Atomistry » Zinc » PDB 6cqg-6d1a » 6csp
Atomistry »
  Zinc »
    PDB 6cqg-6d1a »
      6csp »

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

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Cyclohexenylhydroxamate, PDB code: 6csp 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) 48.28 / 1.24
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.700, 91.830, 96.549, 90.00, 90.00, 90.00
R / Rfree (%) 12.7 / 15.3

Other elements in 6csp:

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

Potassium (K) 4 atoms
Chlorine (Cl) 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 Cyclohexenylhydroxamate (pdb code 6csp). 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 Cyclohexenylhydroxamate, PDB code: 6csp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6csp

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


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

b:5.9
occ:1.00
H13 A:FBM807 1.8 8.5 1.0
OD2 A:ASP705 1.9 5.8 1.0
O04 A:FBM807 2.0 7.1 1.0
OD1 A:ASP612 2.1 4.5 1.0
ND1 A:HIS614 2.1 5.2 1.0
O01 A:FBM807 2.2 10.1 1.0
N03 A:FBM807 2.7 9.7 1.0
C02 A:FBM807 2.7 10.0 1.0
CG A:ASP612 2.8 5.0 1.0
OD2 A:ASP612 2.8 5.3 1.0
CE1 A:HIS614 2.9 5.1 1.0
CG A:ASP705 3.0 4.5 1.0
HE1 A:HIS614 3.1 6.1 1.0
HB2 A:HIS614 3.1 5.8 1.0
CG A:HIS614 3.2 4.2 1.0
H A:HIS614 3.3 5.4 1.0
HA3 A:GLY743 3.4 5.4 1.0
OD1 A:ASP705 3.4 5.2 1.0
H12 A:FBM807 3.4 11.6 1.0
HG12 A:VAL613 3.4 5.5 1.0
HE2 A:HIS573 3.4 6.9 1.0
HH A:TYR745 3.6 9.6 1.0
CB A:HIS614 3.6 4.8 1.0
HE2 A:TYR745 3.8 7.1 1.0
N A:HIS614 4.0 4.5 1.0
H A:VAL613 4.0 4.9 1.0
NE2 A:HIS614 4.1 6.5 1.0
C05 A:FBM807 4.1 9.4 1.0
NE2 A:HIS573 4.2 5.7 1.0
H A:GLY743 4.2 5.3 1.0
CB A:ASP612 4.2 4.2 1.0
HE1 A:HIS573 4.2 6.6 1.0
CD2 A:HIS614 4.2 5.7 1.0
H1 A:FBM807 4.2 12.1 1.0
CB A:ASP705 4.3 4.8 1.0
CA A:GLY743 4.3 4.5 1.0
CG1 A:VAL613 4.3 4.6 1.0
HG13 A:VAL613 4.4 5.5 1.0
HB3 A:HIS614 4.4 5.8 1.0
N A:VAL613 4.4 4.1 1.0
OH A:TYR745 4.4 8.0 1.0
CA A:HIS614 4.4 4.2 1.0
HB2 A:ASP705 4.4 5.8 1.0
HB3 A:ASP705 4.5 5.8 1.0
HB3 A:ASP612 4.5 5.0 1.0
H A:GLY744 4.6 6.9 1.0
CE1 A:HIS573 4.6 5.5 1.0
CE2 A:TYR745 4.6 5.9 1.0
O A:HOH1173 4.6 16.2 1.0
N A:GLY743 4.7 4.5 1.0
C10 A:FBM807 4.7 10.1 1.0
NE2 A:HIS574 4.7 6.0 1.0
H2 A:FBM807 4.8 12.1 1.0
HB2 A:ASP612 4.8 5.0 1.0
HG11 A:VAL613 4.8 5.5 1.0
HA2 A:GLY743 4.8 5.4 1.0
HE2 A:HIS614 4.9 7.8 1.0
HA A:ASP612 4.9 4.9 1.0
C A:ASP612 4.9 4.0 1.0
HA3 A:GLY703 4.9 4.8 1.0
C A:VAL613 4.9 4.5 1.0
CA A:ASP612 4.9 4.0 1.0
CZ A:TYR745 5.0 6.3 1.0

