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Calcium in PDB 4ly1: Structure of Human HDAC2 in Complex with Inhibitor 4-(Acetylamino)-N- [2-Amino-5-(Thiophen-2-Yl)Phenyl]Benzamide

Enzymatic activity of Structure of Human HDAC2 in Complex with Inhibitor 4-(Acetylamino)-N- [2-Amino-5-(Thiophen-2-Yl)Phenyl]Benzamide

All present enzymatic activity of Structure of Human HDAC2 in Complex with Inhibitor 4-(Acetylamino)-N- [2-Amino-5-(Thiophen-2-Yl)Phenyl]Benzamide:
3.5.1.98;

Protein crystallography data

The structure of Structure of Human HDAC2 in Complex with Inhibitor 4-(Acetylamino)-N- [2-Amino-5-(Thiophen-2-Yl)Phenyl]Benzamide, PDB code: 4ly1 was solved by R.Fong, P.J.Lupardus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.57 / 1.57
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.034, 97.490, 138.922, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 18.7

Other elements in 4ly1:

The structure of Structure of Human HDAC2 in Complex with Inhibitor 4-(Acetylamino)-N- [2-Amino-5-(Thiophen-2-Yl)Phenyl]Benzamide also contains other interesting chemical elements:

Zinc (Zn) 3 atoms
Sodium (Na) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Human HDAC2 in Complex with Inhibitor 4-(Acetylamino)-N- [2-Amino-5-(Thiophen-2-Yl)Phenyl]Benzamide (pdb code 4ly1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of Human HDAC2 in Complex with Inhibitor 4-(Acetylamino)-N- [2-Amino-5-(Thiophen-2-Yl)Phenyl]Benzamide, PDB code: 4ly1:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4ly1

Go back to Calcium Binding Sites List in 4ly1
Calcium binding site 1 out of 3 in the Structure of Human HDAC2 in Complex with Inhibitor 4-(Acetylamino)-N- [2-Amino-5-(Thiophen-2-Yl)Phenyl]Benzamide


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 Inhibitor 4-(Acetylamino)-N- [2-Amino-5-(Thiophen-2-Yl)Phenyl]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:14.3
occ:1.00
 OD1 A:ASP179 2.6 14.1 1.0
O A:PHE203 2.6 13.9 1.0
O A:ASP181 2.6 12.6 1.0
O A:HIS183 2.7 12.8 1.0
O A:ASP179 2.9 13.1 1.0
OG A:SER202 2.9 13.8 1.0
CG A:ASP179 3.4 13.1 1.0
C A:ASP179 3.5 13.9 1.0
C A:PHE203 3.6 14.3 1.0
C A:ASP181 3.6 13.7 1.0
N A:ASP181 3.7 11.7 1.0
C A:HIS183 3.7 14.7 1.0
N A:PHE203 3.7 12.5 1.0
CB A:HIS204 3.8 12.9 1.0
CB A:ASP179 3.9 11.5 1.0
CB A:ASP181 4.0 11.4 1.0
CA A:ASP181 4.1 10.9 1.0
CB A:SER202 4.1 13.7 1.0
N A:ILE180 4.1 11.6 1.0
C A:ILE180 4.1 11.0 1.0
OD2 A:ASP179 4.2 14.5 1.0
ND1 A:HIS204 4.3 14.6 1.0
CA A:ILE180 4.3 10.2 1.0
CA A:ASP179 4.3 11.1 1.0
CA A:HIS204 4.3 11.8 1.0
CA A:SER202 4.3 10.2 1.0
N A:GLY185 4.4 12.3 1.0
C A:SER202 4.4 14.4 1.0
CA A:PHE203 4.4 11.2 1.0
N A:HIS204 4.4 12.8 1.0
CA A:HIS184 4.4 12.4 1.0
N A:HIS183 4.5 11.7 1.0
N A:HIS184 4.5 13.6 1.0
O A:HOH501 4.5 14.8 1.0
CG A:HIS204 4.6 14.4 1.0
C A:ILE182 4.6 12.5 1.0
C A:HIS184 4.7 14.4 1.0
CA A:HIS183 4.7 11.1 1.0
N A:ILE182 4.7 10.9 1.0
CE1 A:HIS145 4.8 12.5 1.0
O A:ILE180 4.9 12.1 1.0
O A:ILE182 5.0 13.0 1.0

Calcium binding site 2 out of 3 in 4ly1

Go back to Calcium Binding Sites List in 4ly1
Calcium binding site 2 out of 3 in the Structure of Human HDAC2 in Complex with Inhibitor 4-(Acetylamino)-N- [2-Amino-5-(Thiophen-2-Yl)Phenyl]Benzamide


