Zinc in PDB 6z6o: Hdac-Tc
Enzymatic activity of Hdac-Tc
All present enzymatic activity of Hdac-Tc:
3.5.1.98;
Zinc Binding Sites:
The binding sites of Zinc atom in the Hdac-Tc
(pdb code 6z6o). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Hdac-Tc, PDB code: 6z6o:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 6z6o
Go back to
Zinc Binding Sites List in 6z6o
Zinc binding site 1 out
of 8 in the Hdac-Tc
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Hdac-Tc within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn801
b:194.8
occ:1.00
|
ND1
|
A:HIS247
|
2.2
|
152.8
|
1.0
|
|
OD2
|
A:ASP245
|
2.2
|
158.4
|
1.0
|
|
OD1
|
A:ASP245
|
2.4
|
158.4
|
1.0
|
|
CE1
|
A:HIS247
|
2.6
|
152.8
|
1.0
|
|
CG
|
A:ASP245
|
2.6
|
158.4
|
1.0
|
|
OD2
|
A:ASP338
|
2.9
|
152.2
|
1.0
|
|
CG
|
A:HIS247
|
3.5
|
152.8
|
1.0
|
|
NE2
|
A:HIS247
|
3.8
|
152.8
|
1.0
|
|
CA
|
A:GLY376
|
3.8
|
167.9
|
1.0
|
|
CG
|
A:ASP338
|
4.0
|
152.2
|
1.0
|
|
CB
|
A:ASP245
|
4.2
|
158.4
|
1.0
|
|
NE2
|
A:HIS205
|
4.2
|
166.4
|
1.0
|
|
CB
|
A:HIS247
|
4.2
|
152.8
|
1.0
|
|
CD2
|
A:HIS247
|
4.3
|
152.8
|
1.0
|
|
N
|
A:GLY376
|
4.5
|
167.9
|
1.0
|
|
N
|
A:HIS247
|
4.6
|
152.8
|
1.0
|
|
CB
|
A:ASP338
|
4.7
|
152.2
|
1.0
|
|
CE1
|
A:HIS205
|
4.8
|
166.4
|
1.0
|
|
NE2
|
A:HIS206
|
4.8
|
167.4
|
1.0
|
|
OD1
|
A:ASP338
|
4.9
|
152.2
|
1.0
|
|
N
|
A:ILE246
|
4.9
|
150.5
|
1.0
|
|
Zinc binding site 2 out
of 8 in 6z6o
Go back to
Zinc Binding Sites List in 6z6o
Zinc binding site 2 out
of 8 in the Hdac-Tc
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Hdac-Tc within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn801
b:181.3
occ:1.00
|
OD2
|
B:ASP338
|
2.1
|
166.2
|
1.0
|
|
ND1
|
B:HIS247
|
2.2
|
153.9
|
1.0
|
|
OD1
|
B:ASP245
|
2.2
|
159.8
|
1.0
|
|
OD2
|
B:ASP245
|
2.5
|
159.8
|
1.0
|
|
CG
|
B:ASP245
|
2.7
|
159.8
|
1.0
|
|
CE1
|
B:HIS247
|
3.0
|
153.9
|
1.0
|
|
CG
|
B:ASP338
|
3.2
|
166.2
|
1.0
|
|
CG
|
B:HIS247
|
3.2
|
153.9
|
1.0
|
|
CB
|
B:HIS247
|
3.7
|
153.9
|
1.0
|
|
OD1
|
B:ASP338
|
3.9
|
166.2
|
1.0
|
|
OH
|
B:TYR378
|
3.9
|
172.6
|
1.0
|
|
NE2
|
B:HIS205
|
4.1
|
176.0
|
1.0
|
|
NE2
|
B:HIS247
|
4.1
|
153.9
|
1.0
|
|
N
|
B:HIS247
|
4.1
|
153.9
|
1.0
|
|
CB
|
B:ASP338
|
4.1
|
166.2
|
1.0
|
|
CE1
|
B:HIS205
|
4.2
|
176.0
|
1.0
|
|
CB
|
B:ASP245
|
4.2
|
159.8
|
1.0
|
|
CD2
|
B:HIS247
|
4.2
|
153.9
|
1.0
|
|
CE2
|
B:TYR378
|
4.4
|
172.6
|
1.0
|
|
CA
|
B:HIS247
|
4.5
|
153.9
|
1.0
|
|
CA
|
B:GLY376
|
4.5
|
183.6
|
1.0
|
|
CZ
|
B:TYR378
|
4.7
|
172.6
|
1.0
|
|
N
|
B:ILE246
|
4.7
|
146.3
|
1.0
|
|
NE2
|
B:HIS206
|
4.7
|
160.9
|
1.0
|
|
CG2
|
B:ILE246
|
4.8
|
146.3
|
1.0
|
|
Zinc binding site 3 out
of 8 in 6z6o
Go back to
Zinc Binding Sites List in 6z6o
Zinc binding site 3 out
of 8 in the Hdac-Tc
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Hdac-Tc within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn801
b:193.7
occ:1.00
|
ND1
|
E:HIS247
|
2.2
|
152.6
|
1.0
|
|
OD2
|
E:ASP245
|
2.2
|
158.3
|
1.0
|
|
OD1
|
E:ASP245
|
2.4
|
158.3
|
1.0
|
|
CE1
|
E:HIS247
|
2.5
|
152.6
|
1.0
|
|
CG
|
E:ASP245
|
2.6
|
158.3
|
1.0
|
|
OD2
|
E:ASP338
|
2.9
|
152.9
|
1.0
|
|
CG
|
E:HIS247
|
3.5
|
152.6
|
1.0
|
|
NE2
|
E:HIS247
|
3.8
|
152.6
|
1.0
|
|
CA
|
E:GLY376
|
3.8
|
168.8
|
1.0
|
|
CG
|
E:ASP338
|
4.0
|
152.9
|
1.0
|
|
CB
|
E:ASP245
|
4.2
|
158.3
|
1.0
|
|
NE2
|
E:HIS205
|
4.2
|
166.0
|
1.0
|
|
CB
|
E:HIS247
|
4.2
|
152.6
|
1.0
|
|
CD2
|
E:HIS247
|
4.3
|
152.6
|
1.0
|
|
N
|
E:GLY376
|
4.5
|
168.8
|
1.0
|
|
N
|
E:HIS247
|
4.6
|
152.6
|
1.0
|
|
CB
|
E:ASP338
|
4.7
|
152.9
|
1.0
|
|
CE1
|
E:HIS205
|
4.8
|
166.0
|
1.0
|
|
NE2
|
E:HIS206
|
4.8
|
167.3
|
1.0
|
|
OD1
|
E:ASP338
|
4.9
|
152.9
|
1.0
|
|
N
|
E:ILE246
|
4.9
|
150.7
|
1.0
|
|
Zinc binding site 4 out
of 8 in 6z6o
Go back to
Zinc Binding Sites List in 6z6o
Zinc binding site 4 out
of 8 in the Hdac-Tc
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Hdac-Tc within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn801
b:185.4
occ:1.00
|
OD2
|
F:ASP338
|
2.1
|
167.5
|
1.0
|
|
ND1
|
F:HIS247
|
2.2
|
155.7
|
1.0
|
|
OD1
|
F:ASP245
|
2.2
|
162.6
|
1.0
|
|
OD2
|
F:ASP245
|
2.5
|
162.6
|
1.0
|
|
CG
|
F:ASP245
|
2.7
|
162.6
|
1.0
|
|
CE1
|
F:HIS247
|
3.0
|
155.7
|
1.0
|
|
CG
|
F:ASP338
|
3.2
|
167.5
|
1.0
|
|
CG
|
F:HIS247
|
3.2
|
155.7
|
1.0
|
|
CB
|
F:HIS247
|
3.7
|
155.7
|
1.0
|
|
OD1
|
F:ASP338
|
3.9
|
167.5
|
1.0
|
|
OH
|
F:TYR378
|
3.9
|
174.5
|
1.0
|
|
NE2
|
F:HIS205
|
4.1
|
177.4
|
1.0
|
|
N
|
F:HIS247
|
4.1
|
155.7
|
1.0
|
|
CB
|
F:ASP338
|
4.1
|
167.5
|
1.0
|
|
NE2
|
F:HIS247
|
4.1
|
155.7
|
1.0
|
|
CE1
|
F:HIS205
|
4.2
|
177.4
|
1.0
|
|
CB
|
F:ASP245
|
4.2
|
162.6
|
1.0
|
|
CD2
|
F:HIS247
|
4.2
|
155.7
|
1.0
|
|
CE2
|
F:TYR378
|
4.4
|
174.5
|
1.0
|
|
CA
|
F:HIS247
|
4.5
|
155.7
|
1.0
|
|
CA
|
F:GLY376
|
4.5
|
185.3
|
1.0
|
|
N
|
F:ILE246
|
4.7
|
148.6
|
1.0
|
|
CZ
|
F:TYR378
|
4.7
|
174.5
|
1.0
|
|
NE2
|
F:HIS206
|
4.7
|
161.7
|
1.0
|
|
CG2
|
F:ILE246
|
4.8
|
148.6
|
1.0
|
|
Zinc binding site 5 out
of 8 in 6z6o
Go back to
Zinc Binding Sites List in 6z6o
Zinc binding site 5 out
of 8 in the Hdac-Tc
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Hdac-Tc within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Zn801
b:193.7
occ:1.00
|
ND1
|
I:HIS247
|
2.2
|
152.6
|
1.0
|
|
OD2
|
I:ASP245
|
2.2
|
157.8
|
1.0
|
|
OD1
|
I:ASP245
|
2.4
|
157.8
|
1.0
|
|
CE1
|
I:HIS247
|
2.6
|
152.6
|
1.0
|
|
CG
|
I:ASP245
|
2.6
|
157.8
|
1.0
|
|
OD2
|
I:ASP338
|
2.9
|
152.0
|
1.0
|
|
CG
|
I:HIS247
|
3.5
|
152.6
|
1.0
|
|
NE2
|
I:HIS247
|
3.8
|
152.6
|
1.0
|
|
CA
|
I:GLY376
|
3.8
|
168.2
|
1.0
|
|
CG
|
I:ASP338
|
4.0
|
152.0
|
1.0
|
|
CB
|
I:ASP245
|
4.2
|
157.8
|
1.0
|
|
NE2
|
I:HIS205
|
4.2
|
166.6
|
1.0
|
|
CB
|
I:HIS247
|
4.2
|
152.6
|
1.0
|
|
CD2
|
I:HIS247
|
4.3
|
152.6
|
1.0
|
|
N
|
I:GLY376
|
4.5
|
168.2
|
1.0
|
|
N
|
I:HIS247
|
4.6
|
152.6
|
1.0
|
|
CB
|
I:ASP338
|
4.7
|
152.0
|
1.0
|
|
CE1
|
I:HIS205
|
4.8
|
166.6
|
1.0
|
|
NE2
|
I:HIS206
|
4.8
|
167.0
|
1.0
|
|
OD1
|
I:ASP338
|
4.9
|
152.0
|
1.0
|
|
N
|
I:ILE246
|
4.9
|
151.0
|
1.0
|
|
Zinc binding site 6 out
of 8 in 6z6o
Go back to
Zinc Binding Sites List in 6z6o
Zinc binding site 6 out
of 8 in the Hdac-Tc
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Hdac-Tc within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Zn801
b:182.0
occ:1.00
|
OD2
|
J:ASP338
|
2.1
|
166.2
|
1.0
|
|
ND1
|
J:HIS247
|
2.2
|
153.5
|
1.0
|
|
OD1
|
J:ASP245
|
2.2
|
160.6
|
1.0
|
|
OD2
|
J:ASP245
|
2.5
|
160.6
|
1.0
|
|
CG
|
J:ASP245
|
2.7
|
160.6
|
1.0
|
|
CE1
|
J:HIS247
|
3.0
|
153.5
|
1.0
|
|
CG
|
J:ASP338
|
3.2
|
166.2
|
1.0
|
|
CG
|
J:HIS247
|
3.2
|
153.5
|
1.0
|
|
CB
|
J:HIS247
|
3.7
|
153.5
|
1.0
|
|
OD1
|
J:ASP338
|
3.9
|
166.2
|
1.0
|
|
OH
|
J:TYR378
|
3.9
|
173.3
|
1.0
|
|
NE2
|
J:HIS205
|
4.1
|
176.5
|
1.0
|
|
NE2
|
J:HIS247
|
4.1
|
153.5
|
1.0
|
|
N
|
J:HIS247
|
4.1
|
153.5
|
1.0
|
|
CB
|
J:ASP338
|
4.1
|
166.2
|
1.0
|
|
CE1
|
J:HIS205
|
4.2
|
176.5
|
1.0
|
|
CB
|
J:ASP245
|
4.2
|
160.6
|
1.0
|
|
CD2
|
J:HIS247
|
4.2
|
153.5
|
1.0
|
|
CE2
|
J:TYR378
|
4.4
|
173.3
|
1.0
|
|
CA
|
J:GLY376
|
4.5
|
183.6
|
1.0
|
|
CA
|
J:HIS247
|
4.5
|
153.5
|
1.0
|
|
CZ
|
J:TYR378
|
4.7
|
173.3
|
1.0
|
|
N
|
J:ILE246
|
4.7
|
146.7
|
1.0
|
|
NE2
|
J:HIS206
|
4.7
|
161.2
|
1.0
|
|
CG2
|
J:ILE246
|
4.8
|
146.7
|
1.0
|
|
Zinc binding site 7 out
of 8 in 6z6o
Go back to
Zinc Binding Sites List in 6z6o
Zinc binding site 7 out
of 8 in the Hdac-Tc