Zinc binding site 2 out of 2 in 6csp

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


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

b:6.0
occ:1.00
H13 B:FBM805 1.8 9.3 1.0
OD2 B:ASP705 2.0 5.8 1.0
O04 B:FBM805 2.0 7.7 1.0
OD1 B:ASP612 2.1 4.3 1.0
ND1 B:HIS614 2.1 5.2 1.0
O01 B:FBM805 2.2 10.3 1.0
N03 B:FBM805 2.7 9.4 1.0
CG B:ASP612 2.8 4.0 1.0
C02 B:FBM805 2.8 9.4 1.0
OD2 B:ASP612 2.8 4.9 1.0
CE1 B:HIS614 3.0 6.3 1.0
CG B:ASP705 3.0 5.2 1.0
HE1 B:HIS614 3.1 7.5 1.0
HB2 B:HIS614 3.1 5.5 1.0
CG B:HIS614 3.2 4.3 1.0
H B:HIS614 3.3 5.3 1.0
HA3 B:GLY743 3.4 5.1 1.0
OD1 B:ASP705 3.4 5.7 1.0
HG12 B:VAL613 3.4 7.3 1.0
HE2 B:HIS573 3.4 6.5 1.0
H12 B:FBM805 3.4 11.3 1.0
HH B:TYR745 3.6 8.7 1.0
CB B:HIS614 3.6 4.6 1.0
HE2 B:TYR745 3.8 7.7 1.0
N B:HIS614 4.0 4.5 1.0
H B:VAL613 4.0 5.2 1.0
NE2 B:HIS614 4.1 6.6 1.0
C05 B:FBM805 4.1 8.8 1.0
NE2 B:HIS573 4.1 5.4 1.0
H B:GLY743 4.2 5.5 1.0
H1 B:FBM805 4.2 11.6 1.0
CB B:ASP612 4.2 3.9 1.0
HE1 B:HIS573 4.2 7.1 1.0
CD2 B:HIS614 4.2 5.7 1.0
CG1 B:VAL613 4.3 6.1 1.0
CA B:GLY743 4.3 4.3 1.0
CB B:ASP705 4.3 4.9 1.0
HG13 B:VAL613 4.3 7.3 1.0
HB3 B:HIS614 4.4 5.5 1.0
OH B:TYR745 4.4 7.2 1.0
N B:VAL613 4.4 4.4 1.0
CA B:HIS614 4.4 4.6 1.0
HB2 B:ASP705 4.5 5.8 1.0
HB3 B:ASP705 4.5 5.8 1.0
HB3 B:ASP612 4.5 4.6 1.0
CE1 B:HIS573 4.6 5.9 1.0
H B:GLY744 4.6 6.5 1.0
CE2 B:TYR745 4.6 6.5 1.0
N B:GLY743 4.6 4.6 1.0
C10 B:FBM805 4.7 9.7 1.0
O B:HOH1206 4.7 18.0 1.0
NE2 B:HIS574 4.8 5.8 1.0
H2 B:FBM805 4.8 11.6 1.0
HB2 B:ASP612 4.8 4.6 1.0
HG11 B:VAL613 4.8 7.3 1.0
HA2 B:GLY743 4.8 5.1 1.0
HE2 B:HIS614 4.9 7.9 1.0
HA B:ASP612 4.9 4.8 1.0
C B:ASP612 4.9 4.4 1.0
C B:VAL613 4.9 4.7 1.0
HA3 B:GLY703 4.9 5.7 1.0
CA B:ASP612 4.9 4.0 1.0
CZ B:TYR745 5.0 6.3 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 11:37:50 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy