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:

Potassium (K) 8 atoms

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: Wed Dec 16 13:21:05 2020

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