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 Inhibitor 4-(Acetylamino)-N- [2-Amino-5-(Thiophen-2-Yl)Phenyl]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:13.3
occ:1.00
 O B:PHE203 2.6 11.1 1.0
O B:ASP181 2.6 10.6 1.0
OD1 B:ASP179 2.6 11.1 1.0
O B:HIS183 2.7 11.1 1.0
OG B:SER202 2.9 12.4 1.0
O B:ASP179 2.9 10.9 1.0
CG B:ASP179 3.4 10.7 1.0
C B:ASP179 3.5 10.7 1.0
C B:ASP181 3.6 10.2 1.0
C B:PHE203 3.6 11.2 1.0
N B:ASP181 3.6 8.4 1.0
C B:HIS183 3.7 12.5 1.0
N B:PHE203 3.8 9.8 1.0
CB B:ASP179 3.8 10.0 1.0
CB B:HIS204 3.9 11.7 1.0
CB B:ASP181 4.0 8.4 1.0
CA B:ASP181 4.0 9.2 1.0
CB B:SER202 4.1 11.4 1.0
N B:ILE180 4.1 10.0 1.0
C B:ILE180 4.1 9.7 1.0
OD2 B:ASP179 4.2 11.2 1.0
ND1 B:HIS204 4.3 13.1 1.0
CA B:ILE180 4.3 8.9 1.0
CA B:ASP179 4.3 9.3 1.0
CA B:HIS204 4.3 10.9 1.0
CA B:SER202 4.3 9.3 1.0
N B:GLY185 4.4 11.0 1.0
N B:HIS204 4.4 11.0 1.0
CA B:PHE203 4.4 9.8 1.0
C B:SER202 4.4 13.6 1.0
CA B:HIS184 4.4 10.4 1.0
N B:HIS183 4.4 10.2 1.0
N B:HIS184 4.5 10.4 1.0
O B:HOH501 4.5 11.4 1.0
CG B:HIS204 4.6 13.3 1.0
C B:ILE182 4.6 11.6 1.0
C B:HIS184 4.7 12.2 1.0
N B:ILE182 4.7 8.7 1.0
CA B:HIS183 4.7 9.3 1.0
CE1 B:HIS145 4.8 10.5 1.0
O B:ILE180 4.9 10.0 1.0
O B:ILE182 5.0 12.3 1.0

Calcium binding site 3 out of 3 in 4ly1

Go back to Calcium Binding Sites List in 4ly1
Calcium binding site 3 out of 3 in the Structure of Human HDAC2 in Complex with Inhibitor 4-(Acetylamino)-N- [2-Amino-5-(Thiophen-2-Yl)Phenyl]Benzamide


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 Inhibitor 4-(Acetylamino)-N- [2-Amino-5-(Thiophen-2-Yl)Phenyl]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca402

b:17.7
occ:1.00
 OD1 C:ASP179 2.6 15.1 1.0
O C:ASP181 2.6 15.5 1.0
O C:PHE203 2.6 16.0 1.0
O C:HIS183 2.7 14.3 1.0
O C:ASP179 2.9 16.6 1.0
OG C:SER202 2.9 16.7 1.0
CG C:ASP179 3.4 17.5 1.0
C C:ASP179 3.5 15.9 1.0
C C:ASP181 3.6 16.4 1.0
C C:PHE203 3.6 16.1 1.0
N C:ASP181 3.7 14.3 1.0
C C:HIS183 3.7 14.7 1.0
N C:PHE203 3.8 14.5 1.0
CB C:HIS204 3.9 14.9 1.0
CB C:ASP179 3.9 15.6 1.0
CA C:ASP181 4.0 14.5 1.0
CB C:ASP181 4.0 14.3 1.0
CB C:SER202 4.1 15.5 1.0
C C:ILE180 4.1 17.3 1.0
N C:ILE180 4.2 13.9 1.0
OD2 C:ASP179 4.2 15.8 1.0
ND1 C:HIS204 4.3 16.9 1.0
CA C:ASP179 4.3 13.5 1.0
CA C:ILE180 4.3 13.8 1.0
CA C:SER202 4.4 13.3 1.0
N C:GLY185 4.4 13.7 1.0
CA C:HIS204 4.4 14.1 1.0
CA C:PHE203 4.4 14.5 1.0
N C:HIS183 4.4 13.2 1.0
N C:HIS204 4.4 13.8 1.0
CA C:HIS184 4.4 13.5 1.0
C C:SER202 4.4 16.7 1.0
N C:HIS184 4.5 13.5 1.0
O C:HOH511 4.5 18.9 1.0
C C:ILE182 4.6 15.7 1.0
CG C:HIS204 4.6 16.4 1.0
N C:ILE182 4.7 14.7 1.0
C C:HIS184 4.7 16.2 1.0
CA C:HIS183 4.7 13.1 1.0
CE1 C:HIS145 4.8 14.8 1.0
O C:ILE180 4.9 16.2 1.0
CA C:ILE182 5.0 14.0 1.0
O C:ILE182 5.0 16.0 1.0

Reference:

B.E.Lauffer, R.Mintzer, R.Fong, S.Mukund, C.Tam, I.Zilberleyb, B.Flicke, A.Ritscher, G.Fedorowicz, R.Vallero, D.F.Ortwine, J.Gunzner, Z.Modrusan, L.Neumann, C.M.Koth, P.J.Lupardus, J.S.Kaminker, C.E.Heise, P.Steiner. Histone Deacetylase (Hdac) Inhibitor Kinetic Rate Constants Correlate with Cellular Histone Acetylation But Not Transcription and Cell Viability. J.Biol.Chem. V. 288 26926 2013.
ISSN: ISSN 0021-9258
PubMed: 23897821
DOI: 10.1074/JBC.M113.490706
Page generated: Wed Jul 9 00:01:34 2025

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