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Calcium in PDB 6wbw: Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor

Enzymatic activity of Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor

All present enzymatic activity of Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor:
3.5.1.98;

Protein crystallography data

The structure of Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor, PDB code: 6wbw 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) 46.33 / 1.46
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 91.970, 98.280, 139.050, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 19.7

Other elements in 6wbw:

The structure of Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor 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 An Ethyl Ketone Inhibitor (pdb code 6wbw). 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 An Ethyl Ketone Inhibitor, PDB code: 6wbw:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6wbw

Go back to Calcium Binding Sites List in 6wbw
Calcium binding site 1 out of 6 in the Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor


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 An Ethyl Ketone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:19.1
occ:1.00
 OD1 A:ASP175 2.5 17.1 1.0
O A:PHE199 2.5 15.2 1.0
O A:ASP177 2.5 15.0 1.0
O A:HIS179 2.8 16.1 1.0
O A:ASP175 2.8 15.0 1.0
OG A:SER198 2.9 16.9 1.0
CG A:ASP175 3.3 15.7 1.0
C A:ASP175 3.4 16.1 1.0
C A:PHE199 3.5 17.0 1.0
C A:ASP177 3.5 14.9 1.0
N A:ASP177 3.6 12.8 1.0
C A:HIS179 3.8 16.8 1.0
N A:PHE199 3.8 14.5 1.0
CB A:ASP175 3.8 15.5 1.0
CB A:HIS200 3.9 15.0 1.0
CB A:ASP177 4.0 13.6 1.0
CA A:ASP177 4.0 12.9 1.0
C A:ILE176 4.1 13.7 1.0
N A:ILE176 4.1 13.6 1.0
CB A:SER198 4.1 15.5 1.0
OD2 A:ASP175 4.2 15.2 1.0
CA A:ASP175 4.2 14.3 1.0
CA A:ILE176 4.3 12.6 1.0
ND1 A:HIS200 4.3 17.1 1.0
CA A:HIS200 4.3 14.2 1.0
CA A:PHE199 4.4 13.8 1.0
N A:HIS200 4.4 14.7 1.0
CA A:HIS180 4.4 13.6 1.0
N A:GLY181 4.4 15.8 1.0
CA A:SER198 4.4 13.4 1.0
N A:HIS179 4.4 13.6 1.0
C A:SER198 4.4 17.5 1.0
N A:HIS180 4.5 14.7 1.0
O A:HOH570 4.5 16.2 1.0
C A:ILE178 4.6 16.1 1.0
CG A:HIS200 4.6 16.2 1.0
N A:ILE178 4.7 14.0 1.0
C A:HIS180 4.7 16.0 1.0
CA A:HIS179 4.7 14.2 1.0
O A:ILE176 4.8 14.6 1.0
CE1 A:HIS141 4.9 15.3 1.0
CA A:ILE178 5.0 13.8 1.0
O A:ILE178 5.0 16.5 1.0

Calcium binding site 2 out of 6 in 6wbw

Go back to Calcium Binding Sites List in 6wbw
Calcium binding site 2 out of 6 in the Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor


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 An Ethyl Ketone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:23.4
occ:1.00
 O A:HOH547 2.5 22.2 1.0
O A:PHE188 2.5 17.3 1.0
O A:VAL194 2.5 19.4 1.0
O A:THR191 2.8 21.3 1.0
O A:HOH680 2.9 22.4 1.0
O A:TYR223 3.2 19.2 1.0
C A:PHE188 3.5 18.6 1.0
CB A:TYR223 3.6 19.1 1.0
C A:VAL194 3.7 18.6 1.0
C A:TYR223 3.8 20.7 1.0
CB A:PHE188 4.0 17.1 1.0
C A:THR191 4.0 21.2 1.0
CA A:TYR223 4.3 17.7 1.0
N A:TYR189 4.4 18.2 1.0
CA A:TYR189 4.4 17.5 1.0
CA A:PHE188 4.4 15.6 1.0
O A:TYR189 4.4 20.7 1.0
CA A:MET195 4.4 16.2 1.0
C A:TYR189 4.4 21.5 1.0
N A:THR191 4.4 20.0 1.0
N A:MET195 4.6 16.5 1.0
N A:THR196 4.6 14.6 1.0
N A:ALA224 4.6 16.6 1.0
O A:GLY220 4.7 20.7 1.0
CG2 A:THR191 4.7 24.1 1.0
CA A:VAL194 4.7 17.1 1.0
CA A:THR191 4.8 19.8 1.0
CA A:GLY220 4.8 20.3 1.0
OG1 A:THR196 4.8 17.0 1.0
N A:VAL194 4.8 17.6 1.0
CB A:VAL194 4.8 19.6 1.0
CG A:TYR223 4.9 19.1 1.0
CG2 A:THR196 4.9 15.5 1.0
C A:MET195 5.0 17.0 1.0

Calcium binding site 3 out of 6 in 6wbw

Go back to Calcium Binding Sites List in 6wbw
Calcium binding site 3 out of 6 in the Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor


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 An Ethyl Ketone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:17.9
occ:1.00
 OD1 B:ASP175 2.5 15.2 1.0
O B:PHE199 2.5 14.8 1.0
O B:ASP177 2.5 12.9 1.0
O B:HIS179 2.8 14.7 1.0
O B:ASP175 2.8 14.6 1.0
OG B:SER198 2.9 15.5 1.0
CG B:ASP175 3.3 15.1 1.0
C B:ASP175 3.4 13.7 1.0
C B:ASP177 3.5 13.8 1.0
C B:PHE199 3.5 15.1 1.0
N B:ASP177 3.6 11.4 1.0
N B:PHE199 3.8 13.2 1.0
CB B:ASP175 3.8 14.3 1.0
C B:HIS179 3.8 15.9 1.0
CB B:HIS200 3.9 14.0 1.0
CA B:ASP177 4.0 12.5 1.0
CB B:ASP177 4.0 12.9 1.0
N B:ILE176 4.1 12.4 1.0
C B:ILE176 4.1 11.8 1.0
CB B:SER198 4.1 14.6 1.0
OD2 B:ASP175 4.2 15.2 1.0
CA B:ILE176 4.2 11.1 1.0
CA B:ASP175 4.2 12.3 1.0
ND1 B:HIS200 4.3 16.4 1.0
CA B:HIS200 4.3 14.1 1.0
N B:HIS200 4.3 13.6 1.0
CA B:PHE199 4.4 12.6 1.0
CA B:HIS180 4.4 13.6 1.0
CA B:SER198 4.4 12.1 1.0
O B:HOH586 4.4 15.0 1.0
C B:SER198 4.4 15.5 1.0
N B:HIS179 4.5 12.7 1.0
N B:GLY181 4.5 14.9 1.0
N B:HIS180 4.5 13.7 1.0
C B:ILE178 4.6 14.7 1.0
CG B:HIS200 4.6 15.7 1.0
N B:ILE178 4.6 11.7 1.0
C B:HIS180 4.7 14.7 1.0
O B:ILE176 4.8 13.7 1.0
CA B:HIS179 4.8 12.3 1.0
O B:ILE178 4.9 14.5 1.0
CA B:ILE178 4.9 12.2 1.0
CE1 B:HIS141 5.0 14.7 1.0

Calcium binding site 4 out of 6 in 6wbw

Go back to Calcium Binding Sites List in 6wbw
Calcium binding site 4 out of 6 in the Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor


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 An Ethyl Ketone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:23.2
occ:1.00
 O B:HOH655 2.4 19.5 1.0
O B:PHE188 2.5 18.9 1.0
O B:VAL194 2.5 19.9 1.0
O B:THR191 2.8 20.8 1.0
O B:HOH749 2.8 21.6 1.0
O B:TYR223 3.1 19.5 1.0
C B:PHE188 3.5 18.7 1.0
CB B:TYR223 3.6 19.0 1.0
C B:VAL194 3.8 19.1 1.0
C B:TYR223 3.8 20.5 1.0
C B:THR191 4.0 21.6 1.0
CB B:PHE188 4.0 16.2 1.0
CA B:TYR223 4.3 17.9 1.0
N B:TYR189 4.3 17.7 1.0
CA B:TYR189 4.3 17.4 1.0
N B:THR191 4.4 21.5 1.0
C B:TYR189 4.4 20.0 1.0
O B:TYR189 4.4 19.5 1.0
CA B:PHE188 4.4 15.7 1.0
CA B:MET195 4.5 15.6 1.0
CG2 B:THR191 4.5 19.1 1.0
N B:MET195 4.6 15.4 1.0
N B:ALA224 4.6 16.5 1.0
N B:THR196 4.6 15.6 1.0
O B:GLY220 4.7 20.5 1.0
CA B:VAL194 4.7 16.3 1.0
CA B:THR191 4.7 20.7 1.0
N B:VAL194 4.8 17.3 1.0
CA B:GLY220 4.8 21.4 1.0
CB B:VAL194 4.8 19.0 1.0
OG1 B:THR196 4.8 17.8 1.0
CG B:TYR223 4.9 19.9 1.0
N B:ASP192 5.0 19.0 1.0
CG2 B:THR196 5.0 15.9 1.0
C B:MET195 5.0 16.2 1.0

Calcium binding site 5 out of 6 in 6wbw

Go back to Calcium Binding Sites List in 6wbw
Calcium binding site 5 out of 6 in the Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor


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 An Ethyl Ketone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:23.9
occ:1.00
 O C:HOH538 2.4 20.0 1.0
O C:VAL194 2.4 19.7 1.0
O C:PHE188 2.5 18.1 1.0
O C:THR191 2.7 18.3 1.0
O C:HOH703 2.9 21.5 1.0
O C:TYR223 3.1 22.1 1.0
C C:PHE188 3.5 18.6 1.0
CB C:TYR223 3.7 19.5 1.0
C C:VAL194 3.7 19.6 1.0
C C:TYR223 3.8 20.8 1.0
C C:THR191 3.9 20.2 1.0
CB C:PHE188 4.0 17.8 1.0
CA C:TYR223 4.3 19.2 1.0
CA C:MET195 4.4 17.9 1.0
N C:THR191 4.4 18.0 1.0
N C:TYR189 4.4 16.6 1.0
CA C:PHE188 4.4 16.3 1.0
CA C:TYR189 4.4 15.5 1.0
CG2 C:THR191 4.4 18.3 1.0
C C:TYR189 4.4 20.2 1.0
O C:TYR189 4.4 18.5 1.0
N C:MET195 4.5 18.1 1.0
N C:ALA224 4.6 18.8 1.0
N C:THR196 4.6 17.2 1.0
O C:GLY220 4.6 20.4 1.0
CA C:THR191 4.7 17.4 1.0
CA C:VAL194 4.7 17.4 1.0
CA C:GLY220 4.8 19.0 1.0
N C:VAL194 4.8 18.2 1.0
OG1 C:THR196 4.8 18.3 1.0
CB C:VAL194 4.8 20.0 1.0
C C:MET195 4.9 19.4 1.0
N C:ASP192 4.9 18.6 1.0
CG C:TYR223 4.9 19.6 1.0

Calcium binding site 6 out of 6 in 6wbw

Go back to Calcium Binding Sites List in 6wbw
Calcium binding site 6 out of 6 in the Structure of Human HDAC2 in Complex with An Ethyl Ketone Inhibitor


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 An Ethyl Ketone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca404

b:23.6
occ:1.00
 O C:ASP177 2.4 19.1 1.0
O C:PHE199 2.5 20.4 1.0
OD1 C:ASP175 2.5 19.5 1.0
O C:HIS179 2.8 17.6 1.0
O C:ASP175 2.9 18.6 1.0
OG C:SER198 2.9 20.5 1.0
CG C:ASP175 3.3 22.0 1.0
C C:ASP175 3.5 19.4 1.0
C C:ASP177 3.5 18.3 1.0
C C:PHE199 3.5 19.2 1.0
N C:ASP177 3.6 17.1 1.0
N C:PHE199 3.7 18.0 1.0
CB C:ASP175 3.8 18.7 1.0
C C:HIS179 3.8 16.8 1.0
CB C:HIS200 3.9 16.5 1.0
CA C:ASP177 4.0 16.2 1.0
CB C:ASP177 4.0 17.1 1.0
C C:ILE176 4.1 20.1 1.0
N C:ILE176 4.1 17.7 1.0
CB C:SER198 4.1 19.0 1.0
OD2 C:ASP175 4.2 19.5 1.0
CA C:ASP175 4.2 17.2 1.0
CA C:ILE176 4.3 17.2 1.0
CA C:PHE199 4.3 18.0 1.0
ND1 C:HIS200 4.4 20.0 1.0
N C:HIS200 4.4 16.8 1.0
CA C:HIS200 4.4 16.4 1.0
CA C:SER198 4.4 16.5 1.0
CA C:HIS180 4.4 16.0 1.0
N C:HIS179 4.4 17.0 1.0
C C:SER198 4.4 19.3 1.0
N C:GLY181 4.4 17.9 1.0
N C:HIS180 4.5 16.9 1.0
O C:HOH578 4.5 20.9 1.0
C C:ILE178 4.6 18.9 1.0
N C:ILE178 4.6 17.0 1.0
CG C:HIS200 4.6 19.0 1.0
C C:HIS180 4.7 19.4 1.0
CA C:HIS179 4.7 16.5 1.0
O C:ILE176 4.8 19.8 1.0
CA C:ILE178 4.9 16.8 1.0
O C:ILE178 5.0 18.4 1.0
CE1 C:HIS141 5.0 18.3 1.0

Reference:

W.Yu, J.Liu, Y.Yu, V.Zhang, D.Clausen, J.Kelly, S.Wolkenberg, D.Beshore, J.L.Duffy, C.C.Chang, R.W.Myers, D.J.Klein, J.Fells, K.Holloway, J.Wu, G.Wu, B.J.Howell, R.J.O.Barnard, J.Kozlowski. Discovery of Ethyl Ketone-Based Hdacs 1, 2, and 3 Selective Inhibitors For Hiv Latency Reactivation. Bioorg.Med.Chem.Lett. 27197 2020.
ISSN: ESSN 1464-3405
PubMed: 32331932
DOI: 10.1016/J.BMCL.2020.127197
Page generated: Tue Jul 16 17:22:51 2024

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