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Sodium 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:

Calcium (Ca) 3 atoms
Zinc (Zn) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 3 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4ly1

Go back to Sodium Binding Sites List in 4ly1
Sodium 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 Sodium with other atoms in the Na 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:Na403

b:13.4
occ:1.00
 O A:HOH520 2.5 20.1 1.0
O A:VAL198 2.5 18.9 1.0
O A:PHE192 2.6 16.5 1.0
O A:THR195 2.8 18.9 1.0
O A:HOH521 2.9 19.8 1.0
O A:TYR227 3.1 18.5 1.0
C A:PHE192 3.5 17.2 1.0
CB A:TYR227 3.6 18.7 1.0
C A:VAL198 3.7 17.8 1.0
C A:TYR227 3.8 20.4 1.0
C A:THR195 4.0 19.3 1.0
CB A:PHE192 4.0 14.8 1.0
CA A:TYR227 4.3 17.8 1.0
N A:TYR193 4.4 16.1 1.0
CA A:TYR193 4.4 15.3 1.0
CA A:MET199 4.4 15.3 1.0
CA A:PHE192 4.4 14.1 1.0
C A:TYR193 4.4 19.7 1.0
O A:TYR193 4.4 19.6 1.0
N A:THR195 4.5 17.9 1.0
N A:MET199 4.6 15.3 1.0
N A:ALA228 4.6 15.9 1.0
N A:THR200 4.6 12.8 1.0
O A:GLY224 4.7 19.9 1.0
CG2 A:THR195 4.7 18.6 1.0
CA A:VAL198 4.7 14.7 1.0
OG1 A:THR200 4.8 15.7 1.0
CA A:GLY224 4.8 19.2 1.0
CA A:THR195 4.8 16.9 1.0
N A:VAL198 4.8 16.1 1.0
CB A:VAL198 4.9 17.2 1.0
C A:MET199 4.9 17.1 1.0
CG A:TYR227 4.9 19.1 1.0
CG2 A:THR200 5.0 15.2 1.0
N A:ASP196 5.0 16.4 1.0

Sodium binding site 2 out of 3 in 4ly1

Go back to Sodium Binding Sites List in 4ly1
Sodium 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 Sodium with other atoms in the Na 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:Na403

b:12.0
occ:1.00
 O B:VAL198 2.5 15.7 1.0
O B:HOH514 2.6 17.4 1.0
O B:PHE192 2.6 15.7 1.0
O B:THR195 2.7 19.1 1.0
O B:HOH535 2.9 18.0 1.0
O B:TYR227 3.0 16.5 1.0
C B:PHE192 3.6 15.7 1.0
CB B:TYR227 3.6 16.2 1.0
C B:TYR227 3.7 17.7 1.0
C B:VAL198 3.7 15.5 1.0
C B:THR195 4.0 18.9 1.0
CB B:PHE192 4.1 13.3 1.0
CA B:TYR227 4.3 15.8 1.0
CA B:TYR193 4.4 14.7 1.0
N B:TYR193 4.4 15.1 1.0
N B:THR195 4.4 17.1 1.0
O B:TYR193 4.5 17.8 1.0
C B:TYR193 4.5 17.6 1.0
CA B:PHE192 4.5 13.5 1.0
CA B:MET199 4.5 12.7 1.0
CG2 B:THR195 4.5 18.8 1.0
N B:ALA228 4.5 13.9 1.0
N B:MET199 4.6 13.1 1.0
N B:THR200 4.6 11.8 1.0
CA B:VAL198 4.7 12.1 1.0
O B:GLY224 4.7 17.8 1.0
CA B:THR195 4.7 15.7 1.0
OG1 B:THR200 4.8 14.6 1.0
CA B:GLY224 4.8 21.2 1.0
N B:VAL198 4.8 13.9 1.0
CB B:VAL198 4.8 14.1 1.0
CG B:TYR227 4.9 17.9 1.0
N B:ASP196 5.0 16.3 1.0
CA B:ALA228 5.0 13.4 1.0
C B:MET199 5.0 14.1 1.0

Sodium binding site 3 out of 3 in 4ly1

Go back to Sodium Binding Sites List in 4ly1
Sodium 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 Sodium with other atoms in the Na 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:Na403

b:11.8
occ:1.00
 O C:VAL198 2.5 16.2 1.0
O C:HOH501 2.5 17.9 1.0
O C:PHE192 2.5 14.9 1.0
O C:THR195 2.8 17.1 1.0
O C:HOH503 2.9 18.5 1.0
O C:TYR227 3.1 16.9 1.0
C C:PHE192 3.6 14.8 1.0
CB C:TYR227 3.7 16.2 1.0
C C:VAL198 3.7 16.6 1.0
C C:TYR227 3.8 17.6 1.0
C C:THR195 4.0 18.4 1.0
CB C:PHE192 4.0 14.3 1.0
CA C:TYR227 4.3 15.1 1.0
CA C:MET199 4.4 14.9 1.0
N C:TYR193 4.4 13.1 1.0
CA C:TYR193 4.4 13.1 1.0
N C:THR195 4.4 14.9 1.0
CA C:PHE192 4.4 13.2 1.0
C C:TYR193 4.4 16.7 1.0
CG2 C:THR195 4.5 15.9 1.0
O C:TYR193 4.5 16.2 1.0
N C:MET199 4.5 14.5 1.0
N C:ALA228 4.6 15.1 1.0
N C:THR200 4.6 14.8 1.0
O C:GLY224 4.6 16.6 1.0
CA C:THR195 4.7 14.7 1.0
CA C:VAL198 4.7 14.3 1.0
CA C:GLY224 4.8 16.3 1.0
OG1 C:THR200 4.8 15.0 1.0
N C:VAL198 4.9 14.4 1.0
CB C:VAL198 4.9 16.1 1.0
C C:MET199 4.9 16.6 1.0
CA C:ALA228 5.0 14.7 1.0
CG C:TYR227 5.0 16.5 1.0
N C:ASP196 5.0 16.6 1.0
CG2 C:THR200 5.0 13.3 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: Mon Oct 7 16:52:37 2024

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