Zinc in PDB 7moz: Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 25)

Enzymatic activity of Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 25)

All present enzymatic activity of Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 25):
3.5.1.98;

Protein crystallography data

The structure of Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 25), PDB code: 7moz was solved by D.J.Klein, W.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.55 / 1.54
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.478, 98.989, 139.489, 90, 90, 90
R / Rfree (%) 17.6 / 20.1

Other elements in 7moz:

The structure of Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 25) also contains other interesting chemical elements:

Calcium (Ca) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 25) (pdb code 7moz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 25), PDB code: 7moz:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 7moz

Go back to Zinc Binding Sites List in 7moz
Zinc binding site 1 out of 3 in the Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 25)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 25) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:13.3
occ:1.00
OD2 A:ASP265 1.9 13.3 1.0
OD1 A:ASP177 2.0 13.1 1.0
O1 A:ZL4411 2.0 13.8 1.0
ND1 A:HIS179 2.0 14.1 1.0
O A:ZL4411 2.5 13.9 1.0
C2 A:ZL4411 2.8 15.1 1.0
CG A:ASP177 2.8 13.1 1.0
CG A:ASP265 2.9 12.6 1.0
CE1 A:HIS179 2.9 14.5 1.0
OD2 A:ASP177 3.0 12.7 1.0
CG A:HIS179 3.2 13.4 1.0
OD1 A:ASP265 3.2 12.2 1.0
CB A:HIS179 3.6 13.1 1.0
C1 A:ZL4411 3.8 16.6 1.0
C3 A:ZL4411 3.8 15.6 1.0
N A:HIS179 3.9 11.3 1.0
C4 A:ZL4411 3.9 15.7 1.0
CA A:GLY302 4.0 13.0 1.0
NE2 A:HIS179 4.1 14.6 1.0
CG2 A:ILE178 4.2 12.0 1.0
CB A:ASP177 4.2 11.7 1.0
CD2 A:HIS179 4.2 13.8 1.0
CB A:ASP265 4.2 13.5 1.0
OH A:TYR304 4.3 13.4 1.0
N A:ILE178 4.3 10.7 1.0
CE2 A:TYR304 4.4 12.8 1.0
CA A:HIS179 4.4 12.3 1.0
NE2 A:HIS141 4.4 14.2 1.0
N A:GLY302 4.4 12.3 1.0
C A:ZL4411 4.8 17.4 1.0
CZ A:TYR304 4.8 13.1 1.0
C A:ILE178 4.8 12.2 1.0
CE1 A:HIS141 4.9 14.2 1.0
NE2 A:HIS142 4.9 14.6 1.0
C A:ASP177 4.9 11.8 1.0
CA A:ASP177 4.9 10.8 1.0
CA A:ILE178 5.0 11.3 1.0

Zinc binding site 2 out of 3 in 7moz

Go back to Zinc Binding Sites List in 7moz
Zinc binding site 2 out of 3 in the Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 25)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 25) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:12.4
occ:1.00
OD2 B:ASP265 1.9 13.2 1.0
OD1 B:ASP177 2.0 11.3 1.0
O1 B:ZL4408 2.0 13.1 1.0
ND1 B:HIS179 2.0 12.3 1.0
O B:ZL4408 2.5 12.1 1.0
C2 B:ZL4408 2.7 13.6 1.0
CG B:ASP177 2.8 11.7 1.0
CE1 B:HIS179 2.9 13.1 1.0
CG B:ASP265 2.9 12.5 1.0
OD2 B:ASP177 3.0 11.8 1.0
CG B:HIS179 3.2 11.8 1.0
OD1 B:ASP265 3.3 11.3 1.0
CB B:HIS179 3.6 11.1 1.0
C1 B:ZL4408 3.8 15.4 1.0
N B:HIS179 3.8 10.8 1.0
C3 B:ZL4408 3.8 14.2 1.0
C4 B:ZL4408 3.9 14.7 1.0
CA B:GLY302 4.0 11.7 1.0
NE2 B:HIS179 4.1 13.3 1.0
CG2 B:ILE178 4.2 11.8 1.0
CD2 B:HIS179 4.2 13.2 1.0
CB B:ASP177 4.2 10.5 1.0
CB B:ASP265 4.3 11.6 1.0
OH B:TYR304 4.3 12.9 1.0
CA B:HIS179 4.3 10.5 1.0
NE2 B:HIS141 4.4 13.6 1.0
N B:ILE178 4.4 9.6 1.0
CE2 B:TYR304 4.4 10.8 1.0
N B:GLY302 4.4 10.7 1.0
C B:ILE178 4.8 11.2 1.0
CE1 B:HIS141 4.8 13.8 1.0
C B:ZL4408 4.8 16.1 1.0
CZ B:TYR304 4.8 11.8 1.0
C B:ASP177 4.9 10.7 1.0
CA B:ASP177 4.9 10.4 1.0
NE2 B:HIS142 4.9 14.9 1.0
CA B:ILE178 5.0 10.1 1.0

