Atomistry » Sodium » PDB 7d5x-7e1z » 7dcs
Atomistry »
  Sodium »
    PDB 7d5x-7e1z »
      7dcs »

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

Go back to Sodium Binding Sites List in 7dcs
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

Go back to Sodium Binding Sites List in 7dcs
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy