Atomistry » Calcium » PDB 7lry-7m41 » 7ltk
Atomistry »
  Calcium »
    PDB 7lry-7m41 »
      7ltk »

Calcium in PDB 7ltk: Structure of Human HDAC2 in Complex with An Inhibitor That Lacks A Zinc Binding Group (Compound 12)

Enzymatic activity of Structure of Human HDAC2 in Complex with An Inhibitor That Lacks A Zinc Binding Group (Compound 12)

All present enzymatic activity of Structure of Human HDAC2 in Complex with An Inhibitor That Lacks A Zinc Binding Group (Compound 12):
3.5.1.98;

Protein crystallography data

The structure of Structure of Human HDAC2 in Complex with An Inhibitor That Lacks A Zinc Binding Group (Compound 12), PDB code: 7ltk 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) 23.20 / 1.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.16, 98.43, 139.2, 90, 90, 90
R / Rfree (%) 17.2 / 19.8

Other elements in 7ltk:

The structure of Structure of Human HDAC2 in Complex with An Inhibitor That Lacks A Zinc Binding Group (Compound 12) 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 That Lacks A Zinc Binding Group (Compound 12) (pdb code 7ltk). 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 That Lacks A Zinc Binding Group (Compound 12), PDB code: 7ltk:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 7ltk

Go back to Calcium Binding Sites List in 7ltk
Calcium binding site 1 out of 6 in the Structure of Human HDAC2 in Complex with An Inhibitor That Lacks A Zinc Binding Group (Compound 12)


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 That Lacks A Zinc Binding Group (Compound 12) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:24.3
occ:1.00
OD1 A:ASP175 2.4 21.3 1.0
O A:PHE199 2.5 20.5 1.0
O A:ASP177 2.5 20.9 1.0
O A:HIS179 2.7 20.7 1.0
O A:ASP175 2.9 19.0 1.0
OG A:SER198 2.9 21.3 1.0
CG A:ASP175 3.3 21.3 1.0
C A:ASP175 3.5 20.5 1.0
C A:ASP177 3.5 20.4 1.0
C A:PHE199 3.6 21.8 1.0
N A:ASP177 3.6 18.3 1.0
C A:HIS179 3.7 21.2 1.0
CB A:ASP175 3.8 20.2 1.0
N A:PHE199 3.8 18.8 1.0
CB A:HIS200 3.9 19.4 1.0
CA A:ASP177 4.0 16.9 1.0
CB A:ASP177 4.0 17.8 1.0
C A:ILE176 4.1 19.4 1.0
CB A:SER198 4.1 20.1 1.0
OD2 A:ASP175 4.1 21.0 1.0
N A:ILE176 4.2 17.7 1.0
CA A:ASP175 4.3 18.0 1.0
ND1 A:HIS200 4.3 22.4 1.0
CA A:ILE176 4.3 16.8 1.0
N A:GLY181 4.4 19.9 1.0
CA A:HIS200 4.4 19.1 1.0
CA A:PHE199 4.4 17.8 1.0
CA A:HIS180 4.4 19.0 1.0
CA A:SER198 4.4 17.7 1.0
N A:HIS200 4.4 19.5 1.0
N A:HIS179 4.4 18.4 1.0
C A:SER198 4.4 21.6 1.0
N A:HIS180 4.5 18.9 1.0
O A:HOH625 4.5 21.6 1.0
C A:ILE178 4.6 21.8 1.0
CG A:HIS200 4.6 21.8 1.0
N A:ILE178 4.7 18.4 1.0
C A:HIS180 4.7 20.5 1.0
CA A:HIS179 4.7 18.3 1.0
O A:ILE176 4.8 19.2 1.0
CE1 A:HIS141 4.9 21.4 1.0
O A:ILE178 4.9 21.1 1.0
CA A:ILE178 5.0 18.1 1.0

