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Sodium 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
Calcium (Ca) 3 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 3 in 6g3o

Go back to Sodium Binding Sites List in 6g3o
Sodium 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 Sodium with other atoms in the Na 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:Na1003

b:43.1
occ:1.00
 O A:VAL198 2.2 47.3 1.0
O A:PHE192 2.3 45.8 1.0
O A:HOH1111 2.5 42.2 1.0
O A:THR195 2.6 44.2 1.0
O A:HOH1128 2.9 46.3 1.0
C A:PHE192 3.3 46.8 1.0
C A:VAL198 3.5 48.8 1.0
O A:TYR227 3.6 48.7 1.0
C A:THR195 3.8 48.9 1.0
CB A:TYR227 3.9 48.4 1.0
CB A:PHE192 3.9 44.6 1.0
C A:TYR227 4.1 48.3 1.0
N A:TYR193 4.2 43.9 1.0
CA A:PHE192 4.2 43.6 1.0
N A:THR195 4.3 48.2 1.0
CG2 A:THR195 4.3 45.3 1.0
CA A:TYR193 4.3 44.4 1.0
N A:MET199 4.4 45.1 1.0
CA A:MET199 4.4 43.2 1.0
C A:TYR193 4.4 51.4 1.0
CA A:VAL198 4.4 44.4 1.0
O A:TYR193 4.4 50.5 1.0
CA A:THR195 4.5 48.2 1.0
CB A:VAL198 4.6 46.9 1.0
CA A:TYR227 4.6 45.6 1.0
N A:VAL198 4.6 46.7 1.0
N A:THR200 4.7 41.3 1.0
N A:ASP196 4.8 46.3 1.0
O A:GLY224 4.8 48.8 1.0
CA A:GLY224 4.8 49.6 1.0
OG1 A:THR200 4.9 40.1 1.0
N A:ALA228 4.9 43.0 1.0
C A:MET199 5.0 43.1 1.0
CG2 A:THR200 5.0 38.6 1.0
N A:THR194 5.0 49.6 1.0

Sodium binding site 2 out of 3 in 6g3o

Go back to Sodium Binding Sites List in 6g3o
Sodium 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 Sodium with other atoms in the Na 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:Na1003

b:53.3
occ:1.00
 O B:VAL198 2.3 40.2 1.0
O B:PHE192 2.3 44.5 1.0
O B:HOH1123 2.5 44.2 1.0
O B:THR195 2.6 48.6 1.0
C B:PHE192 3.4 44.6 1.0
O B:TYR227 3.4 49.0 1.0
C B:VAL198 3.5 39.7 1.0
CB B:TYR227 3.8 45.9 1.0
C B:THR195 3.8 46.9 1.0
C B:TYR227 4.0 47.8 1.0
CB B:PHE192 4.0 36.9 1.0
N B:TYR193 4.2 42.9 1.0
CA B:PHE192 4.3 37.8 1.0
CA B:TYR193 4.3 43.9 1.0
CA B:MET199 4.4 36.4 1.0
N B:MET199 4.4 36.6 1.0
C B:TYR193 4.4 50.0 1.0
N B:THR195 4.4 41.7 1.0
O B:TYR193 4.4 51.6 1.0
CG2 B:THR195 4.4 37.6 1.0
CA B:VAL198 4.5 35.9 1.0
CA B:TYR227 4.5 44.8 1.0
CA B:THR195 4.6 41.2 1.0
O B:GLY224 4.6 49.2 1.0
N B:THR200 4.7 34.9 1.0
CB B:VAL198 4.7 36.4 1.0
N B:VAL198 4.7 38.3 1.0
N B:ALA228 4.7 43.4 1.0
CA B:GLY224 4.8 48.3 1.0
N B:ASP196 4.8 44.3 1.0
OG1 B:THR200 4.8 42.7 1.0
C B:MET199 5.0 38.5 1.0
N B:THR194 5.0 47.6 1.0

Sodium binding site 3 out of 3 in 6g3o

Go back to Sodium Binding Sites List in 6g3o
Sodium 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 Sodium with other atoms in the Na 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:Na1003

b:43.7
occ:1.00
 O C:PHE192 2.2 39.7 1.0
O C:VAL198 2.3 38.1 1.0
O C:THR195 2.3 37.3 1.0
O C:HOH1115 2.5 35.6 1.0
O C:HOH1131 3.0 46.4 1.0
C C:PHE192 3.3 39.4 1.0
C C:VAL198 3.5 41.1 1.0
C C:THR195 3.5 38.4 1.0
O C:TYR227 3.7 43.1 1.0
CB C:TYR227 3.7 39.3 1.0
CB C:PHE192 4.0 38.5 1.0
N C:THR195 4.1 35.0 1.0
CG2 C:THR195 4.2 27.4 1.0
C C:TYR227 4.2 44.1 1.0
N C:TYR193 4.3 35.2 1.0
CA C:PHE192 4.3 35.8 1.0
CA C:THR195 4.3 35.3 1.0
C C:TYR193 4.3 39.4 1.0
O C:TYR193 4.3 38.0 1.0
CA C:TYR193 4.4 34.0 1.0
N C:MET199 4.4 40.5 1.0
CA C:VAL198 4.4 37.1 1.0
CA C:MET199 4.5 41.8 1.0
CA C:GLY224 4.5 36.9 1.0
N C:ASP196 4.5 35.4 1.0
N C:VAL198 4.5 38.2 1.0
CA C:TYR227 4.6 40.5 1.0
CB C:VAL198 4.6 39.1 1.0
O C:GLY224 4.7 42.1 1.0
CA C:ASP196 4.8 37.5 1.0
CB C:THR195 4.8 40.3 1.0
N C:THR194 4.8 37.5 1.0
CG C:TYR227 4.9 41.5 1.0
N C:THR200 4.9 42.2 1.0
N C:ALA228 5.0 39.9 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: Tue Oct 8 08:54:54 2024

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