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Calcium in PDB 7mox: Structure of HDAC2 in Complex with An Inhibitor (Compound 14)

Enzymatic activity of Structure of HDAC2 in Complex with An Inhibitor (Compound 14)

All present enzymatic activity of Structure of HDAC2 in Complex with An Inhibitor (Compound 14):
3.5.1.98;

Protein crystallography data

The structure of Structure of HDAC2 in Complex with An Inhibitor (Compound 14), PDB code: 7mox 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) 24.42 / 1.69
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.56, 99.19, 139.78, 90, 90, 90
R / Rfree (%) 17.6 / 20.2

Other elements in 7mox:

The structure of Structure of HDAC2 in Complex with An Inhibitor (Compound 14) also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of HDAC2 in Complex with An Inhibitor (Compound 14) (pdb code 7mox). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of HDAC2 in Complex with An Inhibitor (Compound 14), PDB code: 7mox:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 7mox

Go back to Calcium Binding Sites List in 7mox
Calcium binding site 1 out of 6 in the Structure of HDAC2 in Complex with An Inhibitor (Compound 14)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of HDAC2 in Complex with An Inhibitor (Compound 14) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:35.7
occ:1.00
 OD1 A:ASP175 2.7 16.4 1.0
O A:ASP177 2.8 15.1 1.0
OG A:SER198 2.9 17.3 1.0
O A:HIS179 2.9 15.5 1.0
O A:PHE199 2.9 15.6 1.0
O A:ASP175 3.0 14.7 1.0
CG A:ASP175 3.3 18.0 1.0
C A:ASP175 3.6 14.4 1.0
C A:PHE199 3.7 16.1 1.0
CB A:ASP175 3.7 16.2 1.0
C A:ASP177 3.8 14.3 1.0
N A:ASP177 3.8 14.0 1.0
N A:PHE199 3.8 14.6 1.0
C A:HIS179 3.8 15.4 1.0
CB A:HIS200 3.8 15.7 1.0
CB A:SER198 4.0 16.1 1.0
OD2 A:ASP175 4.1 19.6 1.0
N A:GLY181 4.1 16.4 1.0
CB A:ASP177 4.1 14.2 1.0
CA A:ASP177 4.2 13.5 1.0
CA A:HIS180 4.2 16.1 1.0
ND1 A:HIS200 4.2 19.3 1.0
CA A:SER198 4.3 15.0 1.0
N A:ILE176 4.3 13.4 1.0
CA A:ASP175 4.3 13.9 1.0
C A:ILE176 4.3 14.7 1.0
C A:SER198 4.4 15.8 1.0
N A:HIS180 4.4 15.4 1.0
CA A:HIS200 4.4 15.5 1.0
N A:HIS200 4.5 15.7 1.0
C A:HIS180 4.5 16.1 1.0
CA A:ILE176 4.5 13.9 1.0
CA A:PHE199 4.5 15.2 1.0
CG A:HIS200 4.5 17.4 1.0
N A:HIS179 4.6 15.1 1.0
C A:ILE178 4.8 15.7 1.0
CE1 A:HIS141 4.8 17.9 1.0
CA A:HIS179 4.9 15.1 1.0
N A:ILE178 4.9 14.2 1.0
O A:HOH627 5.0 18.0 1.0

Calcium binding site 2 out of 6 in 7mox

Go back to Calcium Binding Sites List in 7mox
Calcium binding site 2 out of 6 in the Structure of HDAC2 in Complex with An Inhibitor (Compound 14)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of HDAC2 in Complex with An Inhibitor (Compound 14) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:45.9
occ:1.00
 O A:PHE188 2.6 19.6 1.0
O A:HOH558 2.7 23.2 1.0
O A:VAL194 2.8 19.1 1.0
O A:HOH675 2.9 23.2 1.0
O A:THR191 3.0 20.9 1.0
O A:TYR223 3.3 19.0 1.0
C A:PHE188 3.5 19.6 1.0
CB A:TYR223 3.7 19.3 1.0
C A:TYR223 3.8 19.3 1.0
C A:VAL194 3.9 18.5 1.0
CB A:PHE188 4.1 18.4 1.0
C A:THR191 4.2 20.8 1.0
N A:TYR189 4.3 20.2 1.0
CA A:TYR189 4.3 21.3 1.0
CA A:TYR223 4.4 19.3 1.0
O A:TYR189 4.4 22.7 1.0
C A:TYR189 4.4 22.2 1.0
CA A:PHE188 4.5 19.0 1.0
CA A:MET195 4.5 17.8 1.0
N A:ALA224 4.6 18.7 1.0
N A:THR191 4.6 22.6 1.0
N A:THR196 4.6 16.6 1.0
O A:GLY220 4.6 21.9 1.0
OG1 A:THR196 4.7 19.7 1.0
N A:MET195 4.7 17.4 1.0
CG2 A:THR191 4.8 23.5 1.0
CA A:GLY220 4.8 23.4 1.0
CA A:VAL194 4.9 18.4 1.0
CB A:VAL194 4.9 19.0 1.0
CG2 A:THR196 4.9 18.3 1.0
CG A:TYR223 4.9 20.2 1.0
CA A:ALA224 5.0 19.5 1.0
CA A:THR191 5.0 21.8 1.0
CB A:ALA224 5.0 19.5 1.0

