Zinc in PDB 6z2k: The Structure of the Tetrameric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex
Enzymatic activity of The Structure of the Tetrameric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex
All present enzymatic activity of The Structure of the Tetrameric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex:
3.5.1.98;
Other elements in 6z2k:
The structure of The Structure of the Tetrameric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the The Structure of the Tetrameric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex
(pdb code 6z2k). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
The Structure of the Tetrameric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex, PDB code: 6z2k:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 6z2k
Go back to
Zinc Binding Sites List in 6z2k
Zinc binding site 1 out
of 4 in the The Structure of the Tetrameric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of The Structure of the Tetrameric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn501
b:0.8
occ:1.00
|
OD1
|
C:ASP176
|
2.0
|
0.8
|
1.0
|
|
OD2
|
C:ASP264
|
2.0
|
0.4
|
1.0
|
|
ND1
|
C:HIS178
|
2.0
|
0.3
|
1.0
|
|
CG
|
C:ASP176
|
2.6
|
0.8
|
1.0
|
|
OD2
|
C:ASP176
|
2.6
|
0.8
|
1.0
|
|
HB2
|
C:HIS178
|
2.7
|
0.3
|
1.0
|
|
CG
|
C:HIS178
|
3.0
|
0.3
|
1.0
|
|
HA3
|
C:GLY301
|
3.0
|
0.0
|
1.0
|
|
CE1
|
C:HIS178
|
3.0
|
0.3
|
1.0
|
|
H
|
C:HIS178
|
3.0
|
0.3
|
1.0
|
|
CG
|
C:ASP264
|
3.1
|
0.4
|
1.0
|
|
HE1
|
C:HIS140
|
3.1
|
0.4
|
1.0
|
|
CB
|
C:HIS178
|
3.3
|
0.3
|
1.0
|
|
HE1
|
C:HIS178
|
3.3
|
0.3
|
1.0
|
|
HG22
|
C:ILE177
|
3.5
|
0.7
|
1.0
|
|
OD1
|
C:ASP264
|
3.5
|
0.4
|
1.0
|
|
N
|
C:HIS178
|
3.8
|
0.3
|
1.0
|
|
CE1
|
C:HIS140
|
3.8
|
0.4
|
1.0
|
|
HH
|
C:TYR303
|
3.9
|
0.0
|
1.0
|
|
H
|
C:GLY301
|
3.9
|
0.0
|
1.0
|
|
CA
|
C:GLY301
|
3.9
|
0.0
|
1.0
|
|
HB3
|
C:HIS178
|
4.0
|
0.3
|
1.0
|
|
CB
|
C:ASP176
|
4.0
|
0.8
|
1.0
|
|
HE2
|
C:TYR303
|
4.1
|
0.0
|
1.0
|
|
NE2
|
C:HIS140
|
4.1
|
0.4
|
1.0
|
|
CD2
|
C:HIS178
|
4.1
|
0.3
|
1.0
|
|
NE2
|
C:HIS178
|
4.1
|
0.3
|
1.0
|
|
CA
|
C:HIS178
|
4.1
|
0.3
