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Zinc in PDB 6wi3: 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: 6wi3 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) 48.80 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.162, 97.593, 139.07, 90, 90, 90
R / Rfree (%) 19.7 / 25.4

Other elements in 6wi3:

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

Sodium (Na) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Histone Deacetylases Complex with Peptide Macrocycles (pdb code 6wi3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Histone Deacetylases Complex with Peptide Macrocycles, PDB code: 6wi3:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6wi3

Go back to Zinc Binding Sites List in 6wi3
Zinc binding site 1 out of 3 in the Histone Deacetylases Complex with Peptide Macrocycles


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Histone Deacetylases Complex with Peptide Macrocycles within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:28.4
occ:1.00
OD1 A:ASP269 2.0 26.1 1.0
OD2 A:ASP181 2.1 31.9 1.0
SH F:U2M500 2.3 24.2 1.0
ND1 A:HIS183 2.3 29.8 1.0
CG A:ASP181 2.8 28.7 1.0
OD1 A:ASP181 2.9 27.2 1.0
CG A:ASP269 3.1 27.8 1.0
CG A:HIS183 3.1 30.5 1.0
CE1 A:HIS183 3.2 29.1 1.0
CZ F:U2M500 3.3 31.7 1.0
CE F:U2M500 3.3 31.9 1.0
CB A:HIS183 3.4 28.2 1.0
OD2 A:ASP269 3.6 33.8 1.0
N A:HIS183 3.8 24.3 1.0
CA A:GLY306 4.1 18.9 1.0
NE2 A:HIS145 4.2 24.9 1.0
CG2 A:ILE182 4.2 21.7 1.0
CD2 A:HIS183 4.2 35.9 1.0
NE2 A:HIS183 4.2 36.6 1.0
CA A:HIS183 4.2 26.6 1.0
CB A:ASP181 4.3 24.2 1.0
CB A:ASP269 4.3 25.6 1.0
NE2 A:HIS146 4.4 30.2 1.0
N A:ILE182 4.5 27.0 1.0
OH A:TYR308 4.5 22.2 1.0
CE2 A:TYR308 4.6 25.1 1.0
CE1 A:HIS145 4.6 22.0 1.0
N A:GLY306 4.6 26.1 1.0
CD F:U2M500 4.8 32.0 1.0
C A:ILE182 4.8 28.2 1.0

Zinc binding site 2 out of 3 in 6wi3

Go back to Zinc Binding Sites List in 6wi3
Zinc binding site 2 out of 3 in the Histone Deacetylases Complex with Peptide Macrocycles


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Histone Deacetylases Complex with Peptide Macrocycles within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:28.7
occ:1.00
OD2 B:ASP269 1.9 23.7 1.0
OD2 B:ASP181 2.1 28.0 1.0
ND1 B:HIS183 2.3 25.3 1.0
SH G:U2M500 2.3 27.3 1.0
OD1 B:ASP181 2.7 27.6 1.0
CG B:ASP181 2.8 31.0 1.0
CG B:ASP269 3.0 28.1 1.0
CG B:HIS183 3.2 23.8 1.0
CE1 B:HIS183 3.2 25.9 1.0
CB B:HIS183 3.4 24.9 1.0
CZ G:U2M500 3.5 32.7 1.0
OD1 B:ASP269 3.5 25.0 1.0
CE G:U2M500 3.7 27.0 1.0
N B:HIS183 3.8 21.2 1.0
CA B:GLY306 4.1 27.0 1.0
CG2 B:ILE182 4.2 22.7 1.0
CA B:HIS183 4.2 24.0 1.0
CB B:ASP181 4.2 21.8 1.0
CD2 B:HIS183 4.3 31.5 1.0
NE2 B:HIS145 4.3 28.5 1.0
NE2 B:HIS183 4.3 34.0 1.0
CB B:ASP269 4.3 17.5 1.0
NE2 B:HIS146 4.4 24.7 1.0
N B:ILE182 4.5 23.6 1.0
N B:GLY306 4.7 26.9 1.0
CE2 B:TYR308 4.7 25.9 1.0
CE1 B:HIS145 4.7 24.2 1.0
OH B:TYR308 4.7 29.9 1.0
C B:ILE182 4.8 26.0 1.0
C B:ASP181 5.0 26.0 1.0

Zinc binding site 3 out of 3 in 6wi3

Go back to Zinc Binding Sites List in 6wi3
Zinc binding site 3 out of 3 in the Histone Deacetylases Complex with Peptide Macrocycles


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Histone Deacetylases Complex with Peptide Macrocycles within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:51.0
occ:1.00
OD2 C:ASP269 2.0 57.7 1.0
OD1 C:ASP181 2.2 50.5 1.0
CD2 C:HIS183 2.3 55.1 1.0
SH H:U2M500 2.7 61.2 1.0
OD2 C:ASP181 2.7 50.2 1.0
CG C:ASP181 2.8 49.8 1.0
CG C:HIS183 3.0 57.4 1.0
CG C:ASP269 3.2 51.6 1.0
CB C:HIS183 3.3 49.8 1.0
NE2 C:HIS183 3.5 49.5 1.0
OD1 C:ASP269 3.7 50.3 1.0
N C:HIS183 3.8 48.9 1.0
CZ H:U2M500 3.9 61.4 1.0
CE H:U2M500 4.0 61.8 1.0
CA C:HIS183 4.1 54.8 1.0
CA C:GLY306 4.2 61.2 1.0
ND1 C:HIS183 4.2 57.9 1.0
NE2 C:HIS145 4.3 45.5 1.0
CB C:ASP181 4.3 46.5 1.0
CG2 C:ILE182 4.3 52.3 1.0
NE2 C:HIS146 4.3 59.2 1.0
CB C:ASP269 4.4 61.1 1.0
CE1 C:HIS183 4.4 64.3 1.0
CE2 C:TYR308 4.6 62.6 1.0
N C:ILE182 4.6 51.5 1.0
OH C:TYR308 4.7 62.9 1.0
N C:GLY306 4.8 62.6 1.0
CE1 C:HIS145 4.8 50.7 1.0
C C:ILE182 4.9 52.4 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: Mon Jul 12 16:39:47 2021

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