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Calcium in PDB 6xdm: Structure of Human HDAC2 in Complex with An Aryl Ketone Inhibitor

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

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

Protein crystallography data

The structure of Structure of Human HDAC2 in Complex with An Aryl Ketone Inhibitor, PDB code: 6xdm was solved by D.J.Klein, J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.76 / 1.56
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.255, 99.495, 139.850, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 18.9

Other elements in 6xdm:

The structure of Structure of Human HDAC2 in Complex with An Aryl Ketone Inhibitor also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Zinc (Zn) 3 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 6 in 6xdm

Go back to Calcium Binding Sites List in 6xdm
Calcium binding site 1 out of 6 in the Structure of Human HDAC2 in Complex with An Aryl 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 Aryl Ketone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:29.2
occ:1.00
 OD1 A:ASP175 2.8 12.6 1.0
O A:ASP177 2.8 11.8 1.0
OG A:SER198 2.9 14.3 1.0
O A:PHE199 2.9 13.4 1.0
O A:HIS179 2.9 12.8 1.0
O A:ASP175 3.0 11.6 1.0
CG A:ASP175 3.3 13.1 1.0
C A:ASP175 3.6 11.6 1.0
C A:PHE199 3.7 13.3 1.0
N A:ASP177 3.8 10.1 1.0
C A:ASP177 3.8 10.9 1.0
N A:PHE199 3.8 12.6 1.0
CB A:ASP175 3.8 12.5 1.0
C A:HIS179 3.8 12.3 1.0
CB A:HIS200 3.8 12.7 1.0
CB A:SER198 4.0 12.7 1.0
OD2 A:ASP175 4.1 14.4 1.0
CB A:ASP177 4.1 11.4 1.0
N A:GLY181 4.1 13.1 1.0
CA A:ASP177 4.2 10.1 1.0
N A:ILE176 4.2 10.8 1.0
CA A:SER198 4.3 12.2 1.0
CA A:HIS180 4.3 12.1 1.0
ND1 A:HIS200 4.3 15.2 1.0
C A:ILE176 4.3 10.9 1.0
CA A:ASP175 4.3 11.1 1.0
C A:SER198 4.3 13.4 1.0
CA A:HIS200 4.4 12.9 1.0
N A:HIS180 4.4 11.8 1.0
CA A:ILE176 4.4 11.1 1.0
N A:HIS200 4.4 12.3 1.0
CA A:PHE199 4.5 13.0 1.0
C A:HIS180 4.5 12.5 1.0
CG A:HIS200 4.5 13.7 1.0
N A:HIS179 4.6 11.4 1.0
C A:ILE178 4.8 11.9 1.0
CA A:HIS179 4.9 11.6 1.0
N A:ILE178 4.9 9.9 1.0
CE1 A:HIS141 4.9 15.1 1.0
O A:HOH603 4.9 16.0 1.0

Calcium binding site 2 out of 6 in 6xdm

Go back to Calcium Binding Sites List in 6xdm
Calcium binding site 2 out of 6 in the Structure of Human HDAC2 in Complex with An Aryl 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 Aryl Ketone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:35.1
occ:1.00
 O A:PHE188 2.7 15.5 1.0
O A:HOH550 2.7 18.1 1.0
O A:VAL194 2.8 16.9 1.0
O A:HOH717 2.9 17.2 1.0
O A:THR191 3.1 16.8 1.0
O A:TYR223 3.2 16.6 1.0
C A:PHE188 3.6 15.9 1.0
CB A:TYR223 3.7 15.6 1.0
C A:TYR223 3.8 16.4 1.0
C A:VAL194 3.9 15.6 1.0
CB A:PHE188 4.1 15.2 1.0
C A:THR191 4.3 16.6 1.0
CA A:TYR189 4.3 16.3 1.0
CA A:TYR223 4.3 15.8 1.0
N A:TYR189 4.4 16.2 1.0
O A:TYR189 4.4 17.6 1.0
C A:TYR189 4.4 17.2 1.0
N A:ALA224 4.5 15.7 1.0
CA A:PHE188 4.5 15.4 1.0
CA A:MET195 4.5 14.7 1.0
N A:THR196 4.6 13.7 1.0
N A:THR191 4.7 17.4 1.0
OG1 A:THR196 4.7 14.5 1.0
O A:GLY220 4.7 17.0 1.0
N A:MET195 4.7 14.5 1.0
CG2 A:THR191 4.7 19.2 1.0
CA A:GLY220 4.8 17.6 1.0
CA A:ALA224 4.9 15.8 1.0
CG2 A:THR196 4.9 15.4 1.0
CA A:VAL194 4.9 15.0 1.0
CB A:ALA224 4.9 15.7 1.0
CB A:VAL194 4.9 15.4 1.0
CG A:TYR223 5.0 16.3 1.0

