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

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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

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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

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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

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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

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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

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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

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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

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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: Wed Mar 3 16:15:06 2021

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