Zinc binding site 3 out of 3 in 7moz

Go back to Zinc Binding Sites List in 7moz
Zinc binding site 3 out of 3 in the Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 25)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 25) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:15.6
occ:1.00
OD1 C:ASP177 2.0 13.2 1.0
OD2 C:ASP265 2.0 15.2 1.0
ND1 C:HIS179 2.0 16.8 1.0
O1 C:ZL4410 2.1 16.1 1.0
O C:ZL4410 2.5 15.7 1.0
C2 C:ZL4410 2.8 16.4 1.0
CG C:ASP177 2.8 14.3 1.0
CG C:ASP265 2.9 15.4 1.0
CE1 C:HIS179 3.0 16.4 1.0
OD2 C:ASP177 3.0 15.7 1.0
CG C:HIS179 3.1 14.3 1.0
OD1 C:ASP265 3.3 15.1 1.0
CB C:HIS179 3.5 13.8 1.0
N C:HIS179 3.8 13.4 1.0
C1 C:ZL4410 3.8 16.5 1.0
C3 C:ZL4410 3.9 16.8 1.0
C4 C:ZL4410 3.9 17.4 1.0
CA C:GLY302 4.0 15.3 1.0
NE2 C:HIS179 4.1 16.1 1.0
CG2 C:ILE178 4.2 15.2 1.0
CD2 C:HIS179 4.2 15.1 1.0
CB C:ASP177 4.2 14.0 1.0
OH C:TYR304 4.2 16.8 1.0
CB C:ASP265 4.3 14.1 1.0
CA C:HIS179 4.3 13.6 1.0
N C:ILE178 4.3 14.1 1.0
CE2 C:TYR304 4.4 16.9 1.0
NE2 C:HIS141 4.4 16.2 1.0
N C:GLY302 4.4 14.5 1.0
C C:ILE178 4.8 13.5 1.0
CZ C:TYR304 4.8 17.3 1.0
CE1 C:HIS141 4.8 17.3 1.0
C C:ZL4410 4.8 16.9 1.0
C C:ASP177 4.9 14.9 1.0
NE2 C:HIS142 4.9 15.4 1.0
CA C:ASP177 4.9 14.3 1.0
CA C:ILE178 5.0 13.7 1.0

Reference:

W.Yu, J.Fells, D.Clausen, J.Liu, D.J.Klein, C.Christine Chung, R.W.Myers, J.Wu, G.Wu, B.J.Howell, R.J.O.Barnard, J.Kozlowski. Discovery of Macrocyclic Hdacs 1, 2, and 3 Selective Inhibitors For Hiv Latency Reactivation. Bioorg.Med.Chem.Lett. V. 47 28168 2021.
ISSN: ESSN 1464-3405
PubMed: 34091041
DOI: 10.1016/J.BMCL.2021.128168
Page generated: Sun Aug 22 09:48:39 2021

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy