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

Go back to Calcium Binding Sites List in 7ltl
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

Go back to Calcium Binding Sites List in 7ltl
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: Fri Jul 19 01:47:28 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy