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Calcium in PDB 7mot: Structure of HDAC2 in Complex with An Inhibitor (Compound 9)

Enzymatic activity of Structure of HDAC2 in Complex with An Inhibitor (Compound 9)

All present enzymatic activity of Structure of HDAC2 in Complex with An Inhibitor (Compound 9):
3.5.1.98;

Protein crystallography data

The structure of Structure of HDAC2 in Complex with An Inhibitor (Compound 9), PDB code: 7mot 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) 22.52 / 1.54
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.417, 99.064, 139.622, 90, 90, 90
R / Rfree (%) 17.8 / 20.3

Other elements in 7mot:

The structure of Structure of HDAC2 in Complex with An Inhibitor (Compound 9) 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 9) (pdb code 7mot). 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 9), PDB code: 7mot:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 7mot

Go back to Calcium Binding Sites List in 7mot
Calcium binding site 1 out of 6 in the Structure of HDAC2 in Complex with An Inhibitor (Compound 9)


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 9) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:29.4
occ:1.00
 OD1 A:ASP175 2.7 13.2 1.0
O A:ASP177 2.8 12.3 1.0
O A:PHE199 2.9 13.8 1.0
OG A:SER198 2.9 14.9 1.0
O A:HIS179 2.9 13.4 1.0
O A:ASP175 3.0 12.1 1.0
CG A:ASP175 3.4 13.3 1.0
C A:ASP175 3.6 11.9 1.0
C A:PHE199 3.7 13.7 1.0
N A:PHE199 3.8 12.7 1.0
C A:ASP177 3.8 11.0 1.0
N A:ASP177 3.8 11.1 1.0
CB A:ASP175 3.8 13.9 1.0
CB A:HIS200 3.8 13.8 1.0
C A:HIS179 3.8 12.5 1.0
CB A:SER198 4.0 12.9 1.0
OD2 A:ASP175 4.1 14.4 1.0
CB A:ASP177 4.2 12.2 1.0
N A:GLY181 4.2 14.1 1.0
CA A:ASP177 4.2 10.7 1.0
ND1 A:HIS200 4.2 14.8 1.0
N A:ILE176 4.2 11.2 1.0
CA A:SER198 4.3 12.4 1.0
CA A:HIS180 4.3 12.4 1.0
C A:ILE176 4.3 11.6 1.0
CA A:ASP175 4.3 11.8 1.0
C A:SER198 4.3 13.3 1.0
CA A:HIS200 4.4 13.4 1.0
N A:HIS180 4.4 11.9 1.0
N A:HIS200 4.4 13.0 1.0
CA A:ILE176 4.4 11.9 1.0
CA A:PHE199 4.4 13.1 1.0
CG A:HIS200 4.5 13.7 1.0
C A:HIS180 4.5 13.5 1.0
N A:HIS179 4.6 11.8 1.0
C A:ILE178 4.7 12.2 1.0
CA A:HIS179 4.9 12.2 1.0
CE1 A:HIS141 4.9 14.3 1.0
O A:HOH610 4.9 16.0 1.0
N A:ILE178 4.9 10.0 1.0

Calcium binding site 2 out of 6 in 7mot

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Calcium binding site 2 out of 6 in the Structure of HDAC2 in Complex with An Inhibitor (Compound 9)


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 9) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:36.3
occ:1.00
 O A:PHE188 2.7 17.0 1.0
O A:VAL194 2.7 17.3 1.0
O A:HOH567 2.7 18.2 1.0
O A:THR191 2.9 17.8 1.0
O A:HOH677 3.0 19.3 1.0
O A:TYR223 3.2 17.0 1.0
CB A:TYR223 3.6 16.8 1.0
C A:PHE188 3.6 16.6 1.0
C A:TYR223 3.8 17.0 1.0
C A:VAL194 3.9 16.2 1.0
CB A:PHE188 4.1 15.4 1.0
C A:THR191 4.2 17.8 1.0
CA A:TYR223 4.3 16.9 1.0
CA A:TYR189 4.4 17.4 1.0
N A:TYR189 4.4 17.0 1.0
O A:TYR189 4.5 18.0 1.0
C A:TYR189 4.5 18.1 1.0
CA A:MET195 4.5 15.0 1.0
CA A:PHE188 4.5 15.7 1.0
N A:ALA224 4.6 15.9 1.0
N A:THR191 4.6 18.6 1.0
N A:THR196 4.6 14.2 1.0
N A:MET195 4.7 15.1 1.0
O A:GLY220 4.7 18.5 1.0
CG2 A:THR191 4.7 20.1 1.0
OG1 A:THR196 4.7 15.5 1.0
CA A:VAL194 4.8 16.1 1.0
CA A:GLY220 4.8 19.5 1.0
CB A:VAL194 4.9 16.3 1.0
CG2 A:THR196 4.9 15.8 1.0
CG A:TYR223 4.9 17.5 1.0
CA A:THR191 4.9 18.3 1.0
CA A:ALA224 5.0 16.4 1.0
N A:VAL194 5.0 16.3 1.0

Calcium binding site 3 out of 6 in 7mot

Go back to Calcium Binding Sites List in 7mot
Calcium binding site 3 out of 6 in the Structure of HDAC2 in Complex with An Inhibitor (Compound 9)


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 9) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:30.3
occ:1.00
 O B:ASP177 2.7 10.7 1.0
OD1 B:ASP175 2.7 13.1 1.0
O B:PHE199 2.9 10.9 1.0
O B:HIS179 2.9 11.7 1.0
OG B:SER198 2.9 12.1 1.0
O B:ASP175 3.0 11.8 1.0
CG B:ASP175 3.3 13.6 1.0
C B:ASP175 3.6 11.1 1.0
C B:ASP177 3.7 10.8 1.0
N B:ASP177 3.7 10.5 1.0
C B:PHE199 3.7 11.4 1.0
C B:HIS179 3.8 11.6 1.0
CB B:ASP175 3.8 11.5 1.0
CB B:HIS200 3.8 12.0 1.0
N B:PHE199 3.8 10.8 1.0
CB B:ASP177 4.0 11.2 1.0
CB B:SER198 4.1 12.4 1.0
CA B:ASP177 4.1 10.8 1.0
OD2 B:ASP175 4.1 13.9 1.0
ND1 B:HIS200 4.2 12.9 1.0
N B:ILE176 4.2 9.6 1.0
CA B:HIS180 4.2 12.0 1.0
N B:GLY181 4.3 12.7 1.0
C B:ILE176 4.3 10.5 1.0
CA B:SER198 4.3 10.8 1.0
CA B:ASP175 4.3 9.6 1.0
N B:HIS180 4.4 12.0 1.0
C B:SER198 4.4 12.2 1.0
CA B:ILE176 4.4 9.5 1.0
CA B:HIS200 4.4 11.5 1.0
N B:HIS200 4.5 11.5 1.0
CA B:PHE199 4.5 10.9 1.0
CG B:HIS200 4.5 12.4 1.0
N B:HIS179 4.5 10.3 1.0
C B:HIS180 4.6 12.3 1.0
C B:ILE178 4.7 10.6 1.0
CA B:HIS179 4.8 10.3 1.0
O B:HOH588 4.8 13.2 1.0
N B:ILE178 4.8 9.6 1.0
CE1 B:HIS141 4.9 13.4 1.0

Calcium binding site 4 out of 6 in 7mot

Go back to Calcium Binding Sites List in 7mot
Calcium binding site 4 out of 6 in the Structure of HDAC2 in Complex with An Inhibitor (Compound 9)


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 9) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca405

b:36.1
occ:1.00
 O B:VAL194 2.6 15.2 1.0
O B:PHE188 2.7 15.4 1.0
O B:HOH655 2.7 18.0 1.0
O B:THR191 2.9 17.4 1.0
O B:HOH720 2.9 16.5 1.0
O B:TYR223 3.1 16.1 1.0
CB B:TYR223 3.6 16.1 1.0
C B:PHE188 3.7 15.2 1.0
C B:VAL194 3.7 14.3 1.0
C B:TYR223 3.8 15.9 1.0
CB B:PHE188 4.1 14.6 1.0
C B:THR191 4.1 17.4 1.0
CA B:TYR223 4.3 16.2 1.0
CA B:MET195 4.4 13.2 1.0
CA B:TYR189 4.5 15.5 1.0
N B:TYR189 4.5 14.8 1.0
O B:TYR189 4.5 16.8 1.0
C B:TYR189 4.5 16.3 1.0
N B:MET195 4.6 13.5 1.0
N B:THR191 4.6 18.0 1.0
CA B:PHE188 4.6 15.1 1.0
N B:THR196 4.6 12.1 1.0
N B:ALA224 4.6 14.8 1.0
CG2 B:THR191 4.7 19.6 1.0
CA B:VAL194 4.7 14.0 1.0
CB B:VAL194 4.7 14.2 1.0
O B:GLY220 4.7 16.7 1.0
OG1 B:THR196 4.8 15.3 1.0
CG B:TYR223 4.8 17.1 1.0
N B:VAL194 4.8 14.7 1.0
CA B:GLY220 4.9 19.6 1.0
CA B:THR191 4.9 18.0 1.0
C B:MET195 4.9 13.2 1.0

