.0
C B:ILE35 3.7 46.8 1.0
CA B:VAL26 3.8 37.2 1.0
C B:LEU25 3.8 38.2 1.0
CA B:ASP32 3.9 44.4 1.0
CA B:ASP28 3.9 52.6 1.0
CG B:ASP32 4.0 52.4 1.0
CA B:THR31 4.0 53.8 1.0
O B:THR31 4.0 55.0 1.0
C B:SER27 4.1 42.0 1.0
N B:SER27 4.1 41.0 1.0
CG2 B:ILE35 4.2 37.2 1.0
CA B:CYS36 4.2 42.7 1.0
CB B:ASP28 4.2 56.6 1.0
N B:THR31 4.2 61.3 1.0
N B:VAL26 4.3 37.6 1.0
N B:CYS36 4.4 37.3 1.0
N B:PRO29 4.5 57.9 1.0
CB B:ASP32 4.6 39.0 1.0
CA B:SER27 4.6 41.5 1.0
CB B:CYS36 4.6 52.1 1.0
O B:SER27 4.7 44.5 1.0
CA B:ILE35 4.8 46.1 1.0
CG2 B:THR31 4.8 41.0 1.0
CA B:PRO29 4.8 56.5 1.0
CB B:ILE35 4.9 42.3 1.0

Sodium binding site 3 out of 5 in 7dcs

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Sodium binding site 3 out of 5 in the Crystal Structure of HSF1 Dna-Binding Domain in Complex with 3-Site Hse Dna (23 Bp)


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 HSF1 Dna-Binding Domain in Complex with 3-Site Hse Dna (23 Bp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na201

b:37.5
occ:0.73
 O C:ASP28 2.3 37.5 1.0
O C:ILE35 2.4 42.5 1.0
OD1 C:ASP32 2.5 54.8 1.0
OG1 C:THR31 2.6 55.8 1.0
O C:VAL26 2.8 45.9 1.0
O C:LEU25 2.9 40.5 1.0
N C:ASP32 3.3 51.4 1.0
C C:ASP28 3.4 46.3 1.0
C C:THR31 3.5 50.9 1.0
C C:VAL26 3.5 44.9 1.0
CA C:ASP32 3.6 49.7 1.0
C C:ILE35 3.6 48.0 1.0
CG C:ASP32 3.6 56.5 1.0
CB C:THR31 3.7 54.7 1.0
N C:ASP28 3.8 53.0 1.0
O C:THR31 3.9 48.1 1.0
CA C:THR31 4.0 53.9 1.0
C C:LEU25 4.0 35.6 1.0
CA C:VAL26 4.0 41.7 1.0
CA C:ASP28 4.0 51.0 1.0
CA C:CYS36 4.0 53.0 1.0
N C:THR31 4.1 60.1 1.0
CB C:ASP32 4.2 48.8 1.0
CG2 C:ILE35 4.3 46.6 1.0
CB C:ASP28 4.3 54.6 1.0
N C:CYS36 4.3 47.0 1.0
C C:SER27 4.3 50.8 1.0
CB C:CYS36 4.3 58.0 1.0
N C:SER27 4.4 47.4 1.0
N C:PRO29 4.4 44.7 1.0
N C:VAL26 4.5 32.5 1.0
OD2 C:ASP32 4.6 64.0 1.0
CA C:PRO29 4.6 52.5 1.0
CA C:ILE35 4.8 50.8 1.0
O C:SER27 4.8 53.0 1.0
CA C:SER27 4.8 47.0 1.0
C C:PRO29 4.9 61.2 1.0
C C:ASP32 4.9 51.7 1.0
CG2 C:THR31 4.9 56.6 1.0
O C:HOH304 4.9 49.9 1.0

Sodium binding site 4 out of 5 in 7dcs

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Sodium binding site 4 out of 5 in the Crystal Structure of HSF1 Dna-Binding Domain in Complex with 3-Site Hse Dna (23 Bp)