|
1.0
|
|
HB3
|
C:ASP176
|
4.2
|
0.8
|
1.0
|
|
H
|
C:ILE177
|
4.3
|
0.7
|
1.0
|
|
HA2
|
C:GLY301
|
4.3
|
0.0
|
1.0
|
|
N
|
C:GLY301
|
4.4
|
0.0
|
1.0
|
|
CB
|
C:ASP264
|
4.4
|
0.4
|
1.0
|
|
CG2
|
C:ILE177
|
4.4
|
0.7
|
1.0
|
|
NE2
|
C:HIS141
|
4.5
|
0.1
|
1.0
|
|
HB3
|
C:ASP264
|
4.5
|
0.4
|
1.0
|
|
HB2
|
C:ASP176
|
4.5
|
0.8
|
1.0
|
|
HB2
|
C:ASP264
|
4.6
|
0.4
|
1.0
|
|
N
|
C:ILE177
|
4.6
|
0.7
|
1.0
|
|
HG21
|
C:ILE177
|
4.6
|
0.7
|
1.0
|
|
OH
|
C:TYR303
|
4.7
|
0.0
|
1.0
|
|
HG23
|
C:ILE177
|
4.7
|
0.7
|
1.0
|
|
CE2
|
C:TYR303
|
4.8
|
0.0
|
1.0
|
|
HA
|
C:HIS178
|
4.8
|
0.3
|
1.0
|
|
HE22
|
C:GLN260
|
4.9
|
0.8
|
1.0
|
|
HE2
|
C:HIS178
|
4.9
|
0.3
|
1.0
|
|
C
|
C:ILE177
|
4.9
|
0.7
|
1.0
|
|
C
|
C:GLY301
|
4.9
|
0.0
|
1.0
|
|
HA
|
C:ASP176
|
4.9
|
0.8
|
1.0
|
|
HD2
|
C:HIS178
|
4.9
|
0.3
|
1.0
|
|
H
|
C:GLY302
|
4.9
|
0.3
|
1.0
|
|
CA
|
C:ASP176
|
4.9
|
0.8
|
1.0
|
|
C
|
C:ASP176
|
4.9
|
0.8
|
1.0
|
|
O
|
C:HIS178
|
5.0
|
0.3
|
1.0
|
|
Zinc binding site 2 out
of 4 in 6z2k
Go back to
Zinc Binding Sites List in 6z2k
Zinc binding site 2 out
of 4 in the The Structure of the Tetrameric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of The Structure of the Tetrameric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn502
b:0.8
occ:1.00
|
OD1
|
E:ASP176
|
2.0
|
0.2
|
1.0
|
|
OD2
|
E:ASP264
|
2.0
|
0.1
|
1.0
|
|
ND1
|
E:HIS178
|
2.0
|
0.6
|
1.0
|
|
CG
|
E:ASP176
|
2.6
|
0.2
|
1.0
|
|
OD2
|
E:ASP176
|
2.6
|
0.2
|
1.0
|
|
HB2
|
E:HIS178
|
2.7
|
0.6
|
1.0
|
|
CG
|
E:HIS178
|
3.0
|
0.6
|
1.0
|
|
HA3
|
E:GLY301
|
3.0
|
0.5
|
1.0
|
|
CE1
|
E:HIS178
|
3.0
|
0.6
|
1.0
|
|
H
|
E:HIS178
|
3.0
|
0.6
|
1.0
|
|
CG
|
E:ASP264
|
3.1
|
0.1
|
1.0
|
|
HE1
|
E:HIS140
|
3.1
|
1.0
|
1.0
|
|
CB
|
E:HIS178
|
3.3
|
0.6
|
1.0
|
|
HE1
|
E:HIS178
|
3.3
|
0.6
|
1.0
|
|
HG22
|
E:ILE177
|
3.5
|
0.1
|
1.0
|
|
OD1
|
E:ASP264
|
3.5
|
0.1
|
1.0
|
|
N
|
E:HIS178
|
3.8
|
0.6
|
1.0
|
|
CE1
|
E:HIS140
|
3.8
|
1.0
|
1.0
|
|
HH
|
E:TYR303
|
3.9
|
0.0
|
1.0
|
|
H
|
E:GLY301
|
3.9
|
0.5
|
1.0
|
|
CA
|
E:GLY301
|
3.9
|
0.5
|
1.0
|
|
HB3
|
E:HIS178
|
4.0
|
0.6
|
1.0
|
|
CB
|
E:ASP176