Calcium binding site 5 out of 6 in 7mot

Go back to Calcium Binding Sites List in 7mot
Calcium binding site 5 out of 6 in the Structure of HDAC2 in Complex with An Inhibitor (Compound 9)


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 9) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca406

b:40.0
occ:1.00
 O C:PHE188 2.6 16.2 1.0
O C:VAL194 2.6 17.6 1.0
O C:HOH606 2.7 19.6 1.0
O C:THR191 2.8 18.2 1.0
O C:HOH684 3.0 18.7 1.0
O C:TYR223 3.2 19.3 1.0
C C:PHE188 3.6 15.8 1.0
CB C:TYR223 3.7 18.3 1.0
C C:VAL194 3.8 17.2 1.0
C C:TYR223 3.8 18.4 1.0
C C:THR191 4.0 18.0 1.0
CB C:PHE188 4.1 15.3 1.0
N C:TYR189 4.4 16.1 1.0
CA C:TYR189 4.4 16.6 1.0
CA C:TYR223 4.4 18.6 1.0
O C:TYR189 4.4 17.4 1.0
C C:TYR189 4.4 16.9 1.0
N C:THR191 4.4 16.5 1.0
CA C:PHE188 4.5 15.2 1.0
CA C:MET195 4.5 17.7 1.0
CG2 C:THR191 4.6 16.9 1.0
N C:MET195 4.6 17.2 1.0
N C:ALA224 4.6 17.7 1.0
N C:THR196 4.7 16.4 1.0
O C:GLY220 4.7 19.2 1.0
CA C:THR191 4.7 17.1 1.0
CA C:VAL194 4.7 16.1 1.0
CA C:GLY220 4.8 19.6 1.0
CB C:VAL194 4.8 16.1 1.0
OG1 C:THR196 4.8 17.4 1.0
N C:VAL194 4.9 16.8 1.0
CG C:TYR223 4.9 19.1 1.0
C C:MET195 5.0 17.0 1.0

Calcium binding site 6 out of 6 in 7mot

Go back to Calcium Binding Sites List in 7mot
Calcium binding site 6 out of 6 in the Structure of HDAC2 in Complex with An Inhibitor (Compound 9)


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 9) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca407

b:34.3
occ:1.00
 O C:ASP177 2.7 16.4 1.0
OD1 C:ASP175 2.8 17.1 1.0
O C:PHE199 2.9 17.0 1.0
OG C:SER198 2.9 16.6 1.0
O C:HIS179 2.9 15.1 1.0
O C:ASP175 3.0 15.6 1.0
CG C:ASP175 3.4 17.3 1.0
C C:ASP175 3.6 15.4 1.0
C C:ASP177 3.7 15.3 1.0
C C:PHE199 3.7 15.6 1.0
N C:ASP177 3.7 15.7 1.0
CB C:ASP175 3.8 14.5 1.0
CB C:HIS200 3.8 14.9 1.0
C C:HIS179 3.8 14.3 1.0
N C:PHE199 3.8 15.2 1.0
CB C:SER198 4.0 15.5 1.0
CB C:ASP177 4.1 15.2 1.0
CA C:ASP177 4.2 14.8 1.0
OD2 C:ASP175 4.2 16.8 1.0
N C:GLY181 4.2 15.7 1.0
C C:ILE176 4.3 15.9 1.0
N C:ILE176 4.3 15.4 1.0
CA C:SER198 4.3 14.7 1.0
ND1 C:HIS200 4.3 17.9 1.0
CA C:HIS180 4.3 14.9 1.0
CA C:ASP175 4.3 14.7 1.0
C C:SER198 4.4 15.2 1.0
CA C:HIS200 4.4 14.8 1.0
CA C:ILE176 4.4 15.4 1.0
N C:HIS180 4.4 14.7 1.0
N C:HIS200 4.4 14.8 1.0
N C:HIS179 4.5 14.1 1.0
CA C:PHE199 4.5 15.0 1.0
CG C:HIS200 4.5 16.4 1.0
C C:HIS180 4.6 15.2 1.0
C C:ILE178 4.7 14.6 1.0
CA C:HIS179 4.8 14.4 1.0
N C:ILE178 4.8 14.5 1.0
O C:HOH599 4.8 17.9 1.0
CE1 C:HIS141 5.0 16.7 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: Fri Jul 19 02:06:06 2024

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