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Hdac-Tc within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Zn801
b:191.1
occ:1.00
|
ND1
|
M:HIS247
|
2.2
|
152.0
|
1.0
|
|
OD2
|
M:ASP245
|
2.2
|
157.8
|
1.0
|
|
OD1
|
M:ASP245
|
2.4
|
157.8
|
1.0
|
|
CE1
|
M:HIS247
|
2.6
|
152.0
|
1.0
|
|
CG
|
M:ASP245
|
2.6
|
157.8
|
1.0
|
|
OD2
|
M:ASP338
|
2.9
|
153.1
|
1.0
|
|
CG
|
M:HIS247
|
3.5
|
152.0
|
1.0
|
|
NE2
|
M:HIS247
|
3.8
|
152.0
|
1.0
|
|
CA
|
M:GLY376
|
3.8
|
167.9
|
1.0
|
|
CG
|
M:ASP338
|
4.0
|
153.1
|
1.0
|
|
CB
|
M:ASP245
|
4.2
|
157.8
|
1.0
|
|
NE2
|
M:HIS205
|
4.2
|
165.5
|
1.0
|
|
CB
|
M:HIS247
|
4.2
|
152.0
|
1.0
|
|
CD2
|
M:HIS247
|
4.3
|
152.0
|
1.0
|
|
N
|
M:GLY376
|
4.5
|
167.9
|
1.0
|
|
N
|
M:HIS247
|
4.6
|
152.0
|
1.0
|
|
CB
|
M:ASP338
|
4.7
|
153.1
|
1.0
|
|
CE1
|
M:HIS205
|
4.8
|
165.5
|
1.0
|
|
NE2
|
M:HIS206
|
4.8
|
166.5
|
1.0
|
|
OD1
|
M:ASP338
|
4.9
|
153.1
|
1.0
|
|
N
|
M:ILE246
|
4.9
|
151.0
|
1.0
|
|
Zinc binding site 8 out
of 8 in 6z6o
Go back to
Zinc Binding Sites List in 6z6o
Zinc binding site 8 out
of 8 in the Hdac-Tc
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Hdac-Tc within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Zn801
b:186.2
occ:1.00
|
OD2
|
N:ASP338
|
2.1
|
167.9
|
1.0
|
|
ND1
|
N:HIS247
|
2.2
|
155.9
|
1.0
|
|
OD1
|
N:ASP245
|
2.2
|
162.2
|
1.0
|
|
OD2
|
N:ASP245
|
2.5
|
162.2
|
1.0
|
|
CG
|
N:ASP245
|
2.7
|
162.2
|
1.0
|
|
CE1
|
N:HIS247
|
3.0
|
155.9
|
1.0
|
|
CG
|
N:ASP338
|
3.2
|
167.9
|
1.0
|
|
CG
|
N:HIS247
|
3.2
|
155.9
|
1.0
|
|
CB
|
N:HIS247
|
3.7
|
155.9
|
1.0
|
|
OD1
|
N:ASP338
|
3.9
|
167.9
|
1.0
|
|
OH
|
N:TYR378
|
3.9
|
176.4
|
1.0
|
|
NE2
|
N:HIS205
|
4.1
|
177.4
|
1.0
|
|
N
|
N:HIS247
|
4.1
|
155.9
|
1.0
|
|
NE2
|
N:HIS247
|
4.1
|
155.9
|
1.0
|
|
CB
|
N:ASP338
|
4.1
|
167.9
|
1.0
|
|
CE1
|
N:HIS205
|
4.2
|
177.4
|
1.0
|
|
CB
|
N:ASP245
|
4.2
|
162.2
|
1.0
|
|
CD2
|
N:HIS247
|
4.2
|
155.9
|
1.0
|
|
CE2
|
N:TYR378
|
4.4
|
176.4
|
1.0
|
|
CA
|
N:GLY376
|
4.5
|
185.2
|
1.0
|
|
CA
|
N:HIS247
|
4.5
|
155.9
|
1.0
|
|
N
|
N:ILE246
|
4.7
|
148.6
|
1.0
|
|
CZ
|
N:TYR378
|
4.7
|
176.4
|
1.0
|
|
NE2
|
N:HIS206
|
4.7
|
162.1
|
1.0
|
|
CG2
|
N:ILE246
|
4.8
|
148.6
|
1.0
|
|
Reference:
J.H.Lee,
D.Bollschweiler,
T.Schafer,
R.Huber.
Structural Basis For the Regulation of Nucleosome Recognition and Hdac Activity By Histone Deacetylase Assemblies. Sci Adv V. 7 2021.
ISSN: ESSN 2375-2548
PubMed: 33523989
DOI: 10.1126/SCIADV.ABD4413
Page generated: Tue Oct 29 15:27:00 2024
|
