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Sodium in PDB 5hdn: Crystal Structure of Heat Shock FACTOR1-Dbd Complex with Ds-Dna and Ttt

Protein crystallography data

The structure of Crystal Structure of Heat Shock FACTOR1-Dbd Complex with Ds-Dna and Ttt, PDB code: 5hdn 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) 41.33 / 1.68
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.415, 127.367, 55.268, 90.00, 100.55, 90.00
R / Rfree (%) 17.4 / 20.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Heat Shock FACTOR1-Dbd Complex with Ds-Dna and Ttt (pdb code 5hdn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Heat Shock FACTOR1-Dbd Complex with Ds-Dna and Ttt, PDB code: 5hdn:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5hdn

Go back to Sodium Binding Sites List in 5hdn
Sodium binding site 1 out of 3 in the Crystal Structure of Heat Shock FACTOR1-Dbd Complex with Ds-Dna and Ttt


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 FACTOR1-Dbd Complex with Ds-Dna and Ttt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:20.4
occ:1.00
 O A:ASP28 2.4 24.5 1.0
O A:ILE35 2.4 17.1 1.0
OD1 A:ASP32 2.4 23.0 1.0
O A:VAL26 2.5 18.7 1.0
OG1 A:THR31 2.5 20.6 1.0
O A:LEU25 2.9 18.1 1.0
C A:VAL26 3.3 17.0 1.0
C A:ASP28 3.4 24.0 1.0
N A:ASP32 3.5 19.8 1.0
CG A:ASP32 3.6 24.5 1.0
C A:ILE35 3.6 14.9 1.0
C A:THR31 3.6 15.9 1.0
CA A:ASP32 3.7 20.6 1.0
CB A:THR31 3.8 21.3 1.0
N A:ASP28 3.8 19.8 1.0
CA A:VAL26 3.8 16.3 1.0
C A:LEU25 4.0 18.1 1.0
CA A:THR31 4.0 19.2 1.0
O A:THR31 4.1 18.2 1.0
CA A:ASP28 4.1 21.3 1.0
CA A:CYS36 4.1 17.1 1.0
N A:THR31 4.1 19.8 1.0
C A:SER27 4.2 21.6 1.0
N A:SER27 4.2 16.6 1.0
O A:HOH375 4.2 26.9 1.0
CB A:ASP32 4.2 21.3 1.0
N A:CYS36 4.3 15.2 1.0
CG2 A:ILE35 4.3 18.3 1.0
N A:VAL26 4.4 16.1 1.0
N A:PRO29 4.4 22.6 1.0
CB A:ASP28 4.5 22.1 1.0
OD2 A:ASP32 4.5 27.9 1.0
CB A:CYS36 4.5 19.8 1.0
CA A:PRO29 4.6 26.6 1.0
CA A:SER27 4.7 18.0 1.0
O A:SER27 4.7 24.7 1.0
CA A:ILE35 4.8 13.7 1.0
C A:PRO29 4.8 28.1 1.0
CG2 A:THR31 4.9 22.2 1.0
O A:PRO29 5.0 29.2 1.0

Sodium binding site 2 out of 3 in 5hdn

Go back to Sodium Binding Sites List in 5hdn
Sodium binding site 2 out of 3 in the Crystal Structure of Heat Shock FACTOR1-Dbd Complex with Ds-Dna and Ttt


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 FACTOR1-Dbd Complex with Ds-Dna and Ttt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:25.6
occ:1.00
 O B:ASP28 2.3 32.3 1.0
OD1 B:ASP32 2.3 32.2 1.0
OG1 B:THR31 2.5 30.8 1.0
O B:ILE35 2.5 21.1 1.0
O B:VAL26 2.6 20.7 1.0
O B:LEU25 3.1 25.4 1.0
C B:ASP28 3.4 30.4 1.0
C B:VAL26 3.4 21.0 1.0
N B:ASP32 3.4 29.7 1.0
CG B:ASP32 3.5 32.2 1.0
C B:THR31 3.6 28.3 1.0
CA B:ASP32 3.7 27.1 1.0
C B:ILE35 3.7 23.5 1.0
CB B:THR31 3.7 31.1 1.0
N B:ASP28 3.8 24.8 1.0
O B:HOH356 3.8 26.1 1.0
CA B:VAL26 3.9 20.9 1.0
CA B:THR31 4.0 31.7 1.0
N B:THR31 4.0 33.0 1.0
CA B:CYS36 4.1 21.0 1.0
CA B:ASP28 4.1 29.8 1.0
O B:THR31 4.1 28.6 1.0
C B:LEU25 4.2 22.9 1.0
CB B:ASP32 4.2 30.1 1.0
N B:SER27 4.3 21.1 1.0
N B:CYS36 4.3 21.6 1.0
N B:PRO29 4.3 32.0 1.0
C B:SER27 4.4 27.5 1.0
OD2 B:ASP32 4.4 35.9 1.0
CG2 B:ILE35 4.4 23.8 1.0
CA B:PRO29 4.5 35.4 1.0
CB B:CYS36 4.5 24.8 1.0
CB B:ASP28 4.5 28.7 1.0
N B:VAL26 4.6 21.2 1.0
C B:PRO29 4.6 36.4 1.0
CA B:SER27 4.8 24.9 1.0
CG2 B:THR31 4.8 33.2 1.0
O B:PRO29 4.8 35.9 1.0
CA B:ILE35 4.8 22.2 1.0

Sodium binding site 3 out of 3 in 5hdn

Go back to Sodium Binding Sites List in 5hdn
Sodium binding site 3 out of 3 in the Crystal Structure of Heat Shock FACTOR1-Dbd Complex with Ds-Dna and Ttt


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 FACTOR1-Dbd Complex with Ds-Dna and Ttt within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na201

b:32.2
occ:0.90
 O D:ILE35 2.4 37.1 1.0
OD1 D:ASP32 2.4 39.7 1.0
OG1 D:THR31 2.4 40.5 1.0
O D:ASP28 2.5 43.4 1.0
O D:VAL26 2.5 35.0 1.0
O D:LEU25 2.8 36.4 1.0
C D:VAL26 3.2 33.9 1.0
C D:ASP28 3.4 44.2 1.0
N D:ASP32 3.4 43.9 1.0
CG D:ASP32 3.5 43.2 1.0
C D:ILE35 3.6 36.1 1.0
C D:THR31 3.6 43.5 1.0
CA D:ASP32 3.6 45.2 1.0
CB D:THR31 3.7 42.4 1.0
N D:ASP28 3.7 40.5 1.0
CA D:VAL26 3.8 32.6 1.0
C D:LEU25 3.9 34.9 1.0
O D:THR31 4.0 42.6 1.0
CA D:THR31 4.0 44.5 1.0
CA D:CYS36 4.0 35.0 1.0
CA D:ASP28 4.0 42.9 1.0
C D:SER27 4.1 37.3 1.0
CB D:ASP32 4.1 44.9 1.0
N D:SER27 4.2 33.8 1.0
N D:THR31 4.2 46.6 1.0
CG2 D:ILE35 4.2 36.6 1.0
O D:HOH345 4.2 32.3 1.0
N D:CYS36 4.3 34.9 1.0
N D:VAL26 4.4 33.0 1.0
OD2 D:ASP32 4.4 43.0 1.0
N D:PRO29 4.4 47.9 1.0
CB D:CYS36 4.4 41.4 1.0
CB D:ASP28 4.5 41.0 1.0
CA D:SER27 4.6 35.8 1.0
O D:SER27 4.6 38.5 1.0
CA D:PRO29 4.7 49.1 1.0
CA D:ILE35 4.7 36.2 1.0
CG2 D:THR31 4.9 43.4 1.0
C D:PRO29 4.9 50.7 1.0
CB D:ILE35 5.0 35.2 1.0
C D:ASP32 5.0 48.4 1.0

Reference:

H.Feng, W.Liu, D.C.Wang. HSF1-Dbd Crystal Structure To Be Published.
Page generated: Tue Dec 15 11:03:08 2020

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