Atomistry » Sodium » PDB 6fmq-6g3o » 6g3o
Atomistry »
  Sodium »
    PDB 6fmq-6g3o »
      6g3o »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy