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Calcium in PDB 6g3o: Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide

Enzymatic activity of Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide

All present enzymatic activity of Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide, PDB code: 6g3o was solved by T.Isabet, M.Aurelly, L.Chantalat, E.Thoreau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.26 / 2.27
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.050, 93.300, 139.420, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 21.9

Other elements in 6g3o:

The structure of Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide also contains other interesting chemical elements:

Fluorine (F) 9 atoms
Zinc (Zn) 3 atoms
Sodium (Na) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide (pdb code 6g3o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide, PDB code: 6g3o:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6g3o

Go back to Calcium Binding Sites List in 6g3o
Calcium binding site 1 out of 3 in the Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:46.0
occ:1.00
 O A:ASP181 2.5 34.7 1.0
O A:PHE203 2.6 35.2 1.0
O A:HIS183 2.6 38.7 1.0
OD1 A:ASP179 2.7 40.7 1.0
O A:ASP179 3.0 36.1 1.0
OG A:SER202 3.0 37.7 1.0
CG A:ASP179 3.4 39.6 1.0
C A:ASP181 3.5 37.7 1.0
C A:PHE203 3.6 37.9 1.0
N A:ASP181 3.6 32.1 1.0
C A:HIS183 3.6 40.4 1.0
C A:ASP179 3.6 36.8 1.0
CB A:HIS204 3.8 34.5 1.0
CB A:ASP179 3.9 35.0 1.0
N A:PHE203 3.9 34.1 1.0
CB A:ASP181 3.9 34.7 1.0
CA A:ASP181 3.9 32.2 1.0
C A:ILE180 4.2 35.5 1.0
OD2 A:ASP179 4.2 42.5 1.0
CA A:HIS204 4.2 33.6 1.0
N A:HIS183 4.3 36.5 1.0
N A:ILE180 4.3 31.4 1.0
CB A:SER202 4.3 37.8 1.0
N A:HIS204 4.3 35.1 1.0
N A:HIS184 4.3 36.5 1.0
ND1 A:HIS204 4.3 39.2 1.0
CA A:HIS184 4.4 34.1 1.0
CA A:ASP179 4.4 33.8 1.0
CA A:ILE180 4.4 30.4 1.0
CA A:PHE203 4.4 33.6 1.0
O A:HOH1116 4.5 33.8 1.0
C A:ILE182 4.5 38.4 1.0
CG A:HIS204 4.5 37.2 1.0
N A:GLY185 4.5 36.0 1.0
N A:ILE182 4.6 34.2 1.0
C A:SER202 4.6 37.0 1.0
CA A:HIS183 4.6 36.6 1.0
CA A:SER202 4.6 34.6 1.0
C A:HIS184 4.8 38.0 1.0
O A:ILE182 4.9 35.9 1.0
CA A:ILE182 4.9 32.6 1.0
O A:ILE180 5.0 34.9 1.0

Calcium binding site 2 out of 3 in 6g3o

Go back to Calcium Binding Sites List in 6g3o
Calcium binding site 2 out of 3 in the Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1002

b:43.3
occ:1.00
 OD1 B:ASP179 2.5 39.0 1.0
O B:ASP181 2.5 33.1 1.0
O B:PHE203 2.6 36.4 1.0
O B:HIS183 2.7 35.1 1.0
O B:ASP179 2.9 36.4 1.0
OG B:SER202 3.1 40.2 1.0
CG B:ASP179 3.3 38.5 1.0
C B:ASP181 3.4 33.1 1.0
N B:ASP181 3.4 33.3 1.0
C B:ASP179 3.5 38.8 1.0
C B:PHE203 3.6 38.9 1.0
C B:HIS183 3.7 35.7 1.0
CB B:ASP179 3.8 36.1 1.0
CA B:ASP181 3.8 31.5 1.0
CB B:ASP181 3.9 31.6 1.0
CB B:HIS204 3.9 34.2 1.0
N B:PHE203 3.9 34.9 1.0
C B:ILE180 4.0 36.4 1.0
OD2 B:ASP179 4.1 46.0 1.0
N B:ILE180 4.1 36.5 1.0
CA B:ASP179 4.2 34.3 1.0
CA B:ILE180 4.3 35.1 1.0
N B:HIS183 4.3 31.8 1.0
CB B:SER202 4.3 38.8 1.0
CA B:HIS204 4.4 35.0 1.0
N B:HIS204 4.4 36.9 1.0
N B:HIS184 4.4 31.6 1.0
ND1 B:HIS204 4.5 38.2 1.0
CA B:HIS184 4.5 32.0 1.0
CA B:PHE203 4.5 34.2 1.0
O B:HOH1134 4.5 35.9 1.0
N B:ILE182 4.5 30.6 1.0
C B:ILE182 4.5 36.2 1.0
N B:GLY185 4.6 32.1 1.0
CA B:SER202 4.6 36.6 1.0
C B:SER202 4.6 40.3 1.0
CA B:HIS183 4.7 32.5 1.0
CG B:HIS204 4.7 37.5 1.0
O B:ILE180 4.8 34.3 1.0
C B:HIS184 4.9 35.7 1.0
CA B:ILE182 4.9 31.9 1.0
O B:ILE182 5.0 36.8 1.0
CE1 B:HIS145 5.0 33.2 1.0