Calcium binding site 3 out of 6 in 7mox

Go back to Calcium Binding Sites List in 7mox
Calcium binding site 3 out of 6 in the Structure of HDAC2 in Complex with An Inhibitor (Compound 14)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of HDAC2 in Complex with An Inhibitor (Compound 14) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:36.8
occ:1.00
 O B:ASP177 2.7 13.6 1.0
OD1 B:ASP175 2.8 16.7 1.0
O B:HIS179 2.8 14.4 1.0
O B:PHE199 2.8 14.1 1.0
OG B:SER198 2.9 16.9 1.0
O B:ASP175 3.1 14.9 1.0
CG B:ASP175 3.4 17.5 1.0
C B:ASP175 3.7 13.9 1.0
C B:ASP177 3.7 12.7 1.0
C B:PHE199 3.7 13.8 1.0
N B:ASP177 3.7 12.4 1.0
C B:HIS179 3.7 14.3 1.0
CB B:HIS200 3.8 14.3 1.0
CB B:ASP175 3.8 14.2 1.0
N B:PHE199 3.9 13.2 1.0
CB B:SER198 4.0 15.7 1.0
CB B:ASP177 4.1 11.7 1.0
OD2 B:ASP175 4.1 19.2 1.0
CA B:ASP177 4.1 12.1 1.0
CA B:HIS180 4.2 15.0 1.0
N B:GLY181 4.2 15.4 1.0
ND1 B:HIS200 4.3 15.7 1.0
N B:ILE176 4.3 12.8 1.0
C B:ILE176 4.3 12.7 1.0
CA B:SER198 4.3 13.7 1.0
N B:HIS180 4.3 14.3 1.0
CA B:ASP175 4.4 12.9 1.0
CA B:HIS200 4.4 14.1 1.0
C B:SER198 4.4 14.6 1.0
N B:HIS200 4.5 13.5 1.0
CA B:ILE176 4.5 12.9 1.0
C B:HIS180 4.5 15.5 1.0
CG B:HIS200 4.5 15.2 1.0
CA B:PHE199 4.5 13.3 1.0
N B:HIS179 4.6 13.1 1.0
C B:ILE178 4.7 13.2 1.0
CA B:HIS179 4.8 13.1 1.0
N B:ILE178 4.8 11.7 1.0
O B:HOH666 4.8 17.2 1.0
CE1 B:HIS141 4.9 16.7 1.0

Calcium binding site 4 out of 6 in 7mox

Go back to Calcium Binding Sites List in 7mox
Calcium binding site 4 out of 6 in the Structure of HDAC2 in Complex with An Inhibitor (Compound 14)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of HDAC2 in Complex with An Inhibitor (Compound 14) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca405

b:42.9
occ:1.00
 O B:HOH648 2.6 21.9 1.0
O B:PHE188 2.6 19.6 1.0
O B:VAL194 2.6 19.6 1.0
O B:HOH638 2.9 22.0 1.0
O B:THR191 2.9 21.8 1.0
O B:TYR223 3.2 18.9 1.0
CB B:TYR223 3.6 20.6 1.0
C B:PHE188 3.6 19.1 1.0
C B:TYR223 3.8 19.3 1.0
C B:VAL194 3.8 18.2 1.0
CB B:PHE188 4.1 19.4 1.0
C B:THR191 4.1 21.9 1.0
CA B:TYR223 4.3 20.0 1.0
CA B:TYR189 4.4 20.6 1.0
N B:TYR189 4.4 19.2 1.0
O B:TYR189 4.4 22.1 1.0
C B:TYR189 4.5 21.5 1.0
CA B:MET195 4.5 16.8 1.0
CA B:PHE188 4.5 19.6 1.0
N B:THR191 4.6 23.2 1.0
N B:ALA224 4.6 18.3 1.0
N B:MET195 4.6 17.2 1.0
N B:THR196 4.6 15.8 1.0
CG2 B:THR191 4.6 23.8 1.0
OG1 B:THR196 4.7 18.5 1.0
O B:GLY220 4.7 21.4 1.0
CA B:VAL194 4.7 17.6 1.0
CB B:VAL194 4.8 18.2 1.0
CA B:GLY220 4.9 23.8 1.0
CA B:THR191 4.9 22.9 1.0
CG B:TYR223 4.9 22.3 1.0
N B:VAL194 4.9 17.4 1.0
CG2 B:THR196 5.0 17.8 1.0
C B:MET195 5.0 16.4 1.0
CA B:ALA224 5.0 18.5 1.0

