Calcium in PDB 7ltg: Structure of Human HDAC2 in Complex with Apicidin

Enzymatic activity of Structure of Human HDAC2 in Complex with Apicidin

All present enzymatic activity of Structure of Human HDAC2 in Complex with Apicidin:
3.5.1.98;

Protein crystallography data

The structure of Structure of Human HDAC2 in Complex with Apicidin, PDB code: 7ltg 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) 26.25 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.27, 98.39, 139.07, 90, 90, 90
R / Rfree (%) 16.8 / 19.8

Other elements in 7ltg:

The structure of Structure of Human HDAC2 in Complex with Apicidin 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 Apicidin (pdb code 7ltg). 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 Apicidin, PDB code: 7ltg:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 7ltg

Go back to Calcium Binding Sites List in 7ltg
Calcium binding site 1 out of 6 in the Structure of Human HDAC2 in Complex with Apicidin


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 Apicidin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:23.9
occ:1.00
 OD1 A:ASP175 2.5 19.6 1.0
O A:ASP177 2.5 17.8 1.0
O A:PHE199 2.6 16.5 1.0
O A:HIS179 2.8 18.7 1.0
O A:ASP175 2.9 18.8 1.0
OG A:SER198 2.9 22.1 1.0
CG A:ASP175 3.3 19.4 1.0
C A:ASP175 3.5 19.2 1.0
C A:ASP177 3.5 17.9 1.0
N A:ASP177 3.6 14.9 1.0
C A:PHE199 3.6 19.3 1.0
CB A:ASP175 3.7 15.7 1.0
C A:HIS179 3.8 18.8 1.0
N A:PHE199 3.8 15.1 1.0
CB A:HIS200 3.9 14.1 1.0
CB A:ASP177 4.0 15.8 1.0
CA A:ASP177 4.0 14.3 1.0
C A:ILE176 4.1 17.7 1.0
N A:ILE176 4.1 15.2 1.0
OD2 A:ASP175 4.1 19.5 1.0
CB A:SER198 4.2 17.2 1.0
CA A:ASP175 4.2 15.0 1.0
CA A:ILE176 4.3 14.1 1.0
ND1 A:HIS200 4.3 19.0 1.0
CA A:HIS180 4.4 16.4 1.0
CA A:HIS200 4.4 14.3 1.0
N A:GLY181 4.4 18.0 1.0
CA A:PHE199 4.4 14.4 1.0
CA A:SER198 4.4 16.4 1.0
N A:HIS200 4.4 16.2 1.0
N A:HIS179 4.4 15.9 1.0
N A:HIS180 4.4 16.3 1.0
C A:SER198 4.5 18.8 1.0
C A:ILE178 4.6 19.0 1.0
O A:HOH523 4.6 18.1 1.0
CG A:HIS200 4.6 17.8 1.0
N A:ILE178 4.7 15.5 1.0
C A:HIS180 4.7 20.2 1.0
CA A:HIS179 4.7 15.6 1.0
O A:ILE176 4.9 15.6 1.0
CE1 A:HIS141 4.9 17.6 1.0
O A:ILE178 5.0 18.8 1.0
CA A:ILE178 5.0 14.1 1.0

Calcium binding site 2 out of 6 in 7ltg

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Calcium binding site 2 out of 6 in the Structure of Human HDAC2 in Complex with Apicidin


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 Apicidin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:25.5
occ:1.00
 O A:HOH517 2.5 21.2 1.0
O A:PHE188 2.5 18.8 1.0
O A:VAL194 2.6 21.0 1.0
O A:THR191 2.8 22.8 1.0
O A:HOH658 2.8 24.0 1.0
O A:TYR223 3.1 21.7 1.0
C A:PHE188 3.6 20.1 1.0
CB A:TYR223 3.7 20.0 1.0
C A:TYR223 3.7 23.1 1.0
C A:VAL194 3.8 21.4 1.0
C A:THR191 4.0 24.4 1.0
CB A:PHE188 4.0 18.0 1.0
CA A:TYR223 4.3 19.2 1.0
N A:TYR189 4.4 19.2 1.0
CA A:TYR189 4.4 19.5 1.0
CA A:PHE188 4.4 16.5 1.0
CA A:MET195 4.5 19.4 1.0
O A:TYR189 4.5 22.7 1.0
C A:TYR189 4.5 23.4 1.0
N A:THR191 4.5 23.0 1.0
N A:MET195 4.6 19.5 1.0
N A:ALA224 4.6 18.9 1.0
N A:THR196 4.6 17.6 1.0
O A:GLY220 4.7 22.4 1.0
CG2 A:THR191 4.7 27.6 1.0
CA A:VAL194 4.7 18.4 1.0
OG1 A:THR196 4.7 19.8 1.0
CA A:THR191 4.8 22.2 1.0
CA A:GLY220 4.8 22.6 1.0
CG2 A:THR196 4.8 15.6 1.0
N A:VAL194 4.9 18.9 1.0
CB A:VAL194 4.9 20.8 1.0
C A:MET195 5.0 21.0 1.0
CG A:TYR223 5.0 20.4 1.0
N A:ASP192 5.0 20.7 1.0

