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: Sat Jul 10 11:32:22 2021

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