Calcium in PDB 7ltl: Structure of Human HDAC2 in Complex with An Inhibitor Lacking A Zinc Binding Group (Compound 19)

Enzymatic activity of Structure of Human HDAC2 in Complex with An Inhibitor Lacking A Zinc Binding Group (Compound 19)

All present enzymatic activity of Structure of Human HDAC2 in Complex with An Inhibitor Lacking A Zinc Binding Group (Compound 19):
3.5.1.98;

Protein crystallography data

The structure of Structure of Human HDAC2 in Complex with An Inhibitor Lacking A Zinc Binding Group (Compound 19), PDB code: 7ltl was solved by D.J.Klein, D.C.Beshore, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.77 / 1.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.35, 98.76, 139.44, 90, 90, 90
R / Rfree (%) 17 / 19.5

Other elements in 7ltl:

The structure of Structure of Human HDAC2 in Complex with An Inhibitor Lacking A Zinc Binding Group (Compound 19) 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 Inhibitor Lacking A Zinc Binding Group (Compound 19) (pdb code 7ltl). 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 Inhibitor Lacking A Zinc Binding Group (Compound 19), PDB code: 7ltl:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 7ltl

Go back to Calcium Binding Sites List in 7ltl
Calcium binding site 1 out of 6 in the Structure of Human HDAC2 in Complex with An Inhibitor Lacking A Zinc Binding Group (Compound 19)


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 Inhibitor Lacking A Zinc Binding Group (Compound 19) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:33.6
occ:1.00
 OD1 A:ASP175 2.7 16.3 1.0
O A:ASP177 2.8 15.0 1.0
O A:HIS179 2.8 15.9 1.0
O A:PHE199 2.8 16.0 1.0
OG A:SER198 2.9 18.3 1.0
O A:ASP175 3.0 16.0 1.0
CG A:ASP175 3.3 17.9 1.0
C A:ASP175 3.6 16.5 1.0
C A:ASP177 3.7 16.6 1.0
C A:PHE199 3.7 16.4 1.0
N A:ASP177 3.8 13.8 1.0
C A:HIS179 3.8 16.8 1.0
N A:PHE199 3.8 14.4 1.0
CB A:ASP175 3.8 16.3 1.0
CB A:HIS200 3.8 14.6 1.0
CB A:SER198 4.0 16.2 1.0
CB A:ASP177 4.1 15.3 1.0
N A:GLY181 4.1 15.7 1.0
OD2 A:ASP175 4.1 17.4 1.0
CA A:ASP177 4.1 14.2 1.0
N A:ILE176 4.2 14.9 1.0
CA A:HIS180 4.3 14.1 1.0
CA A:SER198 4.3 13.7 1.0
C A:ILE176 4.3 16.1 1.0
ND1 A:HIS200 4.3 17.6 1.0
CA A:ASP175 4.4 14.1 1.0
CA A:HIS200 4.4 15.1 1.0
C A:SER198 4.4 17.0 1.0
N A:HIS180 4.4 14.7 1.0
N A:HIS200 4.5 14.4 1.0
C A:HIS180 4.5 16.1 1.0
CA A:ILE176 4.5 13.8 1.0
CA A:PHE199 4.5 14.0 1.0
N A:HIS179 4.5 14.1 1.0
CG A:HIS200 4.6 16.6 1.0
C A:ILE178 4.7 17.6 1.0
CA A:HIS179 4.8 14.2 1.0
N A:ILE178 4.8 13.8 1.0
CE1 A:HIS141 4.9 18.2 1.0
O A:HOH555 4.9 18.2 1.0
CA A:GLY181 5.0 15.7 1.0

Calcium binding site 2 out of 6 in 7ltl

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Calcium binding site 2 out of 6 in the Structure of Human HDAC2 in Complex with An Inhibitor Lacking A Zinc Binding Group (Compound 19)


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 Inhibitor Lacking A Zinc Binding Group (Compound 19) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:39.2
occ:1.00
 O A:VAL194 2.6 21.1 1.0
O A:PHE188 2.6 20.1 1.0
O A:HOH535 2.7 21.6 1.0
O A:HOH679 2.9 21.1 1.0
O A:THR191 3.0 21.2 1.0
O A:TYR223 3.2 20.4 1.0
C A:PHE188 3.6 19.4 1.0
CB A:TYR223 3.7 18.3 1.0
C A:TYR223 3.8 21.9 1.0
C A:VAL194 3.8 20.9 1.0
CB A:PHE188 4.1 17.9 1.0
C A:THR191 4.2 22.4 1.0
CA A:TYR223 4.3 18.4 1.0
N A:TYR189 4.4 18.6 1.0
CA A:TYR189 4.4 18.0 1.0
O A:TYR189 4.4 21.1 1.0
CA A:PHE188 4.5 17.1 1.0
C A:TYR189 4.5 21.8 1.0
CA A:MET195 4.5 17.9 1.0
N A:ALA224 4.6 18.8 1.0
N A:THR196 4.6 17.2 1.0
N A:MET195 4.6 17.7 1.0
N A:THR191 4.6 21.4 1.0
OG1 A:THR196 4.7 18.7 1.0
CG2 A:THR191 4.7 24.5 1.0
O A:GLY220 4.7 21.3 1.0
CA A:VAL194 4.8 18.0 1.0
CG2 A:THR196 4.9 16.7 1.0
CB A:VAL194 4.9 20.9 1.0
CA A:GLY220 4.9 21.4 1.0
N A:VAL194 4.9 19.0 1.0
CA A:ALA224 4.9 18.3 1.0
CA A:THR191 4.9 21.4 1.0
CG A:TYR223 4.9 19.7 1.0
CB A:ALA224 5.0 19.2 1.0
C A:MET195 5.0 19.1 1.0

Calcium binding site 3 out of 6 in 7ltl

Go back to Calcium Binding Sites List in 7ltl
Calcium binding site 3 out of 6 in the Structure of Human HDAC2 in Complex with An Inhibitor Lacking A Zinc Binding Group (Compound 19)


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 Inhibitor Lacking A Zinc Binding Group (Compound 19) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca405

b:31.6
occ:1.00
 O B:ASP177 2.7 13.2 1.0
OD1 B:ASP175 2.8 16.3 1.0
O B:PHE199 2.9 14.4 1.0
O B:HIS179 2.9 14.8 1.0
OG B:SER198 2.9 15.7 1.0
O B:ASP175 3.1 14.9 1.0
CG B:ASP175 3.4 16.2 1.0
C B:ASP175 3.6 14.8 1.0
C B:ASP177 3.7 13.3 1.0
C B:PHE199 3.7 15.0 1.0
N B:ASP177 3.7 11.8 1.0
N B:PHE199 3.8 13.9 1.0
C B:HIS179 3.8 16.2 1.0
CB B:ASP175 3.8 15.0 1.0
CB B:HIS200 3.8 13.8 1.0
CB B:SER198 4.0 14.8 1.0
CB B:ASP177 4.1 13.2 1.0
OD2 B:ASP175 4.1 16.5 1.0
CA B:ASP177 4.1 12.1 1.0
N B:GLY181 4.2 15.3 1.0
N B:ILE176 4.2 11.9 1.0
CA B:HIS180 4.3 14.2 1.0
ND1 B:HIS200 4.3 16.9 1.0
C B:ILE176 4.3 12.5 1.0
CA B:SER198 4.3 12.3 1.0
CA B:ASP175 4.4 12.8 1.0
CA B:HIS200 4.4 13.6 1.0
C B:SER198 4.4 16.9 1.0
N B:HIS180 4.4 14.2 1.0
CA B:ILE176 4.4 12.2 1.0
N B:HIS200 4.4 14.3 1.0
CA B:PHE199 4.5 13.1 1.0
N B:HIS179 4.5 13.6 1.0
CG B:HIS200 4.5 16.1 1.0
C B:HIS180 4.5 15.4 1.0
C B:ILE178 4.7 16.0 1.0
N B:ILE178 4.8 11.6 1.0
O B:HOH646 4.8 16.1 1.0
CA B:HIS179 4.8 12.9 1.0
CE1 B:HIS141 4.9 17.4 1.0

Calcium binding site 4 out of 6 in 7ltl

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Calcium binding site 4 out of 6 in the Structure of Human HDAC2 in Complex with An Inhibitor Lacking A Zinc Binding Group (Compound 19)


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 Inhibitor Lacking A Zinc Binding Group (Compound 19) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca406

b:39.1
occ:1.00
 O B:HOH612 2.6 19.7 1.0
O B:PHE188 2.7 19.3 1.0
O B:VAL194 2.7 19.2 1.0
O B:HOH749 2.9 21.1 1.0
O B:THR191 2.9 20.8 1.0
O B:TYR223 3.2 19.9 1.0
CB B:TYR223 3.6 17.4 1.0
C B:PHE188 3.7 19.2 1.0
C B:TYR223 3.8 20.5 1.0
C B:VAL194 3.8 19.1 1.0
CB B:PHE188 4.1 17.1 1.0
C B:THR191 4.2 22.2 1.0
CA B:TYR223 4.3 16.3 1.0
CA B:TYR189 4.4 17.8 1.0
O B:TYR189 4.4 20.6 1.0
N B:TYR189 4.4 17.3 1.0
C B:TYR189 4.4 21.6 1.0
CA B:MET195 4.5 15.0 1.0
N B:ALA224 4.6 18.1 1.0
CA B:PHE188 4.6 15.9 1.0
N B:THR191 4.6 20.7 1.0
N B:MET195 4.6 16.4 1.0
CG2 B:THR191 4.6 20.4 1.0
N B:THR196 4.6 14.1 1.0
O B:GLY220 4.7 20.0 1.0
OG1 B:THR196 4.7 18.6 1.0
CA B:VAL194 4.8 15.7 1.0
CB B:VAL194 4.8 18.1 1.0
CA B:GLY220 4.8 21.9 1.0
CG B:TYR223 4.9 20.0 1.0
N B:VAL194 4.9 17.0 1.0
CA B:THR191 4.9 20.2 1.0
CA B:ALA224 5.0 17.1 1.0
CG2 B:THR196 5.0 16.0 1.0

Calcium binding site 5 out of 6 in 7ltl

Go back to Calcium Binding Sites List in 7ltl
Calcium binding site 5 out of 6 in the Structure of Human HDAC2 in Complex with An Inhibitor Lacking A Zinc Binding Group (Compound 19)


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 Inhibitor Lacking A Zinc Binding Group (Compound 19) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca407

b:40.7
occ:1.00
 O C:PHE188 2.6 19.8 1.0
O C:VAL194 2.6 21.5 1.0
O C:HOH588 2.7 23.1 1.0
O C:THR191 2.8 20.1 1.0
O C:HOH701 3.0 23.1 1.0
O C:TYR223 3.3 21.4 1.0
C C:PHE188 3.6 20.1 1.0
CB C:TYR223 3.7 20.1 1.0
C C:VAL194 3.8 22.2 1.0
C C:TYR223 3.9 21.6 1.0
C C:THR191 4.0 22.9 1.0
CB C:PHE188 4.1 18.0 1.0
N C:TYR189 4.3 17.3 1.0
CA C:TYR189 4.3 17.5 1.0
CA C:TYR223 4.4 19.5 1.0
C C:TYR189 4.4 21.1 1.0
O C:TYR189 4.4 20.4 1.0
CA C:PHE188 4.4 17.1 1.0
N C:THR191 4.5 18.4 1.0
CA C:MET195 4.5 20.5 1.0
CG2 C:THR191 4.6 19.2 1.0
N C:ALA224 4.6 19.2 1.0
N C:THR196 4.6 19.0 1.0
N C:MET195 4.7 19.3 1.0
O C:GLY220 4.7 21.8 1.0
OG1 C:THR196 4.7 19.8 1.0
CA C:THR191 4.8 18.4 1.0
CA C:VAL194 4.8 18.1 1.0
CA C:GLY220 4.8 20.7 1.0
CB C:VAL194 4.8 20.3 1.0
N C:VAL194 4.9 18.4 1.0
CG2 C:THR196 4.9 18.2 1.0
CA C:ALA224 5.0 19.1 1.0
CG C:TYR223 5.0 20.1 1.0
C C:MET195 5.0 21.4 1.0

Calcium binding site 6 out of 6 in 7ltl

Go back to Calcium Binding Sites List in 7ltl
Calcium binding site 6 out of 6 in the Structure of Human HDAC2 in Complex with An Inhibitor Lacking A Zinc Binding Group (Compound 19)


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 Inhibitor Lacking A Zinc Binding Group (Compound 19) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca408

b:40.7
occ:1.00
 O C:ASP177 2.7 19.8 1.0
OD1 C:ASP175 2.8 20.8 1.0
O C:PHE199 2.8 18.6 1.0
O C:HIS179 2.9 19.3 1.0
OG C:SER198 2.9 21.1 1.0
O C:ASP175 3.0 19.6 1.0
CG C:ASP175 3.4 24.0 1.0
C C:ASP175 3.6 18.8 1.0
C C:PHE199 3.7 18.7 1.0
C C:ASP177 3.7 19.1 1.0
N C:ASP177 3.7 18.4 1.0
CB C:HIS200 3.8 17.0 1.0
C C:HIS179 3.8 18.9 1.0
N C:PHE199 3.8 18.4 1.0
CB C:ASP175 3.8 19.5 1.0
CB C:SER198 4.0 19.9 1.0
CB C:ASP177 4.1 17.8 1.0
CA C:ASP177 4.1 17.1 1.0
N C:GLY181 4.2 17.9 1.0
OD2 C:ASP175 4.2 20.2 1.0
CA C:HIS180 4.3 17.2 1.0
ND1 C:HIS200 4.3 20.3 1.0
C C:ILE176 4.3 20.1 1.0
CA C:SER198 4.3 17.0 1.0
N C:ILE176 4.3 18.0 1.0
CA C:ASP175 4.4 18.0 1.0
C C:SER198 4.4 20.1 1.0
CA C:HIS200 4.4 16.6 1.0
N C:HIS180 4.4 18.0 1.0
N C:HIS200 4.4 16.3 1.0
CA C:ILE176 4.5 17.4 1.0
CA C:PHE199 4.5 17.6 1.0
N C:HIS179 4.5 17.6 1.0
CG C:HIS200 4.5 19.8 1.0
C C:HIS180 4.5 19.3 1.0
C C:ILE178 4.7 19.6 1.0
N C:ILE178 4.8 17.6 1.0
CA C:HIS179 4.8 17.9 1.0
O C:HOH556 4.8 22.5 1.0
CE1 C:HIS141 4.9 20.7 1.0

Reference:

D.C.Beshore, G.C.Adam, R.J.O.Barnard, C.Burlein, S.N.Gallicchio, M.K.Holloway, D.Krosky, W.Lemaire, R.W.Myers, S.Patel, M.A.Plotkin, D.A.Powell, V.Rada, C.D.Cox, P.J.Coleman, D.J.Klein, S.E.Wolkenberg. Redefining the Histone Deacetylase Inhibitor Pharmacophore: High Potency with No Zinc Cofactor Interaction. Acs Med.Chem.Lett. V. 12 540 2021.
ISSN: ISSN 1948-5875
PubMed: 33854701
DOI: 10.1021/ACSMEDCHEMLETT.1C00074
Page generated: Sat Jul 10 11:32:12 2021

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