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Calcium in PDB 7mos: Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 4)

Enzymatic activity of Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 4)

All present enzymatic activity of Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 4):
3.5.1.98;

Protein crystallography data

The structure of Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 4), PDB code: 7mos 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) 80.75 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.447, 98.947, 139.708, 90, 90, 90
R / Rfree (%) 18.3 / 20.8

Other elements in 7mos:

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

Calcium binding site 1 out of 6 in 7mos

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Calcium binding site 1 out of 6 in the Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 4)


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 A Macrocyclic Inhibitor (Compound 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:35.6
occ:1.00
 OD1 A:ASP175 2.7 15.9 1.0
O A:ASP177 2.8 16.0 1.0
O A:HIS179 2.9 15.5 1.0
O A:PHE199 2.9 16.0 1.0
OG A:SER198 2.9 17.1 1.0
O A:ASP175 3.0 15.5 1.0
CG A:ASP175 3.3 16.9 1.0
C A:ASP175 3.6 14.7 1.0
C A:ASP177 3.7 15.2 1.0
C A:PHE199 3.7 16.7 1.0
CB A:ASP175 3.8 15.6 1.0
N A:ASP177 3.8 14.5 1.0
C A:HIS179 3.8 15.6 1.0
N A:PHE199 3.8 15.7 1.0
CB A:HIS200 3.9 16.9 1.0
CB A:SER198 4.1 16.0 1.0
OD2 A:ASP175 4.1 17.5 1.0
CB A:ASP177 4.1 15.3 1.0
N A:GLY181 4.1 16.6 1.0
CA A:ASP177 4.2 14.2 1.0
CA A:HIS180 4.2 16.2 1.0
N A:ILE176 4.2 13.6 1.0
ND1 A:HIS200 4.3 18.1 1.0
CA A:SER198 4.3 15.8 1.0
CA A:ASP175 4.3 13.9 1.0
C A:ILE176 4.3 14.8 1.0
N A:HIS180 4.4 15.1 1.0
C A:SER198 4.4 16.4 1.0
CA A:HIS200 4.4 17.1 1.0
N A:HIS200 4.5 16.8 1.0
CA A:ILE176 4.5 14.1 1.0
C A:HIS180 4.5 16.4 1.0
CA A:PHE199 4.5 16.4 1.0
CG A:HIS200 4.6 17.3 1.0
N A:HIS179 4.6 14.7 1.0
C A:ILE178 4.7 15.6 1.0
CE1 A:HIS141 4.8 18.2 1.0
N A:ILE178 4.8 14.5 1.0
CA A:HIS179 4.8 15.4 1.0
O A:HOH606 4.9 18.5 1.0

Calcium binding site 2 out of 6 in 7mos

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Calcium binding site 2 out of 6 in the Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 4)


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 A Macrocyclic Inhibitor (Compound 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca408

b:46.1
occ:1.00
 O A:PHE188 2.6 20.9 1.0
O A:HOH548 2.6 21.8 1.0
O A:VAL194 2.8 20.7 1.0
O A:HOH645 2.8 22.7 1.0
O A:THR191 3.1 21.2 1.0
O A:TYR223 3.2 20.4 1.0
C A:PHE188 3.5 20.7 1.0
CB A:TYR223 3.7 20.4 1.0
C A:TYR223 3.8 20.6 1.0
C A:VAL194 3.9 19.8 1.0
CB A:PHE188 4.1 19.4 1.0
N A:TYR189 4.3 20.9 1.0
CA A:TYR189 4.3 21.9 1.0
C A:THR191 4.3 21.5 1.0
CA A:TYR223 4.4 20.6 1.0
C A:TYR189 4.4 22.5 1.0
O A:TYR189 4.4 23.2 1.0
CA A:PHE188 4.5 19.9 1.0
CA A:MET195 4.5 18.6 1.0
N A:ALA224 4.5 19.3 1.0
N A:THR196 4.6 17.0 1.0
OG1 A:THR196 4.6 21.0 1.0
N A:THR191 4.6 22.9 1.0
O A:GLY220 4.7 23.2 1.0
N A:MET195 4.7 18.5 1.0
CG2 A:THR191 4.8 23.3 1.0
CA A:GLY220 4.8 24.2 1.0
CA A:VAL194 4.9 19.6 1.0
CA A:ALA224 4.9 19.9 1.0
CB A:VAL194 4.9 20.1 1.0
CG2 A:THR196 4.9 19.2 1.0
CB A:ALA224 4.9 20.0 1.0
CG A:TYR223 5.0 21.2 1.0

Calcium binding site 3 out of 6 in 7mos

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Calcium binding site 3 out of 6 in the Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 4)


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 A Macrocyclic Inhibitor (Compound 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca406

b:39.4
occ:1.00
 OD1 B:ASP175 2.7 15.5 1.0
O B:ASP177 2.7 13.8 1.0
O B:HIS179 2.8 14.3 1.0
OG B:SER198 2.9 17.0 1.0
O B:PHE199 2.9 13.9 1.0
O B:ASP175 3.1 14.8 1.0
CG B:ASP175 3.3 16.7 1.0
C B:ASP175 3.6 14.4 1.0
C B:ASP177 3.7 13.4 1.0
C B:HIS179 3.7 14.1 1.0
N B:ASP177 3.7 13.7 1.0
C B:PHE199 3.8 14.3 1.0
CB B:HIS200 3.8 15.4 1.0
CB B:ASP175 3.8 15.0 1.0
N B:PHE199 3.9 13.4 1.0
CB B:ASP177 4.1 13.3 1.0
CB B:SER198 4.1 15.4 1.0
OD2 B:ASP175 4.1 18.2 1.0
CA B:ASP177 4.1 13.1 1.0
CA B:HIS180 4.2 14.3 1.0
N B:GLY181 4.2 14.8 1.0
ND1 B:HIS200 4.3 15.5 1.0
N B:ILE176 4.3 13.3 1.0
N B:HIS180 4.3 13.4 1.0
C B:ILE176 4.3 13.7 1.0
CA B:ASP175 4.4 13.6 1.0
CA B:SER198 4.4 13.5 1.0
CA B:HIS200 4.4 15.2 1.0
N B:HIS200 4.5 14.5 1.0
C B:SER198 4.5 14.5 1.0
C B:HIS180 4.5 14.8 1.0
CA B:ILE176 4.5 13.3 1.0
CG B:HIS200 4.5 15.2 1.0
N B:HIS179 4.5 13.7 1.0
CA B:PHE199 4.5 14.2 1.0
C B:ILE178 4.7 13.9 1.0
CA B:HIS179 4.8 13.7 1.0
N B:ILE178 4.8 12.6 1.0
CE1 B:HIS141 4.9 17.3 1.0
O B:HOH641 4.9 16.4 1.0

Calcium binding site 4 out of 6 in 7mos

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Calcium binding site 4 out of 6 in the Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 4)


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 A Macrocyclic Inhibitor (Compound 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca407

b:41.4
occ:1.00
 O B:VAL194 2.6 18.3 1.0
O B:HOH646 2.6 20.0 1.0
O B:PHE188 2.7 19.0 1.0
O B:HOH663 2.9 20.8 1.0
O B:THR191 2.9 21.8 1.0
O B:TYR223 3.2 19.1 1.0
CB B:TYR223 3.6 21.0 1.0
C B:PHE188 3.6 18.7 1.0
C B:VAL194 3.7 17.6 1.0
C B:TYR223 3.8 19.6 1.0
CB B:PHE188 4.1 19.4 1.0
C B:THR191 4.1 21.5 1.0
CA B:TYR223 4.3 20.7 1.0
N B:TYR189 4.4 18.5 1.0
CA B:TYR189 4.4 19.6 1.0
O B:TYR189 4.5 21.0 1.0
CA B:MET195 4.5 17.1 1.0
C B:TYR189 4.5 20.5 1.0
CA B:PHE188 4.5 19.4 1.0
N B:MET195 4.6 17.3 1.0
N B:ALA224 4.6 18.5 1.0
N B:THR196 4.6 15.9 1.0
N B:THR191 4.6 22.2 1.0
OG1 B:THR196 4.7 18.6 1.0
CA B:VAL194 4.7 16.9 1.0
CG2 B:THR191 4.7 22.9 1.0
CB B:VAL194 4.7 17.7 1.0
O B:GLY220 4.7 21.0 1.0
N B:VAL194 4.8 16.6 1.0
CG B:TYR223 4.9 22.4 1.0
CA B:GLY220 4.9 23.2 1.0
CA B:THR191 4.9 22.1 1.0
C B:MET195 4.9 16.7 1.0
CG2 B:THR196 4.9 17.5 1.0

