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Zinc in PDB 5efh: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trifluoroketone Transition State Analogue

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trifluoroketone Transition State Analogue

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trifluoroketone Transition State Analogue:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trifluoroketone Transition State Analogue, PDB code: 5efh was solved by Y.Hai, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.71 / 2.16
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.659, 92.414, 96.158, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 24.2

Other elements in 5efh:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trifluoroketone Transition State Analogue also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Potassium (K) 4 atoms
Bromine (Br) 7 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trifluoroketone Transition State Analogue (pdb code 5efh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trifluoroketone Transition State Analogue, PDB code: 5efh:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5efh

Go back to Zinc Binding Sites List in 5efh
Zinc binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trifluoroketone Transition State Analogue


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 6 Catalytic Domain 2 in Complex with Trifluoroketone Transition State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2001

b:16.1
occ:1.00
O13 D:FKS2004 1.9 11.5 1.0
OD2 D:ASP705 2.0 12.0 1.0
OD1 D:ASP612 2.1 9.8 1.0
ND1 D:HIS614 2.2 13.2 1.0
O14 D:FKS2004 2.4 11.7 1.0
C11 D:FKS2004 2.7 12.3 1.0
OD2 D:ASP612 2.7 10.8 1.0
CG D:ASP612 2.7 11.2 1.0
CE1 D:HIS614 3.0 13.9 1.0
CG D:ASP705 3.1 12.1 1.0
CG D:HIS614 3.3 13.6 1.0
OD1 D:ASP705 3.5 11.8 1.0
F16 D:FKS2004 3.5 14.6 1.0
C12 D:FKS2004 3.7 14.1 1.0
CB D:HIS614 3.7 13.4 1.0
C10 D:FKS2004 3.8 12.3 1.0
C9 D:FKS2004 3.8 12.5 1.0
N D:HIS614 3.9 13.6 1.0
CA D:GLY743 4.1 11.0 1.0
NE2 D:HIS614 4.2 14.8 1.0
CB D:ASP612 4.2 10.8 1.0
N D:VAL613 4.3 12.7 1.0
OH D:TYR745 4.3 11.5 1.0
CD2 D:HIS614 4.3 14.6 1.0
CB D:ASP705 4.3 12.5 1.0
NE2 D:HIS573 4.4 11.5 1.0
CG1 D:VAL613 4.4 11.7 1.0
F17 D:FKS2004 4.4 14.4 1.0
CA D:HIS614 4.4 13.8 1.0
CE2 D:TYR745 4.4 11.4 1.0
N D:GLY743 4.6 10.6 1.0
F15 D:FKS2004 4.7 14.8 1.0
CE1 D:HIS573 4.8 11.7 1.0
NE2 D:HIS574 4.8 13.1 1.0
C D:ASP612 4.8 13.6 1.0
C D:VAL613 4.9 14.2 1.0
CZ D:TYR745 4.9 11.3 1.0
N D:GLY744 4.9 11.7 1.0
C D:GLY743 4.9 11.1 1.0
CA D:ASP612 4.9 11.3 1.0
CA D:VAL613 5.0 13.7 1.0

Zinc binding site 2 out of 2 in 5efh

Go back to Zinc Binding Sites List in 5efh
Zinc binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trifluoroketone Transition State Analogue


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Trifluoroketone Transition State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:17.0
occ:1.00
O13 A:FKS2004 1.9 9.7 1.0
OD2 A:ASP705 2.0 15.8 1.0
OD1 A:ASP612 2.1 11.9 1.0
ND1 A:HIS614 2.2 13.8 1.0
O14 A:FKS2004 2.6 9.8 1.0
C11 A:FKS2004 2.7 11.1 1.0
CG A:ASP612 2.8 11.2 1.0
OD2 A:ASP612 2.8 10.7 1.0
CG A:ASP705 3.0 16.1 1.0
CE1 A:HIS614 3.1 14.6 1.0
CG A:HIS614 3.2 14.4 1.0
OD1 A:ASP705 3.3 16.2 1.0
F16 A:FKS2004 3.5 14.7 1.0
CB A:HIS614 3.6 14.1 1.0
C12 A:FKS2004 3.7 14.0 1.0
C9 A:FKS2004 3.8 11.6 1.0
N A:HIS614 3.8 13.9 1.0
C10 A:FKS2004 3.9 11.2 1.0
CA A:GLY743 4.2 12.5 1.0
CG1 A:VAL613 4.2 14.9 1.0
CB A:ASP612 4.2 11.2 1.0
OH A:TYR745 4.2 14.7 1.0
NE2 A:HIS614 4.2 16.0 1.0
NE2 A:HIS573 4.3 9.4 1.0
N A:VAL613 4.3 14.2 1.0
CD2 A:HIS614 4.3 15.6 1.0
CB A:ASP705 4.3 16.4 1.0
CE2 A:TYR745 4.3 15.1 1.0
CA A:HIS614 4.4 14.9 1.0
F17 A:FKS2004 4.4 14.9 1.0
CE1 A:HIS573 4.6 9.5 1.0
N A:GLY743 4.7 12.2 1.0
CZ A:TYR745 4.8 14.4 1.0
C A:VAL613 4.8 14.7 1.0
F15 A:FKS2004 4.8 14.9 1.0
C A:ASP612 4.8 13.8 1.0
N A:GLY744 4.9 13.5 1.0
CA A:ASP612 4.9 11.8 1.0
C A:GLY743 5.0 12.8 1.0
CA A:VAL613 5.0 14.4 1.0
NE2 A:HIS574 5.0 10.6 1.0

Reference:

Y.Hai, D.W.Christianson. Histone Deacetylase 6 Structure and Molecular Basis of Catalysis and Inhibition. Nat.Chem.Biol. V. 12 741 2016.
ISSN: ESSN 1552-4469
PubMed: 27454933
DOI: 10.1038/NCHEMBIO.2134
Page generated: Sun Oct 27 15:15:04 2024

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