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 HSF1 Dna-Binding Domain in Complex with 3-Site Hse Dna (23 Bp) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na201

b:33.9
occ:0.91
 O D:ILE35 2.4 38.8 1.0
O D:ASP28 2.5 41.4 1.0
OD1 D:ASP32 2.5 40.5 1.0
O D:VAL26 2.7 31.2 1.0
OG1 D:THR31 2.7 35.7 1.0
O D:LEU25 3.0 33.5 1.0
C D:VAL26 3.4 32.4 1.0
N D:ASP32 3.4 28.9 1.0
C D:ASP28 3.5 41.9 1.0
C D:THR31 3.6 37.5 1.0
C D:ILE35 3.6 32.4 1.0
CA D:ASP32 3.6 32.3 1.0
CG D:ASP32 3.7 39.0 1.0
N D:ASP28 3.8 35.0 1.0
CB D:THR31 3.9 37.7 1.0
CA D:VAL26 3.9 28.7 1.0
O D:THR31 4.0 43.2 1.0
CA D:CYS36 4.1 33.5 1.0
C D:LEU25 4.1 33.6 1.0
CA D:ASP28 4.1 37.3 1.0
CA D:THR31 4.1 38.8 1.0
CG2 D:ILE35 4.2 23.1 1.0
C D:SER27 4.2 32.0 1.0
CB D:ASP32 4.3 32.2 1.0
N D:SER27 4.3 29.3 1.0
N D:CYS36 4.3 29.9 1.0
N D:THR31 4.3 42.9 1.0
CB D:CYS36 4.4 41.2 1.0
CB D:ASP28 4.5 33.6 1.0
N D:VAL26 4.5 25.2 1.0
N D:PRO29 4.6 39.5 1.0
CA D:SER27 4.7 32.1 1.0
CA D:ILE35 4.7 27.0 1.0
OD2 D:ASP32 4.7 43.3 1.0
O D:SER27 4.8 37.0 1.0
CA D:PRO29 4.8 38.0 1.0
C D:ASP32 4.9 34.1 1.0
CB D:ILE35 4.9 23.0 1.0
N D:ILE35 5.0 37.5 1.0

Sodium binding site 5 out of 5 in 7dcs

Go back to Sodium Binding Sites List in 7dcs
Sodium binding site 5 out of 5 in the Crystal Structure of HSF1 Dna-Binding Domain in Complex with 3-Site Hse Dna (23 Bp)


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 HSF1 Dna-Binding Domain in Complex with 3-Site Hse Dna (23 Bp) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na201

b:60.1
occ:0.84
 O F:ASP28 2.3 68.7 1.0
O F:ILE35 2.4 65.3 1.0
O F:VAL26 2.5 65.5 1.0
OD1 F:ASP32 2.6 78.0 1.0
OG1 F:THR31 2.8 71.1 1.0
O F:LEU25 3.0 60.5 1.0
C F:VAL26 3.2 63.1 1.0
C F:ASP28 3.4 73.7 1.0
C F:ILE35 3.5 64.7 1.0
N F:ASP32 3.6 72.2 1.0
N F:ASP28 3.6 69.7 1.0
C F:THR31 3.7 70.7 1.0
CG F:ASP32 3.7 79.3 1.0
CA F:ASP32 3.8 74.0 1.0
CA F:VAL26 3.8 60.6 1.0
CA F:ASP28 3.9 71.8 1.0
CA F:CYS36 3.9 69.7 1.0
CG2 F:ILE35 4.0 72.4 1.0
C F:SER27 4.0 67.5 1.0
CB F:THR31 4.0 69.7 1.0
C F:LEU25 4.0 62.6 1.0
O F:THR31 4.1 66.5 1.0
N F:SER27 4.1 60.3 1.0
N F:CYS36 4.1 63.7 1.0
CA F:THR31 4.3 71.9 1.0
CB F:ASP28 4.3 72.8 1.0
O F:HOH303 4.3 61.7 1.0
CB F:ASP32 4.4 74.7 1.0
N F:PRO29 4.4 76.9 1.0
N F:VAL26 4.4 66.4 1.0
N F:THR31 4.4 76.0 1.0
CA F:SER27 4.4 62.5 1.0
CB F:CYS36 4.5 79.4 1.0
O F:SER27 4.5 68.8 1.0
CA F:ILE35 4.6 66.7 1.0
CA F:PRO29 4.7 76.5 1.0
CB F:ILE35 4.7 70.8 1.0
OD2 F:ASP32 4.7 83.6 1.0
CG1 F:ILE35 4.9 76.1 1.0
C F:PRO29 5.0 79.6 1.0

Reference:

F.Na, L.Wei. Crystal Structure of HSF1 Dna-Binding Domain in Complex with 3-Site Hse Dna (23 Bp) To Be Published.
Page generated: Tue Oct 8 16:32:07 2024

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