Sodium in PDB 7kut: Crystal Structure of Danio Rerio Histone Deacetylase 10 H137A Mutant in Complex with N-Acetylputrescine (Tetrahedral Intermediate)

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

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 10 H137A Mutant in Complex with N-Acetylputrescine (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 N-Acetylputrescine (Tetrahedral Intermediate), PDB code: 7kut 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) 60.50 / 2.05
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 80.248, 80.248, 245.96, 90, 90, 120
R / Rfree (%) 17.6 / 21.9

Other elements in 7kut:

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

Potassium (K) 2 atoms
Zinc (Zn) 1 atom

Sodium Binding Sites:

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

Sodium binding site 1 out of 1 in 7kut

Go back to Sodium Binding Sites List in 7kut
Sodium binding site 1 out of 1 in the Crystal Structure of Danio Rerio Histone Deacetylase 10 H137A Mutant in Complex with N-Acetylputrescine (Tetrahedral Intermediate)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Danio Rerio Histone Deacetylase 10 H137A Mutant in Complex with N-Acetylputrescine (Tetrahedral Intermediate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na718

b:74.2
occ:0.99
 O A:HOH1112 2.5 63.8 1.0
O A:HOH1055 2.6 49.0 1.0
O A:HOH868 2.7 52.1 1.0
O A:HOH1035 2.8 51.3 1.0
O A:HOH1106 3.0 55.4 1.0
O A:HOH940 3.1 34.9 1.0
OD2 A:ASP22 4.3 47.0 1.0
O A:TYR92 4.3 35.2 1.0
O A:HOH825 4.4 41.7 1.0
OE1 A:GLU24 4.6 58.7 1.0
CA A:LYS90 4.7 43.0 1.0
CG A:LYS90 4.8 47.7 1.0
N A:ALA94 4.8 25.7 1.0
O A:SER89 4.9 31.8 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: Wed Mar 3 15:35:23 2021

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