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Calcium in PDB 6xeb: Structure of Human HDAC2 in Complex with Ketone Inhibitor (Compound E)

Enzymatic activity of Structure of Human HDAC2 in Complex with Ketone Inhibitor (Compound E)

All present enzymatic activity of Structure of Human HDAC2 in Complex with Ketone Inhibitor (Compound E):
3.5.1.98;

Protein crystallography data

The structure of Structure of Human HDAC2 in Complex with Ketone Inhibitor (Compound E), PDB code: 6xeb was solved by D.J.Klein, D.Clausen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.93 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.390, 99.030, 139.580, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 19.3

Other elements in 6xeb:

The structure of Structure of Human HDAC2 in Complex with Ketone Inhibitor (Compound E) also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Human HDAC2 in Complex with Ketone Inhibitor (Compound E) (pdb code 6xeb). 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 Human HDAC2 in Complex with Ketone Inhibitor (Compound E), PDB code: 6xeb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6xeb

Go back to Calcium Binding Sites List in 6xeb
Calcium binding site 1 out of 6 in the Structure of Human HDAC2 in Complex with Ketone Inhibitor (Compound E)


Mono view


Stereo pair view

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

b:30.0
occ:1.00
 OD1 A:ASP175 2.7 13.9 1.0
O A:ASP177 2.8 13.2 1.0
O A:PHE199 2.8 14.7 1.0
O A:HIS179 2.9 14.5 1.0
OG A:SER198 2.9 16.2 1.0
O A:ASP175 3.0 13.2 1.0
CG A:ASP175 3.4 14.1 1.0
C A:ASP175 3.6 13.1 1.0
C A:PHE199 3.7 14.5 1.0
C A:ASP177 3.7 12.2 1.0
N A:PHE199 3.8 13.5 1.0
N A:ASP177 3.8 12.1 1.0
CB A:HIS200 3.8 14.8 1.0
CB A:ASP175 3.8 14.8 1.0
C A:HIS179 3.8 13.5 1.0
CB A:SER198 4.0 14.1 1.0
OD2 A:ASP175 4.1 14.7 1.0
CB A:ASP177 4.2 13.0 1.0
N A:GLY181 4.2 14.8 1.0
CA A:ASP177 4.2 11.7 1.0
N A:ILE176 4.2 12.2 1.0
ND1 A:HIS200 4.3 15.8 1.0
CA A:HIS180 4.3 12.9 1.0
CA A:SER198 4.3 13.7 1.0
C A:ILE176 4.3 12.5 1.0
CA A:ASP175 4.3 12.9 1.0
C A:SER198 4.4 14.4 1.0
CA A:HIS200 4.4 14.1 1.0
N A:HIS200 4.4 13.7 1.0
N A:HIS180 4.4 12.8 1.0
CA A:ILE176 4.4 12.5 1.0
CA A:PHE199 4.4 13.7 1.0
CG A:HIS200 4.5 14.6 1.0
C A:HIS180 4.5 14.1 1.0
N A:HIS179 4.6 12.7 1.0
C A:ILE178 4.7 13.4 1.0
CA A:HIS179 4.8 13.2 1.0
N A:ILE178 4.9 11.2 1.0
O A:HOH603 4.9 16.7 1.0
CE1 A:HIS141 4.9 15.4 1.0

Calcium binding site 2 out of 6 in 6xeb

Go back to Calcium Binding Sites List in 6xeb
Calcium binding site 2 out of 6 in the Structure of Human HDAC2 in Complex with Ketone Inhibitor (Compound E)


Mono view


Stereo pair view

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

b:37.7
occ:1.00
 O A:PHE188 2.7 17.6 1.0
O A:VAL194 2.7 18.4 1.0
O A:HOH558 2.8 19.1 1.0
O A:THR191 3.0 18.7 1.0
O A:HOH697 3.0 19.8 1.0
O A:TYR223 3.2 17.9 1.0
CB A:TYR223 3.6 17.9 1.0
C A:PHE188 3.6 17.3 1.0
C A:TYR223 3.8 17.9 1.0
C A:VAL194 3.8 17.2 1.0
CB A:PHE188 4.1 16.1 1.0
C A:THR191 4.2 18.9 1.0
CA A:TYR223 4.3 17.9 1.0
CA A:TYR189 4.4 18.2 1.0
N A:TYR189 4.4 17.7 1.0
O A:TYR189 4.5 19.2 1.0
C A:TYR189 4.5 19.2 1.0
CA A:MET195 4.5 16.1 1.0
CA A:PHE188 4.5 16.5 1.0
N A:ALA224 4.6 16.7 1.0
N A:THR191 4.6 19.7 1.0
N A:THR196 4.6 15.2 1.0
N A:MET195 4.7 16.2 1.0
O A:GLY220 4.7 19.4 1.0
CG2 A:THR191 4.7 21.2 1.0
OG1 A:THR196 4.7 16.3 1.0
CA A:VAL194 4.8 17.2 1.0
CA A:GLY220 4.8 20.1 1.0
CB A:VAL194 4.8 17.3 1.0
CG2 A:THR196 4.9 16.1 1.0
CG A:TYR223 4.9 18.7 1.0
CA A:THR191 4.9 19.3 1.0
N A:VAL194 5.0 17.3 1.0
CA A:ALA224 5.0 17.1 1.0
C A:MET195 5.0 16.1 1.0

Calcium binding site 3 out of 6 in 6xeb

Go back to Calcium Binding Sites List in 6xeb
Calcium binding site 3 out of 6 in the Structure of Human HDAC2 in Complex with Ketone Inhibitor (Compound E)


Mono view


Stereo pair view

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

b:31.0
occ:1.00
 O B:ASP177 2.7 11.6 1.0
OD1 B:ASP175 2.7 13.6 1.0
O B:PHE199 2.8 11.7 1.0
O B:HIS179 2.9 12.9 1.0
OG B:SER198 2.9 13.5 1.0
O B:ASP175 3.0 12.9 1.0
CG B:ASP175 3.3 14.3 1.0
C B:ASP175 3.6 12.3 1.0
C B:ASP177 3.7 11.6 1.0
N B:ASP177 3.7 11.5 1.0
C B:PHE199 3.7 12.2 1.0
C B:HIS179 3.8 12.7 1.0
CB B:ASP175 3.8 12.5 1.0
CB B:HIS200 3.8 13.0 1.0
N B:PHE199 3.8 11.9 1.0
CB B:ASP177 4.0 11.8 1.0
CB B:SER198 4.1 13.6 1.0
CA B:ASP177 4.1 11.5 1.0
OD2 B:ASP175 4.2 14.8 1.0
N B:ILE176 4.2 10.4 1.0
CA B:HIS180 4.3 12.8 1.0
ND1 B:HIS200 4.3 14.3 1.0
C B:ILE176 4.3 11.6 1.0
N B:GLY181 4.3 13.9 1.0
CA B:ASP175 4.3 10.8 1.0
CA B:SER198 4.3 11.7 1.0
CA B:ILE176 4.4 10.5 1.0
N B:HIS180 4.4 12.7 1.0
C B:SER198 4.4 13.1 1.0
CA B:HIS200 4.4 12.6 1.0
N B:HIS200 4.5 12.5 1.0
N B:HIS179 4.5 11.9 1.0
CA B:PHE199 4.5 11.9 1.0
CG B:HIS200 4.5 13.5 1.0
C B:HIS180 4.6 13.3 1.0
C B:ILE178 4.7 12.1 1.0
O B:HOH617 4.8 14.0 1.0
CA B:HIS179 4.8 11.5 1.0
N B:ILE178 4.8 10.9 1.0
CE1 B:HIS141 4.9 14.5 1.0

Calcium binding site 4 out of 6 in 6xeb

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Calcium binding site 4 out of 6 in the Structure of Human HDAC2 in Complex with Ketone Inhibitor (Compound E)


Mono view


Stereo pair view

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

b:36.9
occ:1.00
 O B:VAL194 2.6 16.1 1.0
O B:PHE188 2.7 16.4 1.0
O B:HOH650 2.7 19.1 1.0
O B:THR191 2.9 18.3 1.0
O B:HOH745 3.0 17.0 1.0
O B:TYR223 3.1 16.9 1.0
CB B:TYR223 3.6 16.8 1.0
C B:PHE188 3.7 16.1 1.0
C B:VAL194 3.7 15.2 1.0
C B:TYR223 3.8 16.9 1.0
C B:THR191 4.1 18.4 1.0
CB B:PHE188 4.1 15.1 1.0
CA B:TYR223 4.3 16.9 1.0
CA B:MET195 4.4 14.2 1.0
CA B:TYR189 4.5 16.9 1.0
O B:TYR189 4.5 18.1 1.0
N B:TYR189 4.5 16.0 1.0
N B:MET195 4.5 14.4 1.0
C B:TYR189 4.6 17.7 1.0
N B:THR196 4.6 13.0 1.0
N B:THR191 4.6 18.9 1.0
CA B:PHE188 4.6 15.7 1.0
N B:ALA224 4.6 15.8 1.0
CG2 B:THR191 4.7 20.2 1.0
CA B:VAL194 4.7 14.8 1.0
O B:GLY220 4.7 17.9 1.0
CB B:VAL194 4.7 15.2 1.0
OG1 B:THR196 4.8 16.5 1.0
CG B:TYR223 4.8 17.9 1.0
N B:VAL194 4.8 15.6 1.0
CA B:GLY220 4.9 20.5 1.0
CA B:THR191 4.9 19.0 1.0
C B:MET195 4.9 14.3 1.0

Calcium binding site 5 out of 6 in 6xeb

Go back to Calcium Binding Sites List in 6xeb
Calcium binding site 5 out of 6 in the Structure of Human HDAC2 in Complex with Ketone Inhibitor (Compound E)


Mono view


Stereo pair view

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

b:39.4
occ:1.00
 O C:PHE188 2.6 17.5 1.0
O C:VAL194 2.6 18.3 1.0
O C:HOH604 2.7 20.4 1.0
O C:THR191 2.8 19.3 1.0
O C:HOH706 3.0 20.0 1.0
O C:TYR223 3.2 19.9 1.0
C C:PHE188 3.6 17.0 1.0
CB C:TYR223 3.7 19.2 1.0
C C:VAL194 3.8 17.9 1.0
C C:TYR223 3.8 19.1 1.0
C C:THR191 4.0 19.0 1.0
CB C:PHE188 4.1 16.3 1.0
CA C:TYR223 4.4 19.6 1.0
N C:TYR189 4.4 17.1 1.0
CA C:TYR189 4.4 17.5 1.0
O C:TYR189 4.4 18.0 1.0
C C:TYR189 4.4 17.8 1.0
N C:THR191 4.4 17.1 1.0
CA C:PHE188 4.5 16.4 1.0
CA C:MET195 4.5 18.8 1.0
CG2 C:THR191 4.6 17.9 1.0
N C:MET195 4.6 18.3 1.0
N C:ALA224 4.6 18.5 1.0
O C:GLY220 4.7 20.4 1.0
N C:THR196 4.7 17.2 1.0
CA C:VAL194 4.7 17.1 1.0
CA C:GLY220 4.7 20.6 1.0
CA C:THR191 4.7 17.9 1.0
CB C:VAL194 4.8 17.2 1.0
OG1 C:THR196 4.9 17.9 1.0
N C:VAL194 4.9 17.7 1.0
CG C:TYR223 4.9 20.0 1.0
CG2 C:THR196 5.0 16.8 1.0
C C:MET195 5.0 17.9 1.0

Calcium binding site 6 out of 6 in 6xeb

Go back to Calcium Binding Sites List in 6xeb
Calcium binding site 6 out of 6 in the Structure of Human HDAC2 in Complex with Ketone Inhibitor (Compound E)


Mono view


Stereo pair view

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

b:35.4
occ:1.00
 O C:ASP177 2.7 17.2 1.0
OD1 C:ASP175 2.8 18.2 1.0
OG C:SER198 2.9 17.4 1.0
O C:PHE199 2.9 17.8 1.0
O C:HIS179 2.9 15.9 1.0
O C:ASP175 3.0 16.6 1.0
CG C:ASP175 3.4 18.5 1.0
C C:ASP175 3.6 16.4 1.0
C C:ASP177 3.7 16.1 1.0
N C:ASP177 3.7 16.7 1.0
C C:PHE199 3.7 16.4 1.0
CB C:ASP175 3.8 15.6 1.0
C C:HIS179 3.8 15.3 1.0
N C:PHE199 3.8 16.1 1.0
CB C:HIS200 3.8 15.7 1.0
CB C:SER198 4.0 16.3 1.0
CB C:ASP177 4.1 16.0 1.0
CA C:ASP177 4.1 15.8 1.0
OD2 C:ASP175 4.2 17.8 1.0
N C:GLY181 4.2 16.4 1.0
CA C:SER198 4.3 15.6 1.0
N C:ILE176 4.3 16.6 1.0
C C:ILE176 4.3 16.8 1.0
ND1 C:HIS200 4.3 18.4 1.0
CA C:HIS180 4.3 15.9 1.0
CA C:ASP175 4.3 15.4 1.0
C C:SER198 4.4 16.3 1.0
CA C:HIS200 4.4 15.7 1.0
CA C:ILE176 4.4 16.3 1.0
N C:HIS180 4.4 15.6 1.0
N C:HIS200 4.5 15.5 1.0
N C:HIS179 4.5 15.2 1.0
CA C:PHE199 4.5 15.9 1.0
CG C:HIS200 4.5 17.1 1.0
C C:HIS180 4.6 16.0 1.0
C C:ILE178 4.7 15.6 1.0
CA C:HIS179 4.8 15.4 1.0
N C:ILE178 4.8 15.4 1.0
O C:HOH606 4.8 19.5 1.0
CE1 C:HIS141 5.0 17.6 1.0

Reference:

D.J.Clausen, J.Liu, W.Yu, J.L.Duffy, C.C.Chung, R.W.Myers, D.J.Klein, J.Fells, K.Holloway, J.Wu, G.Wu, B.J.Howell, R.J.O.Barnard, J.Kozlowski. Development of A Selective Hdac Inhibitor Aimed at Reactivating the Hiv Latent Reservoir. Bioorg.Med.Chem.Lett. V. 30 27367 2020.
ISSN: ESSN 1464-3405
PubMed: 32738976
DOI: 10.1016/J.BMCL.2020.127367
Page generated: Tue Jul 16 18:00:51 2024

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