Calcium binding site 5 out of 6 in 7mox

Go back to Calcium Binding Sites List in 7mox
Calcium binding site 5 out of 6 in the Structure of HDAC2 in Complex with An Inhibitor (Compound 14)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of HDAC2 in Complex with An Inhibitor (Compound 14) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca406

b:45.7
occ:1.00
 O C:PHE188 2.6 19.0 1.0
O C:HOH564 2.6 22.3 1.0
O C:VAL194 2.6 20.4 1.0
O C:THR191 2.9 21.4 1.0
O C:HOH647 2.9 23.2 1.0
O C:TYR223 3.3 22.2 1.0
C C:PHE188 3.5 19.1 1.0
CB C:TYR223 3.7 23.2 1.0
C C:VAL194 3.8 20.9 1.0
C C:TYR223 3.9 22.5 1.0
CB C:PHE188 4.1 19.0 1.0
C C:THR191 4.1 20.9 1.0
N C:TYR189 4.3 19.5 1.0
CA C:TYR189 4.3 20.0 1.0
O C:TYR189 4.4 20.7 1.0
C C:TYR189 4.4 20.4 1.0
CA C:TYR223 4.4 23.2 1.0
CA C:PHE188 4.4 18.6 1.0
N C:THR191 4.5 19.8 1.0
CA C:MET195 4.5 21.7 1.0
N C:MET195 4.6 21.0 1.0
CG2 C:THR191 4.6 20.7 1.0
N C:ALA224 4.6 21.3 1.0
N C:THR196 4.7 20.8 1.0
O C:GLY220 4.7 23.3 1.0
OG1 C:THR196 4.7 20.8 1.0
CA C:VAL194 4.8 20.1 1.0
CA C:GLY220 4.8 23.8 1.0
CA C:THR191 4.8 20.1 1.0
CB C:VAL194 4.8 20.2 1.0
CG2 C:THR196 4.9 19.5 1.0
N C:VAL194 4.9 20.1 1.0
C C:MET195 5.0 21.1 1.0
CG C:TYR223 5.0 24.1 1.0

Calcium binding site 6 out of 6 in 7mox

Go back to Calcium Binding Sites List in 7mox
Calcium binding site 6 out of 6 in the Structure of HDAC2 in Complex with An Inhibitor (Compound 14)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of HDAC2 in Complex with An Inhibitor (Compound 14) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca407

b:44.3
occ:1.00
 OD1 C:ASP175 2.7 22.3 1.0
O C:ASP177 2.7 21.1 1.0
O C:HIS179 2.8 19.3 1.0
OG C:SER198 2.9 20.9 1.0
O C:PHE199 3.0 20.2 1.0
O C:ASP175 3.1 19.9 1.0
CG C:ASP175 3.3 23.8 1.0
C C:ASP175 3.7 20.3 1.0
C C:ASP177 3.7 20.2 1.0
N C:ASP177 3.7 20.9 1.0
C C:HIS179 3.8 19.0 1.0
CB C:ASP175 3.8 19.9 1.0
C C:PHE199 3.8 19.6 1.0
CB C:HIS200 3.8 20.6 1.0
N C:PHE199 3.9 18.8 1.0
CB C:SER198 4.0 19.7 1.0
CB C:ASP177 4.0 19.4 1.0
OD2 C:ASP175 4.1 22.8 1.0
CA C:ASP177 4.1 19.9 1.0
N C:GLY181 4.2 19.4 1.0
CA C:HIS180 4.2 19.5 1.0
C C:ILE176 4.3 21.1 1.0
N C:ILE176 4.3 20.6 1.0
CA C:SER198 4.3 18.8 1.0
ND1 C:HIS200 4.3 22.3 1.0
N C:HIS180 4.4 18.9 1.0
CA C:ASP175 4.4 19.7 1.0
C C:SER198 4.5 19.3 1.0
CA C:HIS200 4.5 20.2 1.0
CA C:ILE176 4.5 20.9 1.0
C C:HIS180 4.5 19.8 1.0
N C:HIS179 4.5 18.8 1.0
N C:HIS200 4.5 19.2 1.0
CG C:HIS200 4.6 21.2 1.0
CA C:PHE199 4.6 19.4 1.0
C C:ILE178 4.7 19.2 1.0
N C:ILE178 4.8 19.4 1.0
CA C:HIS179 4.8 18.9 1.0
CE1 C:HIS141 4.8 23.8 1.0
O C:HOH605 4.9 24.0 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: Fri Jul 19 02:06:16 2024

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