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Zinc in PDB 5iwg: HDAC2 with Ligand BRD4884

Enzymatic activity of HDAC2 with Ligand BRD4884

All present enzymatic activity of HDAC2 with Ligand BRD4884:
3.5.1.98;

Protein crystallography data

The structure of HDAC2 with Ligand BRD4884, PDB code: 5iwg was solved by S.Steinbacher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.35 / 1.66
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.297, 98.013, 139.250, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 20.8

Other elements in 5iwg:

The structure of HDAC2 with Ligand BRD4884 also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Calcium (Ca) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the HDAC2 with Ligand BRD4884 (pdb code 5iwg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the HDAC2 with Ligand BRD4884, PDB code: 5iwg:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 5iwg

Go back to Zinc Binding Sites List in 5iwg
Zinc binding site 1 out of 3 in the HDAC2 with Ligand BRD4884


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of HDAC2 with Ligand BRD4884 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:13.1
occ:1.00
OD2 A:ASP269 2.0 12.8 1.0
OD1 A:ASP181 2.0 12.0 1.0
N10 A:IWX403 2.1 11.8 1.0
ND1 A:HIS183 2.2 14.7 1.0
O1 A:IWX403 2.7 13.3 1.0
CG A:ASP181 2.8 11.8 1.0
CG A:ASP269 2.9 12.8 1.0
OD2 A:ASP181 3.0 11.6 1.0
CE1 A:HIS183 3.1 15.1 1.0
C9 A:IWX403 3.2 12.6 1.0
CG A:HIS183 3.2 14.9 1.0
OD1 A:ASP269 3.3 12.3 1.0
C2 A:IWX403 3.6 15.1 1.0
CB A:HIS183 3.6 14.2 1.0
C8 A:IWX403 3.9 11.6 1.0
N A:HIS183 4.0 13.5 1.0
C4 A:IWX403 4.0 13.2 1.0
N3 A:IWX403 4.1 14.6 1.0
CA A:GLY306 4.2 13.2 1.0
NE2 A:HIS183 4.2 15.6 1.0
CG2 A:ILE182 4.2 13.8 1.0
NE2 A:HIS145 4.2 14.7 1.0
CB A:ASP181 4.2 11.8 1.0
CD2 A:HIS183 4.3 15.4 1.0
CB A:ASP269 4.3 13.2 1.0
CA A:HIS183 4.4 13.9 1.0
N A:GLY306 4.4 12.9 1.0
C18 A:IWX403 4.6 16.7 1.0
N A:ILE182 4.6 12.5 1.0
NE2 A:HIS146 4.6 15.1 1.0
CE1 A:HIS145 4.7 14.1 1.0
OH A:TYR308 4.8 14.4 1.0
CE2 A:TYR308 4.9 14.2 1.0
C A:ILE182 5.0 13.4 1.0
CA A:ASP181 5.0 11.8 1.0

Zinc binding site 2 out of 3 in 5iwg

Go back to Zinc Binding Sites List in 5iwg
Zinc binding site 2 out of 3 in the HDAC2 with Ligand BRD4884