Calcium binding site 3 out of 6 in 7ltg

Go back to Calcium Binding Sites List in 7ltg
Calcium binding site 3 out of 6 in the Structure of Human HDAC2 in Complex with Apicidin


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 Apicidin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:23.1
occ:1.00
 O B:ASP177 2.4 15.1 1.0
O B:PHE199 2.5 15.0 1.0
OD1 B:ASP175 2.6 17.5 1.0
O B:HIS179 2.8 16.5 1.0
OG B:SER198 2.9 17.9 1.0
O B:ASP175 2.9 16.1 1.0
CG B:ASP175 3.3 17.8 1.0
C B:ASP177 3.5 17.0 1.0
C B:ASP175 3.5 17.0 1.0
N B:ASP177 3.5 14.5 1.0
C B:PHE199 3.6 16.3 1.0
N B:PHE199 3.8 15.0 1.0
CB B:ASP175 3.8 15.3 1.0
C B:HIS179 3.8 17.3 1.0
CB B:HIS200 3.9 14.7 1.0
CA B:ASP177 4.0 13.7 1.0
CB B:ASP177 4.0 14.3 1.0
C B:ILE176 4.0 16.5 1.0
N B:ILE176 4.1 14.0 1.0
CB B:SER198 4.1 15.3 1.0
OD2 B:ASP175 4.2 20.9 1.0
CA B:ILE176 4.2 13.3 1.0
CA B:ASP175 4.2 14.5 1.0
CA B:HIS200 4.3 13.4 1.0
N B:HIS200 4.4 13.5 1.0
ND1 B:HIS200 4.4 19.8 1.0
CA B:SER198 4.4 14.1 1.0
CA B:HIS180 4.4 13.8 1.0
CA B:PHE199 4.4 14.3 1.0
C B:SER198 4.5 18.5 1.0
N B:HIS180 4.5 14.7 1.0
N B:HIS179 4.5 12.9 1.0
N B:GLY181 4.5 16.9 1.0
O B:HOH586 4.5 17.5 1.0
C B:ILE178 4.6 15.9 1.0
N B:ILE178 4.6 12.1 1.0
CG B:HIS200 4.6 18.4 1.0
C B:HIS180 4.8 18.1 1.0
O B:ILE176 4.8 15.8 1.0
CA B:HIS179 4.8 12.6 1.0
CA B:ILE178 4.9 11.8 1.0
O B:ILE178 4.9 16.1 1.0
CE1 B:HIS141 5.0 16.6 1.0

Calcium binding site 4 out of 6 in 7ltg

Go back to Calcium Binding Sites List in 7ltg
Calcium binding site 4 out of 6 in the Structure of Human HDAC2 in Complex with Apicidin


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 Apicidin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:24.7
occ:1.00
 O B:PHE188 2.5 19.1 1.0
O B:VAL194 2.5 21.3 1.0
O B:HOH529 2.5 18.0 1.0
O B:THR191 2.8 21.3 1.0
O B:HOH675 2.8 23.8 1.0
O B:TYR223 3.1 22.8 1.0
C B:PHE188 3.5 19.7 1.0
CB B:TYR223 3.6 19.7 1.0
C B:VAL194 3.7 21.7 1.0
C B:TYR223 3.8 24.0 1.0
C B:THR191 4.0 23.9 1.0
CB B:PHE188 4.0 18.4 1.0
CA B:TYR223 4.3 20.3 1.0
N B:TYR189 4.3 17.9 1.0
CA B:TYR189 4.4 17.2 1.0
CA B:PHE188 4.4 17.7 1.0
CA B:MET195 4.4 19.1 1.0
N B:THR191 4.4 23.7 1.0
C B:TYR189 4.4 20.5 1.0
O B:TYR189 4.5 21.0 1.0
N B:MET195 4.5 18.4 1.0
N B:ALA224 4.6 21.7 1.0
CG2 B:THR191 4.6 23.4 1.0
O B:GLY220 4.6 25.9 1.0
N B:THR196 4.7 16.9 1.0
CA B:VAL194 4.7 19.0 1.0
CA B:THR191 4.7 22.6 1.0
OG1 B:THR196 4.8 23.4 1.0
CA B:GLY220 4.8 25.4 1.0
N B:VAL194 4.9 19.5 1.0
CB B:VAL194 4.9 21.2 1.0
CG2 B:THR196 4.9 16.2 1.0
CG B:TYR223 4.9 21.5 1.0
C B:MET195 5.0 20.2 1.0
CA B:ALA224 5.0 21.4 1.0
N B:ASP192 5.0 21.6 1.0