Calcium binding site 2 out of 6 in 7ltk

Go back to Calcium Binding Sites List in 7ltk
Calcium binding site 2 out of 6 in the Structure of Human HDAC2 in Complex with An Inhibitor That Lacks A Zinc Binding Group (Compound 12)


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 That Lacks A Zinc Binding Group (Compound 12) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:29.6
occ:1.00
O A:HOH561 2.5 24.4 1.0
O A:VAL194 2.5 24.9 1.0
O A:PHE188 2.5 23.3 1.0
O A:THR191 2.8 27.3 1.0
O A:HOH685 2.9 28.4 1.0
O A:TYR223 3.1 24.2 1.0
C A:PHE188 3.5 24.5 1.0
CB A:TYR223 3.6 24.9 1.0
C A:VAL194 3.7 24.1 1.0
C A:TYR223 3.8 25.9 1.0
C A:THR191 4.0 26.7 1.0
CB A:PHE188 4.0 21.6 1.0
CA A:TYR223 4.3 23.0 1.0
N A:TYR189 4.4 23.0 1.0
CA A:MET195 4.4 22.4 1.0
CA A:TYR189 4.4 22.4 1.0
O A:TYR189 4.4 25.9 1.0
CA A:PHE188 4.4 20.7 1.0
N A:THR191 4.4 25.2 1.0
C A:TYR189 4.5 26.0 1.0
N A:MET195 4.5 21.3 1.0
N A:THR196 4.6 20.2 1.0
N A:ALA224 4.6 21.6 1.0
O A:GLY220 4.7 26.2 1.0
CA A:VAL194 4.7 21.4 1.0
CG2 A:THR191 4.7 26.9 1.0
CA A:THR191 4.7 24.1 1.0
CA A:GLY220 4.8 25.6 1.0
N A:VAL194 4.8 22.6 1.0
OG1 A:THR196 4.8 22.1 1.0
CB A:VAL194 4.8 24.2 1.0
CG A:TYR223 4.9 24.7 1.0
CG2 A:THR196 4.9 20.8 1.0
C A:MET195 4.9 23.8 1.0
N A:ASP192 5.0 23.8 1.0

Calcium binding site 3 out of 6 in 7ltk

Go back to Calcium Binding Sites List in 7ltk
Calcium binding site 3 out of 6 in the Structure of Human HDAC2 in Complex with An Inhibitor That Lacks A Zinc Binding Group (Compound 12)


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 That Lacks A Zinc Binding Group (Compound 12) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:22.6
occ:1.00
O B:ASP177 2.5 17.7 1.0
OD1 B:ASP175 2.5 19.4 1.0
O B:PHE199 2.5 17.9 1.0
O B:HIS179 2.7 19.1 1.0
OG B:SER198 2.9 19.1 1.0
O B:ASP175 3.0 18.8 1.0
CG B:ASP175 3.3 19.3 1.0
C B:ASP177 3.5 17.9 1.0
C B:ASP175 3.5 18.6 1.0
C B:PHE199 3.5 19.1 1.0
N B:ASP177 3.6 15.3 1.0
C B:HIS179 3.7 19.7 1.0
CB B:ASP175 3.8 16.8 1.0
N B:PHE199 3.8 17.8 1.0
CB B:HIS200 3.9 17.9 1.0
CA B:ASP177 4.0 15.6 1.0
CB B:ASP177 4.1 16.9 1.0
CB B:SER198 4.1 18.5 1.0
N B:ILE176 4.1 17.2 1.0
C B:ILE176 4.1 17.1 1.0
OD2 B:ASP175 4.2 19.5 1.0
ND1 B:HIS200 4.3 20.2 1.0
CA B:ASP175 4.3 15.0 1.0
CA B:HIS200 4.3 17.2 1.0
CA B:ILE176 4.3 16.3 1.0
CA B:HIS180 4.3 18.1 1.0
N B:GLY181 4.4 19.7 1.0
N B:HIS200 4.4 17.3 1.0
CA B:SER198 4.4 16.0 1.0
N B:HIS180 4.4 18.3 1.0
CA B:PHE199 4.4 17.1 1.0
N B:HIS179 4.5 17.2 1.0
C B:SER198 4.5 19.7 1.0
O B:HOH618 4.5 18.6 1.0
C B:ILE178 4.6 18.6 1.0
CG B:HIS200 4.6 20.0 1.0
C B:HIS180 4.6 19.6 1.0
N B:ILE178 4.6 15.6 1.0
CA B:HIS179 4.7 15.6 1.0
O B:ILE176 4.9 17.2 1.0
O B:ILE178 4.9 19.2 1.0
CE1 B:HIS141 4.9 19.6 1.0
CA B:ILE178 5.0 15.7 1.0

Calcium binding site 4 out of 6 in 7ltk

Go back to Calcium Binding Sites List in 7ltk
Calcium binding site 4 out of 6 in the Structure of Human HDAC2 in Complex with An Inhibitor That Lacks A Zinc Binding Group (Compound 12)


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 That Lacks A Zinc Binding Group (Compound 12) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:28.8
occ:1.00
O B:HOH610 2.4 23.6 1.0
O B:VAL194 2.5 23.9 1.0
O B:PHE188 2.5 22.8 1.0
O B:THR191 2.7 26.6 1.0
O B:HOH689 2.8 26.3 1.0
O B:TYR223 3.1 23.9 1.0
C B:PHE188 3.6 22.5 1.0
CB B:TYR223 3.6 23.2 1.0
C B:VAL194 3.7 22.9 1.0
C B:TYR223 3.8 26.2 1.0
C B:THR191 3.9 26.7 1.0
CB B:PHE188 4.0 21.8 1.0
CA B:TYR223 4.3 22.4 1.0
CA B:TYR189 4.4 21.3 1.0
N B:TYR189 4.4 21.2 1.0
N B:THR191 4.4 25.3 1.0
C B:TYR189 4.4 24.8 1.0
O B:TYR189 4.5 24.2 1.0
CA B:PHE188 4.5 21.6 1.0
CA B:MET195 4.5 19.6 1.0
N B:MET195 4.5 20.0 1.0
CG2 B:THR191 4.5 26.2 1.0
N B:ALA224 4.6 21.7 1.0
CA B:VAL194 4.7 20.4 1.0
CA B:THR191 4.7 24.1 1.0
N B:THR196 4.7 19.3 1.0
O B:GLY220 4.7 24.4 1.0
CA B:GLY220 4.8 28.2 1.0
N B:VAL194 4.8 21.1 1.0
CB B:VAL194 4.8 22.5 1.0
OG1 B:THR196 4.8 21.4 1.0
CG B:TYR223 4.9 24.5 1.0
N B:ASP192 4.9 24.2 1.0
C B:MET195 5.0 22.2 1.0

Calcium binding site 5 out of 6 in 7ltk

Go back to Calcium Binding Sites List in 7ltk
Calcium binding site 5 out of 6 in the Structure of Human HDAC2 in Complex with An Inhibitor That Lacks A Zinc Binding Group (Compound 12)


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 That Lacks A Zinc Binding Group (Compound 12) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:30.6
occ:1.00
O C:HOH595 2.4 23.5 1.0
O C:VAL194 2.5 24.6 1.0
O C:PHE188 2.5 21.2 1.0
O C:THR191 2.7 23.6 1.0
O C:HOH650 2.9 28.8 1.0
O C:TYR223 3.1 26.3 1.0
C C:PHE188 3.6 22.9 1.0
CB C:TYR223 3.7 25.0 1.0
C C:VAL194 3.7 26.1 1.0
C C:TYR223 3.8 27.2 1.0
C C:THR191 3.9 25.4 1.0
CB C:PHE188 4.0 21.9 1.0
CA C:TYR223 4.3 24.8 1.0
CA C:MET195 4.4 23.7 1.0
N C:TYR189 4.4 21.2 1.0
N C:THR191 4.4 23.4 1.0
CA C:TYR189 4.4 20.7 1.0
CA C:PHE188 4.4 20.3 1.0
O C:TYR189 4.4 24.1 1.0
C C:TYR189 4.5 24.8 1.0
CG2 C:THR191 4.5 22.1 1.0
N C:MET195 4.5 23.4 1.0
N C:ALA224 4.6 23.9 1.0
N C:THR196 4.6 23.2 1.0
O C:GLY220 4.7 25.1 1.0
CA C:VAL194 4.7 22.2 1.0
CA C:THR191 4.7 22.5 1.0
CA C:GLY220 4.8 23.6 1.0
OG1 C:THR196 4.8 24.0 1.0
N C:VAL194 4.8 23.2 1.0
CB C:VAL194 4.9 24.0 1.0
C C:MET195 4.9 26.4 1.0
CG C:TYR223 5.0 25.1 1.0
CG2 C:THR196 5.0 23.2 1.0
N C:ASP192 5.0 23.7 1.0
CA C:ALA224 5.0 24.1 1.0

Calcium binding site 6 out of 6 in 7ltk

Go back to Calcium Binding Sites List in 7ltk
Calcium binding site 6 out of 6 in the Structure of Human HDAC2 in Complex with An Inhibitor That Lacks A Zinc Binding Group (Compound 12)


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 That Lacks A Zinc Binding Group (Compound 12) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:29.8
occ:1.00
OD1 C:ASP175 2.5 25.5 1.0
O C:ASP177 2.5 25.3 1.0
O C:PHE199 2.6 25.6 1.0
O C:HIS179 2.7 22.9 1.0
O C:ASP175 2.9 23.8 1.0
OG C:SER198 2.9 27.0 1.0
CG C:ASP175 3.3 28.8 1.0
C C:ASP177 3.5 25.1 1.0
C C:ASP175 3.5 25.2 1.0
N C:ASP177 3.6 24.4 1.0
C C:PHE199 3.6 25.4 1.0
C C:HIS179 3.7 23.6 1.0
N C:PHE199 3.8 23.8 1.0
CB C:ASP175 3.8 24.5 1.0
CB C:HIS200 3.9 23.0 1.0
CA C:ASP177 4.0 22.3 1.0
CB C:ASP177 4.1 22.5 1.0
C C:ILE176 4.1 28.3 1.0
CB C:SER198 4.1 22.7 1.0
N C:ILE176 4.1 23.8 1.0
OD2 C:ASP175 4.2 26.5 1.0
CA C:ASP175 4.3 22.5 1.0
CA C:ILE176 4.3 23.1 1.0
N C:HIS179 4.4 22.6 1.0
CA C:PHE199 4.4 23.8 1.0
ND1 C:HIS200 4.4 26.8 1.0
N C:GLY181 4.4 22.1 1.0
CA C:SER198 4.4 21.4 1.0
CA C:HIS200 4.4 22.0 1.0
CA C:HIS180 4.4 22.7 1.0
N C:HIS200 4.4 21.8 1.0
N C:HIS180 4.4 22.7 1.0
C C:SER198 4.4 25.2 1.0
O C:HOH545 4.5 27.6 1.0
C C:ILE178 4.5 24.3 1.0
N C:ILE178 4.6 22.1 1.0
CG C:HIS200 4.7 25.5 1.0
C C:HIS180 4.7 24.8 1.0
CA C:HIS179 4.7 22.2 1.0
O C:ILE176 4.8 27.6 1.0
CA C:ILE178 4.9 22.4 1.0
CE1 C:HIS141 4.9 26.1 1.0
O C:ILE178 4.9 24.2 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: Wed Jul 9 23:18:30 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy