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Potassium in PDB 6uhv: Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 6-[(3-Aminopropyl)Amino]-N-Hydroxyhexanamide

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 6-[(3-Aminopropyl)Amino]-N-Hydroxyhexanamide

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 6-[(3-Aminopropyl)Amino]-N-Hydroxyhexanamide:
3.5.1.48; 3.5.1.62;

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 6-[(3-Aminopropyl)Amino]-N-Hydroxyhexanamide, PDB code: 6uhv was solved by C.J.Herbst-Gervasoni, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.72 / 2.53
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.525, 80.525, 245.874, 90.00, 90.00, 120.00
R / Rfree (%) 20.4 / 24.6

Other elements in 6uhv:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 6-[(3-Aminopropyl)Amino]-N-Hydroxyhexanamide also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 6-[(3-Aminopropyl)Amino]-N-Hydroxyhexanamide (pdb code 6uhv). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 6-[(3-Aminopropyl)Amino]-N-Hydroxyhexanamide, PDB code: 6uhv:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 6uhv

Go back to Potassium Binding Sites List in 6uhv
Potassium binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 6-[(3-Aminopropyl)Amino]-N-Hydroxyhexanamide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 6-[(3-Aminopropyl)Amino]-N-Hydroxyhexanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K703

b:36.2
occ:1.00
 O A:ASP174 2.7 36.6 1.0
O A:TRP196 2.7 36.3 1.0
O A:HIS176 2.7 32.8 1.0
O A:ASP172 2.8 41.0 1.0
OD2 A:ASP172 2.9 35.1 1.0
OG A:SER195 3.1 33.7 1.0
CG A:ASP172 3.1 36.6 1.0
C A:ASP172 3.6 38.6 1.0
C A:ASP174 3.6 35.9 1.0
OD1 A:ASP172 3.6 43.2 1.0
CB A:ASP172 3.6 30.2 1.0
N A:ASP174 3.7 33.0 1.0
C A:HIS176 3.8 35.4 1.0
C A:TRP196 3.8 39.5 1.0
CA A:ASP174 4.0 32.4 1.0
CB A:SER195 4.0 35.8 1.0
N A:TRP196 4.0 33.3 1.0
CB A:ASP174 4.0 35.2 1.0
CA A:ASP172 4.2 34.8 1.0
CA A:SER195 4.3 33.4 1.0
C A:TRP173 4.3 33.8 1.0
N A:TRP173 4.4 38.1 1.0
CA A:HIS177 4.4 38.6 1.0
N A:HIS176 4.4 39.8 1.0
CB A:HIS197 4.4 30.5 1.0
N A:HIS177 4.5 33.0 1.0
C A:SER195 4.5 38.2 1.0
N A:GLY178 4.5 32.3 1.0
CA A:TRP173 4.5 31.0 1.0
ND1 A:HIS197 4.5 40.8 1.0
CA A:TRP196 4.6 35.5 1.0
N A:VAL175 4.6 37.4 1.0
CD1 A:TRP196 4.7 31.8 1.0
OH A:TYR193 4.7 35.3 1.0
CA A:HIS176 4.8 35.7 1.0
N A:HIS197 4.8 38.2 1.0
CA A:HIS197 4.8 33.7 1.0
C A:VAL175 4.8 38.6 1.0
CE1 A:HIS136 4.9 33.4 1.0
ND1 A:HIS136 4.9 31.4 1.0
OD2 A:ASP174 4.9 38.9 1.0
C A:HIS177 4.9 34.7 1.0
CG A:HIS197 5.0 37.6 1.0

Potassium binding site 2 out of 2 in 6uhv

Go back to Potassium Binding Sites List in 6uhv
Potassium binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 6-[(3-Aminopropyl)Amino]-N-Hydroxyhexanamide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Danio Rerio Histone Deacetylase 10 in Complex with 6-[(3-Aminopropyl)Amino]-N-Hydroxyhexanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K704

b:62.9
occ:1.00
 O A:VAL191 2.7 44.8 1.0
O A:PHE185 2.7 44.2 1.0
O A:HOH812 2.9 55.5 1.0
O A:PHE224 2.9 38.9 1.0
O A:HOH863 2.9 36.3 1.0
O A:ASP188 3.6 46.7 1.0
C A:PHE224 3.6 42.3 1.0
C A:PHE185 3.7 38.6 1.0
CB A:PHE185 3.8 40.7 1.0
C A:VAL191 3.9 43.3 1.0
CB A:PHE224 3.9 44.3 1.0
N A:TYR193 4.1 39.2 1.0
N A:ASN225 4.3 38.1 1.0
CB A:TYR193 4.4 31.7 1.0
CA A:PHE185 4.4 41.0 1.0
CA A:PHE224 4.4 45.1 1.0
CB A:ASN225 4.5 36.6 1.0
CA A:LEU192 4.5 38.5 1.0
CA A:ASN225 4.5 39.0 1.0
N A:LEU192 4.6 39.7 1.0
C A:ASP188 4.7 46.6 1.0
N A:GLU186 4.7 45.4 1.0
C A:LEU192 4.8 41.5 1.0
O A:GLU186 4.8 42.9 1.0
CA A:GLU186 4.8 44.3 1.0
OD1 A:ASN225 4.8 35.4 1.0
CA A:TYR193 4.9 37.2 1.0
CB A:VAL191 4.9 42.5 1.0
CA A:VAL191 4.9 42.1 1.0
C A:GLU186 4.9 49.2 1.0
CG1 A:VAL191 5.0 36.5 1.0

Reference:

C.J.Herbst-Gervasoni, D.W.Christianson. Binding of N8-Acetylspermidine Analogues to Histone Deacetylase 10 Reveals Molecular Strategies For Blocking Polyamine Deacetylation. Biochemistry 2019.
ISSN: ISSN 0006-2960
PubMed: 31746596
DOI: 10.1021/ACS.BIOCHEM.9B00906
Page generated: Mon Aug 12 17:48:50 2024

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