Calcium binding site 3 out of 6 in 6xdm

Go back to Calcium Binding Sites List in 6xdm
Calcium binding site 3 out of 6 in the Structure of Human HDAC2 in Complex with An Aryl 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 Aryl Ketone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:30.2
occ:1.00
 O B:ASP177 2.7 9.8 1.0
OD1 B:ASP175 2.8 12.6 1.0
O B:PHE199 2.8 11.3 1.0
OG B:SER198 2.9 12.4 1.0
O B:HIS179 2.9 11.7 1.0
O B:ASP175 3.1 11.0 1.0
CG B:ASP175 3.4 12.5 1.0
C B:ASP175 3.6 10.6 1.0
C B:PHE199 3.7 10.9 1.0
C B:ASP177 3.7 9.2 1.0
N B:ASP177 3.8 9.3 1.0
C B:HIS179 3.8 11.5 1.0
N B:PHE199 3.8 10.7 1.0
CB B:ASP175 3.8 10.9 1.0
CB B:HIS200 3.8 11.4 1.0
CB B:SER198 4.0 12.1 1.0
CB B:ASP177 4.1 9.1 1.0
OD2 B:ASP175 4.1 13.1 1.0
CA B:ASP177 4.1 8.8 1.0
ND1 B:HIS200 4.2 13.2 1.0
N B:GLY181 4.2 12.2 1.0
N B:ILE176 4.3 9.5 1.0
CA B:HIS180 4.3 11.5 1.0
C B:ILE176 4.3 9.6 1.0
CA B:SER198 4.3 10.8 1.0
CA B:ASP175 4.4 9.2 1.0
C B:SER198 4.4 12.3 1.0
N B:HIS180 4.4 11.6 1.0
CA B:HIS200 4.4 11.0 1.0
CA B:ILE176 4.4 9.4 1.0
N B:HIS200 4.4 11.2 1.0
CA B:PHE199 4.5 10.4 1.0
CG B:HIS200 4.5 12.7 1.0
N B:HIS179 4.5 9.7 1.0
C B:HIS180 4.5 11.9 1.0
C B:ILE178 4.7 10.3 1.0
O B:HOH625 4.8 13.7 1.0
CA B:HIS179 4.8 9.8 1.0
N B:ILE178 4.8 9.1 1.0
CE1 B:HIS141 4.9 13.9 1.0

Calcium binding site 4 out of 6 in 6xdm

Go back to Calcium Binding Sites List in 6xdm
Calcium binding site 4 out of 6 in the Structure of Human HDAC2 in Complex with An Aryl 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 Aryl Ketone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:35.7
occ:1.00
 O B:VAL194 2.7 15.2 1.0
O B:HOH672 2.7 18.4 1.0
O B:PHE188 2.7 15.5 1.0
O B:HOH745 2.9 17.2 1.0
O B:THR191 3.0 17.1 1.0
O B:TYR223 3.1 16.1 1.0
CB B:TYR223 3.6 16.2 1.0
C B:TYR223 3.7 15.8 1.0
C B:PHE188 3.7 14.8 1.0
C B:VAL194 3.8 14.4 1.0
CB B:PHE188 4.2 14.3 1.0
C B:THR191 4.2 17.2 1.0
CA B:TYR223 4.3 16.0 1.0
CA B:TYR189 4.4 15.5 1.0
CA B:MET195 4.5 13.6 1.0
O B:TYR189 4.5 17.9 1.0
N B:TYR189 4.5 14.5 1.0
C B:TYR189 4.5 16.9 1.0
N B:ALA224 4.5 14.5 1.0
N B:THR196 4.6 12.7 1.0
N B:MET195 4.6 13.2 1.0
CA B:PHE188 4.6 14.5 1.0
N B:THR191 4.6 17.8 1.0
OG1 B:THR196 4.7 14.4 1.0
CG2 B:THR191 4.7 18.5 1.0
O B:GLY220 4.7 17.1 1.0
CA B:VAL194 4.8 14.0 1.0
CB B:VAL194 4.8 14.3 1.0
CG B:TYR223 4.9 17.0 1.0
CA B:GLY220 4.9 19.7 1.0
N B:VAL194 4.9 14.0 1.0
C B:MET195 4.9 13.5 1.0
CA B:ALA224 4.9 14.4 1.0
CA B:THR191 5.0 17.3 1.0

Calcium binding site 5 out of 6 in 6xdm

Go back to Calcium Binding Sites List in 6xdm
Calcium binding site 5 out of 6 in the Structure of Human HDAC2 in Complex with An Aryl 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 Aryl Ketone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:38.0
occ:1.00
 O C:VAL194 2.7 17.1 1.0
O C:PHE188 2.7 16.0 1.0
O C:HOH617 2.7 19.3 1.0
O C:THR191 2.9 16.3 1.0
O C:HOH664 3.0 18.3 1.0
O C:TYR223 3.2 18.2 1.0
C C:PHE188 3.6 15.5 1.0
CB C:TYR223 3.7 17.6 1.0
C C:TYR223 3.8 17.5 1.0
C C:VAL194 3.8 16.9 1.0
CB C:PHE188 4.1 15.2 1.0
C C:THR191 4.1 16.1 1.0
CA C:TYR223 4.3 17.6 1.0
CA C:TYR189 4.4 16.1 1.0
N C:TYR189 4.4 15.8 1.0
O C:TYR189 4.4 16.5 1.0
C C:TYR189 4.5 16.5 1.0
CA C:MET195 4.5 17.2 1.0
CA C:PHE188 4.5 15.3 1.0
N C:THR191 4.5 15.0 1.0
N C:ALA224 4.5 17.3 1.0
N C:THR196 4.6 16.6 1.0
CG2 C:THR191 4.6 15.5 1.0
N C:MET195 4.6 16.8 1.0
OG1 C:THR196 4.7 16.0 1.0
O C:GLY220 4.7 17.9 1.0
CA C:VAL194 4.8 15.8 1.0
CB C:VAL194 4.8 15.9 1.0
CA C:GLY220 4.8 18.4 1.0
CA C:THR191 4.9 15.3 1.0
CG2 C:THR196 4.9 16.8 1.0
CA C:ALA224 4.9 17.6 1.0
C C:MET195 4.9 17.0 1.0
CG C:TYR223 4.9 18.5 1.0
N C:VAL194 5.0 15.6 1.0

Calcium binding site 6 out of 6 in 6xdm

Go back to Calcium Binding Sites List in 6xdm
Calcium binding site 6 out of 6 in the Structure of Human HDAC2 in Complex with An Aryl 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 Aryl Ketone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:34.8
occ:1.00
 O C:ASP177 2.7 15.8 1.0
OD1 C:ASP175 2.8 17.3 1.0
O C:PHE199 2.9 16.3 1.0
OG C:SER198 2.9 16.2 1.0
O C:HIS179 2.9 14.9 1.0
O C:ASP175 3.0 15.4 1.0
CG C:ASP175 3.4 18.3 1.0
C C:ASP175 3.6 15.6 1.0
C C:ASP177 3.7 15.5 1.0
N C:ASP177 3.7 16.2 1.0
C C:PHE199 3.7 16.0 1.0
CB C:ASP175 3.8 15.3 1.0
C C:HIS179 3.8 14.4 1.0
CB C:HIS200 3.8 15.2 1.0
N C:PHE199 3.8 15.8 1.0
CB C:SER198 4.0 15.4 1.0
CB C:ASP177 4.1 15.7 1.0
CA C:ASP177 4.1 15.6 1.0
OD2 C:ASP175 4.2 17.6 1.0
N C:GLY181 4.3 16.4 1.0
C C:ILE176 4.3 16.3 1.0
CA C:HIS180 4.3 14.9 1.0
CA C:SER198 4.3 14.7 1.0
ND1 C:HIS200 4.3 18.0 1.0
N C:ILE176 4.3 15.4 1.0
CA C:ASP175 4.4 14.9 1.0
C C:SER198 4.4 15.7 1.0
N C:HIS180 4.4 14.7 1.0
CA C:HIS200 4.4 15.2 1.0
CA C:ILE176 4.4 16.0 1.0
N C:HIS200 4.5 15.1 1.0
CA C:PHE199 4.5 16.0 1.0
N C:HIS179 4.5 14.0 1.0
CG C:HIS200 4.5 16.1 1.0
C C:HIS180 4.6 15.7 1.0
C C:ILE178 4.7 14.8 1.0
N C:ILE178 4.8 14.7 1.0
CA C:HIS179 4.8 13.6 1.0
O C:HOH591 4.8 18.7 1.0
CE1 C:HIS141 5.0 17.8 1.0

Reference:

J.Liu, J.Kelly, W.Yu, D.Clausen, Y.Yu, H.Kim, J.L.Duffy, C.C.Chung, R.W.Myers, S.Carroll, D.J.Klein, J.Fells, M.K.Holloway, J.Wu, G.Wu, B.J.Howell, R.J.O.Barnard, J.A.Kozlowski. Selective Class I Hdac Inhibitors Based on Aryl Ketone Zinc Binding Induce Hiv-1 Protein For Clearance. Acs Med.Chem.Lett. V. 11 1476 2020.
ISSN: ISSN 1948-5875
PubMed: 32676157
DOI: 10.1021/ACSMEDCHEMLETT.0C00302
Page generated: Tue Jul 16 18:00:48 2024

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