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Sodium in PDB 6j6w: Mutant K23N of Heat Shock Factor 4-Dbd

Protein crystallography data

The structure of Mutant K23N of Heat Shock Factor 4-Dbd, PDB code: 6j6w was solved by Z.Y.Xiao, L.W.Cui, S.Wang, W.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.17 / 1.69
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 44.632, 65.047, 80.556, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 20.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Mutant K23N of Heat Shock Factor 4-Dbd (pdb code 6j6w). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Mutant K23N of Heat Shock Factor 4-Dbd, PDB code: 6j6w:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6j6w

Go back to Sodium Binding Sites List in 6j6w
Sodium binding site 1 out of 4 in the Mutant K23N of Heat Shock Factor 4-Dbd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mutant K23N of Heat Shock Factor 4-Dbd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:11.7
occ:1.00
 OD1 A:ASP34 2.3 12.7 1.0
OG1 A:THR33 2.4 11.2 1.0
O A:VAL28 2.4 8.6 1.0
O A:ILE37 2.4 10.2 1.0
O A:ASP30 2.5 14.4 1.0
O A:LEU27 3.1 10.3 1.0
C A:VAL28 3.3 8.8 1.0
N A:ASP34 3.4 13.8 1.0
CG A:ASP34 3.4 17.9 1.0
C A:ASP30 3.5 12.6 1.0
C A:THR33 3.5 11.9 1.0
CA A:ASP34 3.6 13.4 1.0
C A:ILE37 3.6 10.2 1.0
N A:ASP30 3.6 10.1 1.0
CB A:THR33 3.7 11.6 1.0
O A:THR33 3.9 12.1 1.0
CA A:VAL28 3.9 8.5 1.0
CA A:THR33 4.0 12.1 1.0
CA A:ASP30 4.0 12.0 1.0
C A:GLY29 4.0 13.9 1.0
CA A:ARG38 4.1 9.3 1.0
CB A:ASP34 4.1 15.9 1.0
O A:HOH354 4.1 10.6 1.0
N A:THR33 4.2 12.0 1.0
N A:GLY29 4.2 8.1 1.0
C A:LEU27 4.2 10.4 1.0
N A:ARG38 4.3 9.7 1.0
CG2 A:ILE37 4.4 10.8 1.0
CB A:ASP30 4.4 14.3 1.0
OD2 A:ASP34 4.4 16.4 1.0
CA A:GLY29 4.5 10.0 1.0
N A:PRO31 4.5 14.9 1.0
N A:VAL28 4.6 8.8 1.0
O A:GLY29 4.6 13.4 1.0
CB A:ARG38 4.6 9.7 1.0
CG2 A:THR33 4.7 13.7 1.0
CA A:ILE37 4.7 10.9 1.0
CA A:PRO31 4.9 16.7 1.0
C A:ASP34 4.9 15.5 1.0
C A:PRO31 5.0 18.4 1.0
N A:ILE37 5.0 11.8 1.0

Sodium binding site 2 out of 4 in 6j6w

Go back to Sodium Binding Sites List in 6j6w
Sodium binding site 2 out of 4 in the Mutant K23N of Heat Shock Factor 4-Dbd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Mutant K23N of Heat Shock Factor 4-Dbd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:24.6
occ:0.49
 O B:HOH342 2.2 20.5 1.0
O A:HOH327 2.6 22.2 1.0
O B:ARG108 2.7 6.1 1.0
NH2 A:ARG110 3.3 31.0 1.0
O A:HOH314 3.3 23.4 1.0
C B:ARG108 3.9 6.2 1.0
CZ A:ARG110 4.2 32.9 1.0
CA B:GLY109 4.5 8.1 1.0
NH1 A:ARG110 4.5 33.0 1.0
CG B:ARG110 4.5 6.9 1.0
CG1 B:VAL107 4.7 6.5 1.0
N B:GLY109 4.7 7.2 1.0
O A:HOH337 4.8 49.9 1.0
C B:GLY109 4.8 9.0 1.0
NE B:ARG110 4.8 18.1 1.0
N B:ARG110 5.0 5.7 1.0
CA B:ARG108 5.0 6.7 1.0
O B:SER42 5.0 10.7 1.0

Sodium binding site 3 out of 4 in 6j6w

Go back to Sodium Binding Sites List in 6j6w
Sodium binding site 3 out of 4 in the Mutant K23N of Heat Shock Factor 4-Dbd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Mutant K23N of Heat Shock Factor 4-Dbd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:12.3
occ:0.28
 O A:HOH336 2.3 24.9 1.0
O A:ARG108 2.8 5.2 1.0
O B:HOH314 3.2 29.6 1.0
NH2 B:ARG110 3.4 24.5 1.0
C A:ARG108 4.0 4.9 1.0
CZ B:ARG110 4.2 22.4 1.0
CA A:GLY109 4.5 6.3 1.0
CG A:ARG110 4.6 5.7 1.0
NH1 B:ARG110 4.6 20.8 1.0
N A:GLY109 4.7 7.2 1.0
CG1 A:VAL107 4.7 7.7 1.0
C A:GLY109 4.8 5.2 1.0
NE A:ARG110 4.8 23.3 1.0
N A:ARG110 5.0 4.9 1.0
O A:SER42 5.0 8.2 1.0

Sodium binding site 4 out of 4 in 6j6w

Go back to Sodium Binding Sites List in 6j6w
Sodium binding site 4 out of 4 in the Mutant K23N of Heat Shock Factor 4-Dbd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Mutant K23N of Heat Shock Factor 4-Dbd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:14.2
occ:1.00
 OD1 B:ASP34 2.3 13.6 1.0
O B:VAL28 2.3 12.2 1.0
OG1 B:THR33 2.4 15.2 1.0
O B:ASP30 2.5 16.4 1.0
O B:ILE37 2.5 13.7 1.0
O B:LEU27 3.0 15.8 1.0
C B:VAL28 3.2 12.3 1.0
N B:ASP34 3.4 15.1 1.0
CG B:ASP34 3.4 12.7 1.0
C B:ASP30 3.5 14.9 1.0
C B:THR33 3.5 15.4 1.0
N B:ASP30 3.5 13.0 1.0
CA B:ASP34 3.6 13.7 1.0
CB B:THR33 3.7 16.3 1.0
C B:ILE37 3.7 13.6 1.0
CA B:VAL28 3.9 12.9 1.0
C B:GLY29 3.9 17.1 1.0
CA B:ASP30 4.0 14.7 1.0
O B:THR33 4.0 15.6 1.0
CA B:THR33 4.0 16.2 1.0
O B:HOH339 4.1 12.3 1.0
C B:LEU27 4.1 17.2 1.0
N B:GLY29 4.1 12.1 1.0
CB B:ASP34 4.1 12.8 1.0
CA B:ARG38 4.1 11.8 1.0
N B:THR33 4.2 15.9 1.0
CB B:ASP30 4.3 14.7 1.0
CA B:GLY29 4.4 13.2 1.0
N B:ARG38 4.4 12.7 1.0
CG2 B:ILE37 4.4 15.8 1.0
OD2 B:ASP34 4.4 16.4 1.0
N B:VAL28 4.5 13.7 1.0
O B:GLY29 4.5 16.2 1.0
N B:PRO31 4.6 15.1 1.0
CB B:ARG38 4.6 11.6 1.0
CG2 B:THR33 4.8 17.1 1.0
CA B:ILE37 4.8 14.6 1.0
CA B:PRO31 4.9 14.2 1.0
C B:ASP34 4.9 15.5 1.0

Reference:

Z.Y.Xiao, L.W.Cui, S.Wang, W.Liu. Structure of the Mutant K23N of Heat Shock Factor 4-Dbd at 1.69 Angstroms Resolution. To Be Published.
Page generated: Tue Oct 8 11:23:28 2024

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