|
4.0
|
0.2
|
1.0
|
|
HE2
|
E:TYR303
|
4.1
|
0.0
|
1.0
|
|
NE2
|
E:HIS140
|
4.1
|
1.0
|
1.0
|
|
CD2
|
E:HIS178
|
4.1
|
0.6
|
1.0
|
|
NE2
|
E:HIS178
|
4.1
|
0.6
|
1.0
|
|
CA
|
E:HIS178
|
4.1
|
0.6
|
1.0
|
|
HB3
|
E:ASP176
|
4.2
|
0.2
|
1.0
|
|
H
|
E:ILE177
|
4.3
|
0.1
|
1.0
|
|
HA2
|
E:GLY301
|
4.3
|
0.5
|
1.0
|
|
N
|
E:GLY301
|
4.4
|
0.5
|
1.0
|
|
CB
|
E:ASP264
|
4.4
|
0.1
|
1.0
|
|
CG2
|
E:ILE177
|
4.4
|
0.1
|
1.0
|
|
NE2
|
E:HIS141
|
4.5
|
0.4
|
1.0
|
|
HB3
|
E:ASP264
|
4.5
|
0.1
|
1.0
|
|
HB2
|
E:ASP176
|
4.5
|
0.2
|
1.0
|
|
HB2
|
E:ASP264
|
4.6
|
0.1
|
1.0
|
|
N
|
E:ILE177
|
4.6
|
0.1
|
1.0
|
|
HG21
|
E:ILE177
|
4.6
|
0.1
|
1.0
|
|
OH
|
E:TYR303
|
4.7
|
0.0
|
1.0
|
|
HG23
|
E:ILE177
|
4.7
|
0.1
|
1.0
|
|
HA
|
E:HIS178
|
4.8
|
0.6
|
1.0
|
|
CE2
|
E:TYR303
|
4.8
|
0.0
|
1.0
|
|
HE22
|
E:GLN260
|
4.9
|
0.3
|
1.0
|
|
HE2
|
E:HIS178
|
4.9
|
0.6
|
1.0
|
|
C
|
E:ILE177
|
4.9
|
0.1
|
1.0
|
|
C
|
E:GLY301
|
4.9
|
0.5
|
1.0
|
|
HA
|
E:ASP176
|
4.9
|
0.2
|
1.0
|
|
HD2
|
E:HIS178
|
4.9
|
0.6
|
1.0
|
|
H
|
E:GLY302
|
4.9
|
0.1
|
1.0
|
|
CA
|
E:ASP176
|
4.9
|
0.2
|
1.0
|
|
C
|
E:ASP176
|
4.9
|
0.2
|
1.0
|
|
O
|
E:HIS178
|
5.0
|
0.6
|
1.0
|
|
Zinc binding site 3 out
of 4 in 6z2k
Go back to
Zinc Binding Sites List in 6z2k
Zinc binding site 3 out
of 4 in the The Structure of the Tetrameric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of The Structure of the Tetrameric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Zn501
b:0.4
occ:1.00
|
OD1
|
K:ASP176
|
2.0
|
0.8
|
1.0
|
|
OD2
|
K:ASP264
|
2.0
|
0.1
|
1.0
|
|
ND1
|
K:HIS178
|
2.0
|
0.9
|
1.0
|
|
CG
|
K:ASP176
|
2.6
|
0.8
|
1.0
|
|
OD2
|
K:ASP176
|
2.6
|
0.8
|
1.0
|
|
HB2
|
K:HIS178
|
2.7
|
0.9
|
1.0
|
|
CG
|
K:HIS178
|
3.0
|
0.9
|
1.0
|
|
HA3
|
K:GLY301
|
3.0
|
0.6
|
1.0
|
|
CE1
|
K:HIS178
|
3.0
|
0.9
|
1.0
|
|
H
|
K:HIS178
|
3.0
|
0.9
|
1.0
|
|
CG
|
K:ASP264
|
3.1
|
0.1
|
1.0
|
|
HE1
|
K:HIS140
|
3.1
|
0.7
|
1.0
|
|
CB
|
K:HIS178
|
3.3
|
0.9
|
1.0
|
|
HE1
|
K:HIS178
|
3.3
|
0.9
|
1.0
|
|
HG22
|
K:ILE177
|
3.5
|
1.0
|
1.0
|
|
OD1
|
K:ASP264
|
3.5
|
0.1
|
1.0
|
|
N
|
K:HIS178
|
3.8
|
0.9
|
1.0
|