Calcium binding site 3 out of 3 in 6g3o

Go back to Calcium Binding Sites List in 6g3o
Calcium binding site 3 out of 3 in the Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human HDAC2 in Complex with (R)-6-[3,4-Dioxo-2- (4-Trifluoromethoxy-Phenylamino)-Cyclobut-1-Enylamino]-Heptanoic Acid Hydroxyamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1002

b:58.4
occ:1.00
 O C:PHE203 2.5 42.6 1.0
O C:ASP181 2.6 43.2 1.0
O C:HIS183 2.6 40.2 1.0
OD1 C:ASP179 2.7 46.4 1.0
OG C:SER202 2.9 38.7 1.0
O C:ASP179 3.0 43.5 1.0
CG C:ASP179 3.4 43.0 1.0
C C:PHE203 3.5 43.3 1.0
C C:ASP181 3.5 45.2 1.0
C C:HIS183 3.6 40.7 1.0
C C:ASP179 3.7 42.7 1.0
N C:ASP181 3.7 39.5 1.0
CB C:HIS204 3.8 38.5 1.0
N C:PHE203 3.9 41.0 1.0
CB C:ASP179 3.9 36.6 1.0
CB C:ASP181 4.0 37.5 1.0
CA C:ASP181 4.0 38.9 1.0
CB C:SER202 4.2 42.4 1.0
CA C:HIS204 4.2 39.5 1.0
OD2 C:ASP179 4.2 38.5 1.0
C C:ILE180 4.2 43.7 1.0
N C:HIS204 4.3 39.8 1.0
N C:HIS183 4.3 38.7 1.0
ND1 C:HIS204 4.3 41.0 1.0
N C:HIS184 4.3 37.2 1.0
CA C:HIS184 4.3 35.4 1.0
N C:ILE180 4.3 38.4 1.0
CA C:PHE203 4.4 40.7 1.0
CA C:ASP179 4.4 37.1 1.0
O C:HOH1128 4.5 49.9 1.0
CA C:ILE180 4.5 38.6 1.0
CA C:SER202 4.5 41.2 1.0
N C:GLY185 4.5 39.1 1.0
CG C:HIS204 4.5 40.5 1.0
C C:ILE182 4.5 44.8 1.0
C C:SER202 4.5 47.0 1.0
CA C:HIS183 4.6 36.9 1.0
N C:ILE182 4.6 41.9 1.0
C C:HIS184 4.7 43.3 1.0
O C:ILE182 4.9 44.7 1.0
CA C:ILE182 4.9 41.6 1.0
O C:ILE180 5.0 44.9 1.0

Reference:

J.F.Fournier, Y.Bhurruth-Alcor, B.Musicki, J.Aubert, M.Aurelly, C.Bouix-Peter, K.Bouquet, L.Chantalat, M.Delorme, B.Drean, G.Duvert, N.Fleury-Bregeot, B.Gauthier, K.Grisendi, C.S.Harris, L.F.Hennequin, T.Isabet, F.Joly, G.Lafitte, C.Millois, R.Morgentin, J.Pascau, D.Piwnica, Y.Rival, C.Soulet, E.Thoreau, L.Tomas. Squaramides As Novel Class I and Iib Histone Deacetylase Inhibitors For Topical Treatment of Cutaneous T-Cell Lymphoma. Bioorg. Med. Chem. Lett. V. 28 2985 2018.
ISSN: ESSN 1464-3405
PubMed: 30122227
DOI: 10.1016/J.BMCL.2018.06.029
Page generated: Wed Jul 9 14:21:31 2025

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