Calcium binding site 5 out of 6 in 7mos

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Calcium binding site 5 out of 6 in the Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 4)


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 A Macrocyclic Inhibitor (Compound 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca406

b:47.2
occ:1.00
 O C:PHE188 2.6 20.3 1.0
O C:VAL194 2.6 21.4 1.0
O C:HOH540 2.6 23.6 1.0
O C:THR191 2.8 22.4 1.0
O C:HOH656 3.0 22.4 1.0
O C:TYR223 3.3 23.0 1.0
C C:PHE188 3.5 20.0 1.0
CB C:TYR223 3.7 23.4 1.0
C C:VAL194 3.8 21.9 1.0
C C:TYR223 3.9 22.9 1.0
C C:THR191 4.0 22.2 1.0
CB C:PHE188 4.0 19.2 1.0
N C:TYR189 4.3 20.3 1.0
O C:TYR189 4.3 20.9 1.0
N C:THR191 4.4 20.7 1.0
CA C:TYR189 4.4 20.7 1.0
CA C:TYR223 4.4 23.5 1.0
C C:TYR189 4.4 20.9 1.0
CA C:PHE188 4.4 19.3 1.0
CA C:MET195 4.5 22.5 1.0
CG2 C:THR191 4.6 20.7 1.0
N C:MET195 4.6 22.2 1.0
N C:ALA224 4.6 21.4 1.0
O C:GLY220 4.7 22.9 1.0
N C:THR196 4.7 21.0 1.0
CA C:VAL194 4.7 21.0 1.0
CA C:THR191 4.7 20.9 1.0
CA C:GLY220 4.7 23.4 1.0
OG1 C:THR196 4.8 21.3 1.0
CB C:VAL194 4.8 20.9 1.0
N C:VAL194 4.9 21.3 1.0
CG2 C:THR196 4.9 19.6 1.0
CG C:TYR223 5.0 23.8 1.0

Calcium binding site 6 out of 6 in 7mos

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Calcium binding site 6 out of 6 in the Structure of HDAC2 in Complex with A Macrocyclic Inhibitor (Compound 4)


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 A Macrocyclic Inhibitor (Compound 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca407

b:43.7
occ:1.00
 OD1 C:ASP175 2.7 21.5 1.0
O C:ASP177 2.7 21.0 1.0
O C:HIS179 2.8 19.3 1.0
OG C:SER198 2.9 21.3 1.0
O C:PHE199 3.0 20.6 1.0
O C:ASP175 3.1 20.8 1.0
CG C:ASP175 3.3 22.9 1.0
C C:ASP177 3.7 20.4 1.0
C C:ASP175 3.7 20.6 1.0
N C:ASP177 3.7 21.1 1.0
C C:HIS179 3.7 19.4 1.0
CB C:ASP175 3.8 19.6 1.0
CB C:HIS200 3.8 19.9 1.0
C C:PHE199 3.8 20.1 1.0
N C:PHE199 3.9 19.9 1.0
CB C:ASP177 4.0 19.2 1.0
CB C:SER198 4.1 19.9 1.0
OD2 C:ASP175 4.1 22.7 1.0
CA C:ASP177 4.1 20.2 1.0
N C:GLY181 4.2 19.6 1.0
CA C:HIS180 4.2 20.0 1.0
CA C:SER198 4.3 19.4 1.0
C C:ILE176 4.3 21.2 1.0
N C:HIS180 4.3 19.5 1.0
N C:ILE176 4.3 20.5 1.0
ND1 C:HIS200 4.3 22.6 1.0
CA C:ASP175 4.4 19.8 1.0
CA C:HIS200 4.4 19.9 1.0
C C:HIS180 4.5 19.6 1.0
C C:SER198 4.5 19.9 1.0
N C:HIS200 4.5 19.2 1.0
N C:HIS179 4.5 19.6 1.0
CA C:ILE176 4.5 20.6 1.0
CG C:HIS200 4.5 21.0 1.0
CA C:PHE199 4.6 20.0 1.0
C C:ILE178 4.7 19.3 1.0
N C:ILE178 4.8 19.6 1.0
CA C:HIS179 4.8 19.5 1.0
CE1 C:HIS141 4.8 23.6 1.0
O C:HOH582 4.9 22.3 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 02:05:57 2024

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