|
CE1
|
K:HIS140
|
3.8
|
0.7
|
1.0
|
|
HH
|
K:TYR303
|
3.9
|
0.2
|
1.0
|
|
H
|
K:GLY301
|
3.9
|
0.6
|
1.0
|
|
CA
|
K:GLY301
|
3.9
|
0.6
|
1.0
|
|
HB3
|
K:HIS178
|
4.0
|
0.9
|
1.0
|
|
CB
|
K:ASP176
|
4.0
|
0.8
|
1.0
|
|
HE2
|
K:TYR303
|
4.1
|
0.2
|
1.0
|
|
NE2
|
K:HIS140
|
4.1
|
0.7
|
1.0
|
|
CD2
|
K:HIS178
|
4.1
|
0.9
|
1.0
|
|
NE2
|
K:HIS178
|
4.1
|
0.9
|
1.0
|
|
CA
|
K:HIS178
|
4.1
|
0.9
|
1.0
|
|
HB3
|
K:ASP176
|
4.2
|
0.8
|
1.0
|
|
H
|
K:ILE177
|
4.3
|
1.0
|
1.0
|
|
HA2
|
K:GLY301
|
4.3
|
0.6
|
1.0
|
|
N
|
K:GLY301
|
4.4
|
0.6
|
1.0
|
|
CB
|
K:ASP264
|
4.4
|
0.1
|
1.0
|
|
CG2
|
K:ILE177
|
4.4
|
1.0
|
1.0
|
|
NE2
|
K:HIS141
|
4.5
|
0.8
|
1.0
|
|
HB3
|
K:ASP264
|
4.5
|
0.1
|
1.0
|
|
HB2
|
K:ASP176
|
4.5
|
0.8
|
1.0
|
|
HB2
|
K:ASP264
|
4.6
|
0.1
|
1.0
|
|
N
|
K:ILE177
|
4.6
|
1.0
|
1.0
|
|
HG21
|
K:ILE177
|
4.6
|
1.0
|
1.0
|
|
OH
|
K:TYR303
|
4.7
|
0.2
|
1.0
|
|
HG23
|
K:ILE177
|
4.7
|
1.0
|
1.0
|
|
CE2
|
K:TYR303
|
4.8
|
0.2
|
1.0
|
|
HA
|
K:HIS178
|
4.8
|
0.9
|
1.0
|
|
HE22
|
K:GLN260
|
4.9
|
0.5
|
1.0
|
|
HE2
|
K:HIS178
|
4.9
|
0.9
|
1.0
|
|
C
|
K:ILE177
|
4.9
|
1.0
|
1.0
|
|
C
|
K:GLY301
|
4.9
|
0.6
|
1.0
|
|
HA
|
K:ASP176
|
4.9
|
0.8
|
1.0
|
|
HD2
|
K:HIS178
|
4.9
|
0.9
|
1.0
|
|
H
|
K:GLY302
|
4.9
|
0.4
|
1.0
|
|
CA
|
K:ASP176
|
4.9
|
0.8
|
1.0
|
|
C
|
K:ASP176
|
4.9
|
0.8
|
1.0
|
|
O
|
K:HIS178
|
5.0
|
0.9
|
1.0
|
|
Zinc binding site 4 out
of 4 in 6z2k
Go back to
Zinc Binding Sites List in 6z2k
Zinc binding site 4 out
of 4 in the The Structure of the Tetrameric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of The Structure of the Tetrameric HDAC1/Mideas/DNTTIP1 Midac Deacetylase Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn501
b:0.4
occ:1.00
|
OD1
|
I:ASP176
|
2.0
|
1.0
|
1.0
|
|
OD2
|
I:ASP264
|
2.0
|
0.3
|
1.0
|
|
ND1
|
I:HIS178
|
2.0
|
1.0
|
1.0
|
|
CG
|
I:ASP176
|
2.6
|
1.0
|
1.0
|
|
OD2
|
I:ASP176
|
2.6
|
1.0
|
1.0
|
|
HB2
|
I:HIS178
|
2.7
|
1.0
|
1.0
|
|
CG
|
I:HIS178
|
3.0
|
1.0
|
1.0
|
|
HA3
|
I:GLY301
|
3.0
|
0.9
|
1.0
|
|
CE1
|
I:HIS178
|
3.0
|
1.0
|
1.0
|
|
H
|
I:HIS178
|
3.0
|
1.0
|
1.0
|
|
CG
|
I:ASP264
|
3.1