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of HDAC2 with Ligand BRD4884 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:10.4
occ:1.00
OD2 B:ASP269 1.9 9.9 1.0
OD1 B:ASP181 2.0 10.4 1.0
N10 B:IWX403 2.2 9.9 1.0
ND1 B:HIS183 2.2 12.0 1.0
O1 B:IWX403 2.8 11.9 1.0
CG B:ASP181 2.8 9.7 1.0
CG B:ASP269 2.9 10.1 1.0
OD2 B:ASP181 3.0 9.5 1.0
CE1 B:HIS183 3.0 12.6 1.0
C9 B:IWX403 3.2 10.2 1.0
CG B:HIS183 3.2 12.0 1.0
OD1 B:ASP269 3.2 9.6 1.0
CB B:HIS183 3.6 11.3 1.0
C2 B:IWX403 3.7 13.3 1.0
C8 B:IWX403 3.9 10.1 1.0
N B:HIS183 3.9 10.6 1.0
C4 B:IWX403 4.0 10.5 1.0
NE2 B:HIS183 4.2 13.5 1.0
N3 B:IWX403 4.2 12.1 1.0
CA B:GLY306 4.2 10.3 1.0
CB B:ASP181 4.2 9.6 1.0
NE2 B:HIS145 4.2 11.3 1.0
CB B:ASP269 4.3 10.3 1.0
CG2 B:ILE182 4.3 11.3 1.0
CD2 B:HIS183 4.3 13.2 1.0
CA B:HIS183 4.4 11.1 1.0
N B:GLY306 4.4 10.3 1.0
N B:ILE182 4.5 9.9 1.0
NE2 B:HIS146 4.6 12.8 1.0
CE1 B:HIS145 4.8 11.1 1.0
OH B:TYR308 4.9 11.9 1.0
C18 B:IWX403 4.9 16.6 1.0
CE2 B:TYR308 4.9 11.4 1.0
C B:ILE182 4.9 10.7 1.0
CA B:ASP181 5.0 9.5 1.0

Zinc binding site 3 out of 3 in 5iwg

Go back to Zinc Binding Sites List in 5iwg
Zinc binding site 3 out of 3 in the HDAC2 with Ligand BRD4884


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of HDAC2 with Ligand BRD4884 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:17.3
occ:1.00
OD2 C:ASP269 1.9 16.5 1.0
OD1 C:ASP181 2.0 17.7 1.0
N10 C:IWX403 2.2 14.7 1.0
ND1 C:HIS183 2.3 19.2 1.0
O1 C:IWX403 2.8 19.1 1.0
CG C:ASP181 2.8 17.7 1.0
CG C:ASP269 2.9 17.6 1.0
OD2 C:ASP181 2.9 17.9 1.0
CE1 C:HIS183 3.2 19.8 1.0
C9 C:IWX403 3.2 15.1 1.0
OD1 C:ASP269 3.2 17.4 1.0
CG C:HIS183 3.3 18.5 1.0
CB C:HIS183 3.6 17.6 1.0
C2 C:IWX403 3.7 19.9 1.0
N C:HIS183 3.9 17.8 1.0
C8 C:IWX403 4.0 14.8 1.0
C4 C:IWX403 4.0 15.7 1.0
N3 C:IWX403 4.2 17.6 1.0
CA C:GLY306 4.2 19.1 1.0
CG2 C:ILE182 4.2 19.4 1.0
NE2 C:HIS183 4.2 19.9 1.0
CB C:ASP269 4.3 18.4 1.0
CB C:ASP181 4.3 17.5 1.0
NE2 C:HIS145 4.3 18.2 1.0
CD2 C:HIS183 4.3 19.4 1.0
CA C:HIS183 4.4 17.5 1.0
N C:GLY306 4.4 18.5 1.0
N C:ILE182 4.5 18.3 1.0
NE2 C:HIS146 4.6 18.6 1.0
CE1 C:HIS145 4.8 18.1 1.0
C18 C:IWX403 4.9 21.1 1.0
C C:ILE182 4.9 18.2 1.0
OH C:TYR308 5.0 20.1 1.0
CA C:ASP181 5.0 17.9 1.0

Reference:

F.F.Wagner, M.Weiwer, S.Steinbacher, A.Schomburg, P.Reinemer, J.P.Gale, A.J.Campbell, S.L.Fisher, W.N.Zhao, S.A.Reis, K.M.Hennig, M.Thomas, P.Muller, M.R.Jefson, D.M.Fass, S.J.Haggarty, Y.L.Zhang, E.B.Holson. Kinetic and Structural Insights Into the Binding of Histone Deacetylase 1 and 2 (HDAC1, 2) Inhibitors. Bioorg.Med.Chem. V. 24 4008 2016.
ISSN: ESSN 1464-3391
PubMed: 27377864
DOI: 10.1016/J.BMC.2016.06.040
Page generated: Wed Dec 16 06:22:51 2020

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