Calcium binding site 5 out of 6 in 7ltg

Go back to Calcium Binding Sites List in 7ltg
Calcium binding site 5 out of 6 in the Structure of Human HDAC2 in Complex with Apicidin


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 Apicidin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:27.9
occ:1.00
 O C:HOH520 2.4 21.5 1.0
O C:VAL194 2.5 26.0 1.0
O C:PHE188 2.5 20.7 1.0
O C:THR191 2.8 24.6 1.0
O C:HOH608 3.0 26.1 1.0
O C:TYR223 3.0 27.2 1.0
C C:PHE188 3.6 23.1 1.0
CB C:TYR223 3.7 24.6 1.0
C C:TYR223 3.7 27.3 1.0
C C:VAL194 3.7 26.2 1.0
C C:THR191 4.0 25.0 1.0
CB C:PHE188 4.1 21.6 1.0
CA C:TYR223 4.3 23.9 1.0
CA C:MET195 4.4 25.1 1.0
N C:TYR189 4.4 19.4 1.0
CA C:TYR189 4.4 19.4 1.0
N C:THR191 4.4 19.4 1.0
CA C:PHE188 4.5 20.3 1.0
C C:TYR189 4.5 23.6 1.0
O C:TYR189 4.5 23.5 1.0
N C:ALA224 4.5 23.2 1.0
N C:MET195 4.5 24.4 1.0
CG2 C:THR191 4.5 18.8 1.0
N C:THR196 4.6 23.8 1.0
O C:GLY220 4.6 24.9 1.0
CA C:VAL194 4.7 20.7 1.0
CA C:THR191 4.7 19.9 1.0
CA C:GLY220 4.7 23.2 1.0
OG1 C:THR196 4.8 23.5 1.0
N C:VAL194 4.8 20.4 1.0
CB C:VAL194 4.8 22.0 1.0
C C:MET195 4.9 26.3 1.0
CG2 C:THR196 4.9 25.2 1.0
CA C:ALA224 4.9 23.6 1.0
CG C:TYR223 5.0 25.2 1.0
CB C:ALA224 5.0 23.9 1.0

Calcium binding site 6 out of 6 in 7ltg

Go back to Calcium Binding Sites List in 7ltg
Calcium binding site 6 out of 6 in the Structure of Human HDAC2 in Complex with Apicidin


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 Apicidin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca403

b:32.7
occ:1.00
 OD1 C:ASP175 2.4 23.4 1.0
O C:ASP177 2.5 23.9 1.0
O C:PHE199 2.6 23.9 1.0
O C:HIS179 2.8 21.0 1.0
O C:ASP175 2.8 25.5 1.0
OG C:SER198 2.9 25.9 1.0
CG C:ASP175 3.3 27.9 1.0
C C:ASP177 3.5 24.9 1.0
C C:ASP175 3.5 25.7 1.0
N C:ASP177 3.6 24.7 1.0
C C:PHE199 3.6 24.3 1.0
C C:HIS179 3.7 23.1 1.0
CB C:ASP175 3.8 21.4 1.0
N C:PHE199 3.8 22.5 1.0
CB C:HIS200 3.9 22.5 1.0
CA C:ASP177 4.0 22.8 1.0
CB C:ASP177 4.1 24.1 1.0
CB C:SER198 4.1 25.3 1.0
C C:ILE176 4.1 28.4 1.0
OD2 C:ASP175 4.2 28.6 1.0
N C:ILE176 4.2 24.2 1.0
CA C:ASP175 4.3 20.6 1.0
ND1 C:HIS200 4.3 28.3 1.0
CA C:HIS180 4.3 20.9 1.0
CA C:ILE176 4.4 23.2 1.0
N C:HIS179 4.4 21.3 1.0
CA C:HIS200 4.4 21.4 1.0
CA C:SER198 4.4 22.5 1.0
N C:GLY181 4.4 21.3 1.0
N C:HIS200 4.4 21.8 1.0
N C:HIS180 4.4 20.5 1.0
CA C:PHE199 4.4 22.7 1.0
C C:SER198 4.5 25.7 1.0
C C:ILE178 4.5 24.2 1.0
O C:HOH537 4.6 24.5 1.0
N C:ILE178 4.6 20.3 1.0
CG C:HIS200 4.6 26.2 1.0
C C:HIS180 4.7 23.4 1.0
CA C:HIS179 4.7 19.9 1.0
O C:ILE176 4.9 27.2 1.0
CA C:ILE178 4.9 20.3 1.0
CE1 C:HIS141 4.9 24.9 1.0
O C:ILE178 5.0 23.0 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 11:32:05 2021

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