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Sodium in PDB 6whz: Histone Deacetylases Complex with Peptide Macrocycles

Enzymatic activity of Histone Deacetylases Complex with Peptide Macrocycles

All present enzymatic activity of Histone Deacetylases Complex with Peptide Macrocycles:
3.5.1.98;

Protein crystallography data

The structure of Histone Deacetylases Complex with Peptide Macrocycles, PDB code: 6whz was solved by A.K.Bera, P.Hosseinzadeh, P.Watson, D.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.90 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.477, 94.802, 138.813, 90, 90, 90
R / Rfree (%) 22.7 / 28.1

Other elements in 6whz:

The structure of Histone Deacetylases Complex with Peptide Macrocycles also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Histone Deacetylases Complex with Peptide Macrocycles (pdb code 6whz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Histone Deacetylases Complex with Peptide Macrocycles, PDB code: 6whz:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6whz

Go back to Sodium Binding Sites List in 6whz
Sodium binding site 1 out of 5 in the Histone Deacetylases Complex with Peptide Macrocycles


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Histone Deacetylases Complex with Peptide Macrocycles within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:25.1
occ:1.00
 OD1 A:ASP179 2.4 33.5 1.0
O A:ASP181 2.5 40.9 1.0
O A:PHE203 2.5 41.1 1.0
O A:ASP179 2.5 38.1 1.0
O A:HIS183 2.7 37.2 1.0
OG A:SER202 2.8 37.1 1.0
CG A:ASP179 3.2 43.0 1.0
C A:ASP179 3.2 35.0 1.0
C A:PHE203 3.4 40.7 1.0
N A:ASP181 3.5 41.9 1.0
C A:ASP181 3.5 33.7 1.0
N A:PHE203 3.5 39.7 1.0
CB A:ASP179 3.6 38.1 1.0
C A:HIS183 3.9 37.8 1.0
C A:ILE180 3.9 46.5 1.0
CA A:ASP181 3.9 31.8 1.0
CB A:SER202 3.9 37.5 1.0
N A:ILE180 3.9 33.3 1.0
CB A:HIS204 4.0 36.1 1.0
CA A:ASP179 4.0 39.4 1.0
CA A:PHE203 4.0 40.2 1.0
C A:SER202 4.1 35.9 1.0
CA A:SER202 4.1 38.0 1.0
CA A:ILE180 4.1 44.8 1.0
OD2 A:ASP179 4.2 41.8 1.0
CB A:ASP181 4.2 36.0 1.0
N A:HIS204 4.3 39.0 1.0
CA A:HIS204 4.4 39.9 1.0
CA A:HIS184 4.4 36.5 1.0
ND1 A:HIS204 4.5 44.6 1.0
N A:GLY185 4.5 40.5 1.0
N A:HIS184 4.6 43.2 1.0
N A:HIS183 4.6 37.9 1.0
O A:ILE180 4.6 41.8 1.0
N A:ILE182 4.7 40.9 1.0
CG A:HIS204 4.7 35.8 1.0
C A:ILE182 4.8 36.8 1.0
C A:HIS184 4.9 35.5 1.0
CB A:PHE203 4.9 30.6 1.0
CA A:HIS183 4.9 39.1 1.0

Sodium binding site 2 out of 5 in 6whz

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Sodium binding site 2 out of 5 in the Histone Deacetylases Complex with Peptide Macrocycles


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Histone Deacetylases Complex with Peptide Macrocycles within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:45.3
occ:1.00
 O A:PHE192 2.4 47.5 1.0
O A:VAL198 2.8 43.3 1.0
O A:TYR227 3.2 49.6 1.0
C A:PHE192 3.4 48.2 1.0
O A:THR195 3.6 51.3 1.0
C A:VAL198 3.9 44.8 1.0
CB A:PHE192 3.9 47.7 1.0
OG1 A:THR200 4.0 46.6 1.0
C A:TYR227 4.1 53.9 1.0
CA A:TYR193 4.1 50.7 1.0
N A:TYR193 4.1 48.9 1.0
CB A:TYR227 4.1 52.1 1.0
N A:THR200 4.3 42.5 1.0
CA A:PHE192 4.3 44.9 1.0
CA A:MET199 4.3 41.3 1.0
C A:TYR193 4.5 55.3 1.0
CG2 A:THR200 4.5 43.1 1.0
N A:MET199 4.6 43.9 1.0
O A:TYR193 4.7 58.1 1.0
O A:GLY224 4.7 57.8 1.0
C A:MET199 4.7 42.9 1.0
CA A:TYR227 4.8 52.8 1.0
C A:THR195 4.8 56.7 1.0
CB A:THR200 4.8 41.0 1.0
N A:ALA228 4.8 50.6 1.0
CB A:ALA228 4.8 47.7 1.0
O A:GLU189 4.9 41.8 1.0
CA A:ALA228 5.0 47.6 1.0
CA A:VAL198 5.0 45.0 1.0

Sodium binding site 3 out of 5 in 6whz

Go back to Sodium Binding Sites List in 6whz
Sodium binding site 3 out of 5 in the Histone Deacetylases Complex with Peptide Macrocycles


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Histone Deacetylases Complex with Peptide Macrocycles within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:30.0
occ:1.00
 O B:ASP181 2.4 31.9 1.0
O B:HIS183 2.5 37.5 1.0
OD1 B:ASP179 2.6 37.9 1.0
OG B:SER202 2.8 39.4 1.0
O B:PHE203 2.9 48.0 1.0
O B:ASP179 3.2 38.3 1.0
C B:HIS183 3.4 36.7 1.0
CG B:ASP179 3.4 38.2 1.0
CB B:HIS204 3.4 46.5 1.0
C B:ASP181 3.5 40.2 1.0
C B:PHE203 3.6 42.0 1.0
CA B:HIS184 3.7 37.5 1.0
N B:ASP181 3.8 36.6 1.0
N B:PHE203 3.9 36.3 1.0
C B:ASP179 3.9 41.1 1.0
N B:GLY185 3.9 42.9 1.0
N B:HIS184 3.9 40.3 1.0
CB B:ASP179 3.9 37.7 1.0
CA B:ASP181 4.0 36.4 1.0
CB B:SER202 4.0 42.0 1.0
ND1 B:HIS204 4.1 43.1 1.0
CA B:HIS204 4.1 49.0 1.0
CG B:HIS204 4.1 44.4 1.0
CB B:ASP181 4.2 35.4 1.0
N B:HIS204 4.2 43.7 1.0
C B:HIS184 4.2 42.9 1.0
OD2 B:ASP179 4.2 38.5 1.0
N B:HIS183 4.3 42.9 1.0
C B:SER202 4.3 42.9 1.0
CA B:SER202 4.4 38.9 1.0
CA B:PHE203 4.4 33.4 1.0
C B:ILE180 4.4 32.4 1.0
CA B:HIS183 4.4 41.1 1.0
CA B:ASP179 4.5 33.8 1.0
C B:ILE182 4.6 47.0 1.0
N B:ILE182 4.6 40.3 1.0
N B:ILE180 4.6 46.0 1.0
CA B:ILE180 4.7 40.8 1.0
CE1 B:HIS145 4.8 40.1 1.0
CA B:ILE182 4.9 40.8 1.0
CA B:GLY185 5.0 45.4 1.0
CB B:HIS184 5.0 39.5 1.0

Sodium binding site 4 out of 5 in 6whz

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Sodium binding site 4 out of 5 in the Histone Deacetylases Complex with Peptide Macrocycles


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Histone Deacetylases Complex with Peptide Macrocycles within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:59.5
occ:1.00
 O B:PHE192 2.4 45.7 1.0
O B:TYR227 2.8 48.9 1.0
O B:VAL198 2.9 56.2 1.0
O B:THR195 3.3 66.5 1.0
C B:TYR227 3.5 53.7 1.0
C B:PHE192 3.5 56.3 1.0
CB B:TYR227 3.6 53.8 1.0
C B:VAL198 4.1 57.4 1.0
CA B:TYR193 4.1 57.3 1.0
O B:GLY224 4.1 59.9 1.0
CA B:TYR227 4.2 58.0 1.0
C B:TYR193 4.2 56.6 1.0
O B:TYR193 4.2 55.9 1.0
CA B:MET199 4.2 52.7 1.0
N B:TYR193 4.3 59.3 1.0
N B:ALA228 4.3 54.5 1.0
CB B:PHE192 4.4 53.6 1.0
N B:THR200 4.5 45.7 1.0
CA B:GLY224 4.5 64.2 1.0
C B:THR195 4.5 61.6 1.0
CB B:ALA228 4.5 58.6 1.0
CA B:ALA228 4.6 51.4 1.0
CA B:PHE192 4.6 54.3 1.0
N B:MET199 4.6 54.7 1.0
OG1 B:THR200 4.7 52.7 1.0
N B:THR194 4.8 61.6 1.0
C B:GLY224 4.8 59.5 1.0
C B:MET199 4.9 49.6 1.0
N B:THR195 4.9 62.7 1.0
CG B:TYR227 4.9 58.5 1.0

Sodium binding site 5 out of 5 in 6whz

Go back to Sodium Binding Sites List in 6whz
Sodium binding site 5 out of 5 in the Histone Deacetylases Complex with Peptide Macrocycles


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Histone Deacetylases Complex with Peptide Macrocycles within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:73.6
occ:1.00
 O C:ASP181 2.5 87.3 1.0
OG C:SER202 2.7 84.3 1.0
O C:HIS183 2.7 82.5 1.0
OD1 C:ASP179 2.7 81.7 1.0
O C:PHE203 2.9 93.1 1.0
O C:ASP179 3.0 85.4 1.0
C C:PHE203 3.4 87.0 1.0
CB C:HIS204 3.5 90.3 1.0
CG C:ASP179 3.5 77.4 1.0
C C:ASP181 3.5 89.8 1.0
C C:HIS183 3.6 79.1 1.0
N C:PHE203 3.6 83.1 1.0
C C:ASP179 3.8 82.8 1.0
N C:ASP181 3.8 87.4 1.0
CB C:SER202 3.9 72.3 1.0
N C:HIS204 3.9 84.6 1.0
CA C:HIS184 3.9 74.7 1.0
CA C:HIS204 3.9 88.4 1.0
CB C:ASP179 4.0 80.3 1.0
C C:SER202 4.0 82.7 1.0
N C:GLY185 4.1 72.3 1.0
CA C:SER202 4.1 76.1 1.0
CA C:ASP181 4.1 86.0 1.0
N C:HIS184 4.1 76.4 1.0
CA C:PHE203 4.2 83.4 1.0
ND1 C:HIS204 4.3 85.3 1.0
CB C:ASP181 4.3 80.2 1.0
C C:ILE180 4.4 81.6 1.0
CG C:HIS204 4.4 90.5 1.0
C C:HIS184 4.4 77.4 1.0
N C:HIS183 4.5 85.2 1.0
OD2 C:ASP179 4.5 74.9 1.0
N C:ILE180 4.5 82.2 1.0
CA C:ASP179 4.5 78.6 1.0
C C:ILE182 4.6 87.3 1.0
N C:ILE182 4.7 84.1 1.0
CA C:ILE180 4.7 81.5 1.0
CA C:HIS183 4.7 80.0 1.0
O C:SER202 4.9 85.7 1.0
CA C:ILE182 5.0 83.5 1.0

Reference:

A.K.Bera, P.Hosseinzadeh, D.Baker. Anchor Extension, A Structure-Guided Approach to Design Macrocycles Targeting Histone Deacetylases To Be Published.
Page generated: Tue Oct 8 14:35:22 2024

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