|
0.3
|
1.0
|
|
HE1
|
I:HIS140
|
3.1
|
0.3
|
1.0
|
|
CB
|
I:HIS178
|
3.3
|
1.0
|
1.0
|
|
HE1
|
I:HIS178
|
3.3
|
1.0
|
1.0
|
|
HG22
|
I:ILE177
|
3.5
|
0.7
|
1.0
|
|
OD1
|
I:ASP264
|
3.5
|
0.3
|
1.0
|
|
N
|
I:HIS178
|
3.8
|
1.0
|
1.0
|
|
CE1
|
I:HIS140
|
3.8
|
0.3
|
1.0
|
|
HH
|
I:TYR303
|
3.9
|
0.4
|
1.0
|
|
H
|
I:GLY301
|
3.9
|
0.9
|
1.0
|
|
CA
|
I:GLY301
|
3.9
|
0.9
|
1.0
|
|
HB3
|
I:HIS178
|
4.0
|
1.0
|
1.0
|
|
CB
|
I:ASP176
|
4.0
|
1.0
|
1.0
|
|
HE2
|
I:TYR303
|
4.1
|
0.4
|
1.0
|
|
NE2
|
I:HIS140
|
4.1
|
0.3
|
1.0
|
|
CD2
|
I:HIS178
|
4.1
|
1.0
|
1.0
|
|
NE2
|
I:HIS178
|
4.1
|
1.0
|
1.0
|
|
CA
|
I:HIS178
|
4.1
|
1.0
|
1.0
|
|
HB3
|
I:ASP176
|
4.2
|
1.0
|
1.0
|
|
H
|
I:ILE177
|
4.3
|
0.7
|
1.0
|
|
HA2
|
I:GLY301
|
4.3
|
0.9
|
1.0
|
|
N
|
I:GLY301
|
4.4
|
0.9
|
1.0
|
|
CB
|
I:ASP264
|
4.4
|
0.3
|
1.0
|
|
CG2
|
I:ILE177
|
4.4
|
0.7
|
1.0
|
|
NE2
|
I:HIS141
|
4.5
|
0.6
|
1.0
|
|
HB3
|
I:ASP264
|
4.5
|
0.3
|
1.0
|
|
HB2
|
I:ASP176
|
4.5
|
1.0
|
1.0
|
|
HB2
|
I:ASP264
|
4.6
|
0.3
|
1.0
|
|
N
|
I:ILE177
|
4.6
|
0.7
|
1.0
|
|
HG21
|
I:ILE177
|
4.6
|
0.7
|
1.0
|
|
OH
|
I:TYR303
|
4.7
|
0.4
|
1.0
|
|
HG23
|
I:ILE177
|
4.7
|
0.7
|
1.0
|
|
HA
|
I:HIS178
|
4.8
|
1.0
|
1.0
|
|
CE2
|
I:TYR303
|
4.9
|
0.4
|
1.0
|
|
HE22
|
I:GLN260
|
4.9
|
0.9
|
1.0
|
|
HE2
|
I:HIS178
|
4.9
|
1.0
|
1.0
|
|
C
|
I:ILE177
|
4.9
|
0.7
|
1.0
|
|
C
|
I:GLY301
|
4.9
|
0.9
|
1.0
|
|
HA
|
I:ASP176
|
4.9
|
1.0
|
1.0
|
|
HD2
|
I:HIS178
|
4.9
|
1.0
|
1.0
|
|
CA
|
I:ASP176
|
4.9
|
1.0
|
1.0
|
|
H
|
I:GLY302
|
4.9
|
0.7
|
1.0
|
|
C
|
I:ASP176
|
4.9
|
1.0
|
1.0
|
|
O
|
I:HIS178
|
5.0
|
1.0
|
1.0
|
|
Reference:
R.E.Turnbull,
L.Fairall,
A.Saleh,
E.Kelsall,
K.L.Morris,
T.J.Ragan,
C.G.Savva,
A.Chandru,
C.J.Millard,
O.V.Makarova,
C.J.Smith,
A.M.Roseman,
A.M.Fry,
S.M.Cowley,
J.W.R.Schwabe.
The Midac Histone Deacetylase Complex Is Essential For Embryonic Development and Has A Unique Multivalent Structure. Nat Commun V. 11 3252 2020.
ISSN: ESSN 2041-1723
PubMed: 32591534
DOI: 10.1038/S41467-020-17078-8
Page generated: Tue Oct 29 15:22:40 2024
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