Zinc in PDB 6csr: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Phenylhydroxamate

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Phenylhydroxamate, PDB code: 6csr was solved by N.J.Porter, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.20 / 1.62
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.890, 91.980, 96.400, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 21.9

Other elements in 6csr:

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

Potassium (K) 4 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 Phenylhydroxamate (pdb code 6csr). 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 Phenylhydroxamate, PDB code: 6csr:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6csr

Go back to Zinc Binding Sites List in 6csr
Zinc binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Phenylhydroxamate


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 Phenylhydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:9.5
occ:1.00
OD2 A:ASP705 2.0 6.8 1.0
O2 A:BHO804 2.0 9.0 1.0
OD1 A:ASP612 2.0 4.2 1.0
ND1 A:HIS614 2.1 6.0 1.0
O1 A:BHO804 2.4 15.6 1.0
N A:BHO804 2.6 12.3 1.0
CG A:ASP612 2.7 5.0 1.0
OD2 A:ASP612 2.8 5.8 1.0
C A:BHO804 2.8 14.0 1.0
CE1 A:HIS614 2.9 6.7 1.0
CG A:ASP705 3.0 6.4 1.0
CG A:HIS614 3.2 6.5 1.0
OD1 A:ASP705 3.4 6.2 1.0
CB A:HIS614 3.6 5.7 1.0
N A:HIS614 3.9 4.4 1.0
NE2 A:HIS614 4.1 7.7 1.0
C1 A:BHO804 4.2 13.6 1.0
NE2 A:HIS573 4.2 6.2 1.0
CB A:ASP612 4.2 5.7 1.0
CD2 A:HIS614 4.2 7.2 1.0
CG1 A:VAL613 4.3 5.7 1.0
CA A:GLY743 4.3 4.9 1.0
CB A:ASP705 4.3 5.4 1.0
N A:VAL613 4.3 5.1 1.0
OH A:TYR745 4.4 10.4 1.0
CA A:HIS614 4.4 5.4 1.0
CE1 A:HIS573 4.5 6.4 1.0
CE2 A:TYR745 4.6 7.5 1.0
N A:GLY743 4.7 4.5 1.0
C6 A:BHO804 4.7 13.9 1.0
NE2 A:HIS574 4.7 5.4 1.0
O A:HOH1107 4.7 20.2 1.0
C A:VAL613 4.8 5.6 1.0
C A:ASP612 4.9 5.1 1.0
CA A:ASP612 4.9 5.0 1.0
CZ A:TYR745 5.0 9.0 1.0

Zinc binding site 2 out of 2 in 6csr

Go back to Zinc Binding Sites List in 6csr
Zinc binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Phenylhydroxamate


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 Phenylhydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:8.9
occ:1.00
OD2 B:ASP705 2.0 7.2 1.0
O2 B:BHO804 2.0 10.6 1.0
OD1 B:ASP612 2.1 5.5 1.0
ND1 B:HIS614 2.1 6.0 1.0
O1 B:BHO804 2.4 12.1 1.0
N B:BHO804 2.6 12.5 1.0
CG B:ASP612 2.7 4.7 1.0
OD2 B:ASP612 2.8 5.1 1.0
C B:BHO804 2.8 12.6 1.0
CE1 B:HIS614 2.9 7.7 1.0
CG B:ASP705 3.0 6.5 1.0
CG B:HIS614 3.2 6.2 1.0
OD1 B:ASP705 3.4 6.4 1.0
CB B:HIS614 3.7 5.8 1.0
N B:HIS614 3.9 6.0 1.0
NE2 B:HIS614 4.1 7.8 1.0
C1 B:BHO804 4.1 12.0 1.0
NE2 B:HIS573 4.2 5.6 1.0
CB B:ASP612 4.2 3.3 1.0
CD2 B:HIS614 4.2 6.9 1.0
CG1 B:VAL613 4.3 4.0 1.0
CA B:GLY743 4.3 4.0 1.0
CB B:ASP705 4.3 5.5 1.0
N B:VAL613 4.3 4.6 1.0
CA B:HIS614 4.4 6.0 1.0
OH B:TYR745 4.4 9.5 1.0
CE1 B:HIS573 4.5 5.7 1.0
CE2 B:TYR745 4.6 8.6 1.0
O B:HOH1080 4.6 17.2 1.0
N B:GLY743 4.7 3.8 1.0
NE2 B:HIS574 4.7 5.0 1.0
C6 B:BHO804 4.7 11.9 1.0
C B:ASP612 4.9 5.2 1.0
C B:VAL613 4.9 6.4 1.0
CA B:ASP612 4.9 3.9 1.0
N B:GLY744 4.9 4.3 1.0
C B:GLY743 5.0 4.4 1.0

Reference:

N.J.Porter, F.F.Wagner, D.W.Christianson. Entropy As A Driver of Selectivity For Inhibitor Binding to Histone Deacetylase 6. Biochemistry V. 57 3916 2018.
ISSN: ISSN 1520-4995
PubMed: 29775292
DOI: 10.1021/ACS.BIOCHEM.8B00367
Page generated: Wed Dec 16 11:37:52 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy