Zinc in PDB 7kus: Crystal Structure of Danio Rerio Histone Deacetylase 10 H137A Mutant in Complex with N8-Acetylspermidine (Tetrahedral Intermediate)

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 H137A Mutant in Complex with N8-Acetylspermidine (Tetrahedral Intermediate)

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 H137A Mutant in Complex with N8-Acetylspermidine (Tetrahedral Intermediate):
3.5.1.48; 3.5.1.62;

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 H137A Mutant in Complex with N8-Acetylspermidine (Tetrahedral Intermediate), PDB code: 7kus 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) 60.60 / 2.00
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.489, 80.489, 245.308, 90, 90, 120
R / Rfree (%) 17.5 / 21.2

Other elements in 7kus:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 10 H137A Mutant in Complex with N8-Acetylspermidine (Tetrahedral Intermediate) also contains other interesting chemical elements:

Potassium (K) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 10 H137A Mutant in Complex with N8-Acetylspermidine (Tetrahedral Intermediate) (pdb code 7kus). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Danio Rerio Histone Deacetylase 10 H137A Mutant in Complex with N8-Acetylspermidine (Tetrahedral Intermediate), PDB code: 7kus:

Zinc binding site 1 out of 1 in 7kus

Go back to Zinc Binding Sites List in 7kus
Zinc binding site 1 out of 1 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 H137A Mutant in Complex with N8-Acetylspermidine (Tetrahedral Intermediate)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Danio Rerio Histone Deacetylase 10 H137A Mutant in Complex with N8-Acetylspermidine (Tetrahedral Intermediate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn705

b:29.3
occ:1.00
 OD2 A:ASP174 1.9 23.2 1.0
O04 A:X54704 2.0 30.5 1.0
OD2 A:ASP267 2.0 30.7 1.0
ND1 A:HIS176 2.1 28.4 1.0
CG A:ASP174 2.6 29.8 1.0
O03 A:X54704 2.7 28.7 1.0
OD1 A:ASP174 2.7 27.9 1.0
C02 A:X54704 2.8 33.8 1.0
CG A:ASP267 3.0 27.5 1.0
CE1 A:HIS176 3.0 29.0 1.0
CG A:HIS176 3.1 28.3 1.0
OD1 A:ASP267 3.2 27.4 1.0
CB A:HIS176 3.5 24.0 1.0
C01 A:X54704 3.6 49.0 1.0
N A:HIS176 3.7 25.2 1.0
N05 A:X54704 4.0 37.2 1.0
CB A:ASP174 4.1 23.7 1.0
N A:VAL175 4.1 25.3 1.0
C06 A:X54704 4.2 35.8 1.0
NE2 A:HIS176 4.2 27.8 1.0
CA A:HIS176 4.2 25.2 1.0
CD2 A:HIS176 4.2 29.1 1.0
NE2 A:HIS136 4.2 27.3 1.0
CG1 A:VAL175 4.3 28.5 1.0
CB A:ASP267 4.3 26.6 1.0
OH A:TYR307 4.3 34.6 1.0
CA A:GLY305 4.4 31.0 1.0
CE2 A:TYR307 4.4 31.5 1.0
C A:VAL175 4.6 29.4 1.0
CE1 A:HIS136 4.6 25.9 1.0
N A:GLY305 4.7 30.2 1.0
C A:ASP174 4.8 28.5 1.0
CA A:ASP174 4.8 26.3 1.0
CA A:VAL175 4.8 26.9 1.0
CZ A:TYR307 4.9 33.6 1.0

Reference:

C.J.Herbst-Gervasoni, D.W.Christianson. X-Ray Crystallographic Snapshots of Substrate Binding in the Active Site of Histone Deacetylase 10. Biochemistry 2021.
ISSN: ISSN 0006-2960
PubMed: 33449614
DOI: 10.1021/ACS.BIOCHEM.0C00936
Page generated: Tue Oct 29 22:31:03 2024

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