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Potassium in PDB 3c0y: Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7

Protein crystallography data

The structure of Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7, PDB code: 3c0y was solved by J.R.Min, A.Schuetz, A.Allali-Hassani, P.Loppnau, N.P.Kwiatkowski, R.Mazitschek, J.Weigelt, M.Sundstrom, C.H.Arrowsmith, A.M.Edwards, M.Vedadi, A.Bochkarev, A.N.Plotnikov, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.44 / 2.10
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 81.750, 81.750, 148.895, 90.00, 90.00, 120.00
R / Rfree (%) 20.2 / 26.4

Other elements in 3c0y:

The structure of Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 (pdb code 3c0y). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7, PDB code: 3c0y:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 3c0y

Go back to Potassium Binding Sites List in 3c0y
Potassium binding site 1 out of 6 in the Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K904

b:34.0
occ:1.00
 O A:ASP707 2.5 23.9 1.0
OG A:SER728 2.6 27.2 1.0
OD1 A:ASP705 2.7 29.9 1.0
O A:HIS709 2.7 28.1 1.0
O A:LEU729 2.9 27.9 1.0
O A:ASP705 3.0 27.1 1.0
CG A:ASP705 3.2 28.7 1.0
C A:ASP705 3.6 27.7 1.0
C A:ASP707 3.6 27.2 1.0
C A:HIS709 3.7 28.2 1.0
C A:LEU729 3.8 28.4 1.0
CB A:ASP705 3.8 27.1 1.0
OD2 A:ASP705 3.8 30.4 1.0
N A:ASP707 3.9 26.5 1.0
CB A:SER728 3.9 25.4 1.0
CB A:HIS730 3.9 26.9 1.0
N A:LEU729 4.0 28.3 1.0
CA A:ASP707 4.2 26.8 1.0
CA A:HIS710 4.2 26.4 1.0
C A:TRP706 4.2 28.2 1.0
N A:TRP706 4.3 28.1 1.0
CB A:ASP707 4.3 26.6 1.0
CA A:SER728 4.3 27.5 1.0
CA A:ASP705 4.3 26.9 1.0
N A:HIS710 4.3 27.2 1.0
CA A:TRP706 4.4 27.9 1.0
N A:GLY711 4.4 25.5 1.0
CA A:HIS730 4.4 29.0 1.0
N A:HIS709 4.5 28.4 1.0
N A:HIS730 4.5 28.5 1.0
CD2 A:HIS730 4.5 27.0 1.0
C A:SER728 4.5 27.8 1.0
CG A:HIS730 4.5 26.0 1.0
CE1 A:HIS669 4.6 23.9 1.0
CA A:LEU729 4.6 28.4 1.0
C A:HIS710 4.7 26.3 1.0
C A:VAL708 4.7 27.8 1.0
N A:VAL708 4.7 26.9 1.0
OH A:TYR726 4.7 23.1 1.0
CA A:HIS709 4.8 28.2 1.0
O A:HOH15 4.8 32.4 1.0
ND1 A:HIS669 4.9 26.1 1.0
O A:TRP706 4.9 29.9 1.0

Potassium binding site 2 out of 6 in 3c0y

Go back to Potassium Binding Sites List in 3c0y
Potassium binding site 2 out of 6 in the Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K905

b:43.4
occ:1.00
 O A:VAL724 2.2 25.7 1.0
O A:HOH41 2.4 32.2 1.0
O A:HOH52 2.4 30.6 1.0
O A:ASP721 2.5 37.8 1.0
O A:PHE718 2.7 28.5 1.0
C A:VAL724 3.4 26.9 1.0
C A:ASP721 3.5 38.1 1.0
O A:PHE755 3.6 30.4 1.0
CB A:PHE755 3.6 30.2 1.0
C A:PHE718 3.7 27.3 1.0
CB A:PHE718 3.9 26.5 1.0
C A:PHE755 4.1 28.8 1.0
N A:ASP721 4.1 37.3 1.0
CA A:ASP721 4.2 37.3 1.0
O A:HOH6 4.2 29.1 1.0
CA A:VAL724 4.2 27.0 1.0
N A:VAL724 4.2 28.7 1.0
CB A:VAL724 4.3 27.8 1.0
CB A:ASP721 4.3 37.1 1.0
CA A:PHE718 4.4 27.3 1.0
N A:LEU725 4.4 27.0 1.0
CA A:PHE755 4.5 29.7 1.0
N A:PRO722 4.5 37.9 1.0
CA A:LEU725 4.6 27.2 1.0
CA A:PRO722 4.7 36.3 1.0
CG A:PHE755 4.7 32.3 1.0
N A:TYR719 4.7 29.0 1.0
C A:TYR719 4.8 31.6 1.0
O A:GLY752 4.8 39.7 1.0
CA A:TYR719 4.9 29.5 1.0
O A:TYR719 4.9 30.8 1.0
N A:TYR726 4.9 25.4 1.0
C A:PRO722 4.9 35.5 1.0
N A:ASN756 4.9 29.0 1.0
CG1 A:VAL724 4.9 24.6 1.0
CA A:GLY752 5.0 39.2 1.0

Potassium binding site 3 out of 6 in 3c0y

Go back to Potassium Binding Sites List in 3c0y
Potassium binding site 3 out of 6 in the Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K904

b:38.3
occ:1.00
 O B:ASP707 2.6 31.7 1.0
OG B:SER728 2.7 33.9 1.0
O B:HIS709 2.7 30.5 1.0
O B:LEU729 2.7 31.8 1.0
OD1 B:ASP705 2.7 26.8 1.0
O B:ASP705 2.9 26.5 1.0
CG B:ASP705 3.3 28.7 1.0
C B:ASP705 3.6 25.9 1.0
C B:HIS709 3.6 30.9 1.0
C B:LEU729 3.7 31.9 1.0
C B:ASP707 3.7 32.6 1.0
N B:ASP707 3.7 32.8 1.0
CB B:HIS730 3.8 30.1 1.0
CB B:ASP705 3.9 26.3 1.0
CB B:SER728 4.0 31.9 1.0
N B:LEU729 4.0 31.6 1.0
OD2 B:ASP705 4.1 31.3 1.0
CA B:HIS710 4.2 30.7 1.0
CA B:ASP707 4.2 31.2 1.0
CD2 B:HIS730 4.2 30.9 1.0
N B:HIS710 4.2 30.2 1.0
C B:TRP706 4.3 32.5 1.0
CB B:ASP707 4.3 31.1 1.0
CA B:SER728 4.3 31.5 1.0
CG B:HIS730 4.3 28.5 1.0
N B:TRP706 4.3 27.7 1.0
N B:GLY711 4.4 28.7 1.0
CA B:HIS730 4.4 32.3 1.0
CA B:ASP705 4.4 26.5 1.0
N B:HIS730 4.4 32.1 1.0
CA B:TRP706 4.5 30.9 1.0
N B:HIS709 4.5 31.8 1.0
C B:SER728 4.5 31.4 1.0
CA B:LEU729 4.5 32.2 1.0
C B:HIS710 4.7 30.6 1.0
CA B:HIS709 4.7 31.5 1.0
CE1 B:HIS669 4.7 31.4 1.0
OH B:TYR726 4.7 30.3 1.0
C B:VAL708 4.7 31.4 1.0
O B:HOH11 4.7 31.0 1.0
N B:VAL708 4.8 33.1 1.0
ND1 B:HIS669 4.9 33.3 1.0

Potassium binding site 4 out of 6 in 3c0y

Go back to Potassium Binding Sites List in 3c0y
Potassium binding site 4 out of 6 in the Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K905

b:46.0
occ:1.00
 O B:ASP721 2.3 34.0 1.0
O B:HOH17 2.4 27.3 1.0
O B:VAL724 2.5 28.7 1.0
O B:PHE718 2.5 27.7 1.0
O B:HOH34 2.6 29.6 1.0
C B:ASP721 3.4 34.1 1.0
O B:PHE755 3.5 29.6 1.0
C B:PHE718 3.6 28.5 1.0
C B:VAL724 3.6 28.6 1.0
CB B:PHE755 3.7 28.6 1.0
N B:ASP721 3.8 35.7 1.0
CA B:ASP721 4.0 34.3 1.0
CB B:PHE718 4.0 27.9 1.0
O B:HOH5 4.1 24.7 1.0
C B:PHE755 4.2 28.9 1.0
CB B:VAL724 4.3 27.5 1.0
CA B:VAL724 4.3 28.6 1.0
CB B:ASP721 4.4 34.3 1.0
CA B:PHE718 4.4 28.8 1.0
N B:VAL724 4.4 30.3 1.0
N B:PRO722 4.5 33.4 1.0
O B:TYR719 4.5 30.7 1.0
N B:TYR719 4.5 30.4 1.0
CA B:PHE755 4.5 29.3 1.0
C B:TYR719 4.5 32.9 1.0
O B:GLY752 4.6 32.4 1.0
CA B:PRO722 4.7 32.8 1.0
N B:LEU725 4.7 27.7 1.0
CA B:TYR719 4.7 31.6 1.0
CG B:PHE755 4.8 30.4 1.0
CG1 B:VAL724 4.8 28.4 1.0
CA B:GLY752 4.9 34.8 1.0
CA B:LEU725 4.9 26.9 1.0
C B:GLN720 4.9 36.8 1.0
N B:GLN720 5.0 34.0 1.0

Potassium binding site 5 out of 6 in 3c0y

Go back to Potassium Binding Sites List in 3c0y
Potassium binding site 5 out of 6 in the Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K904

b:46.0
occ:1.00
 O C:ASP707 2.7 37.2 1.0
O C:HIS709 2.7 37.1 1.0
OD1 C:ASP705 2.7 37.5 1.0
O C:LEU729 2.7 36.9 1.0
OG C:SER728 2.8 37.9 1.0
O C:ASP705 2.9 35.6 1.0
CG C:ASP705 3.2 36.2 1.0
C C:ASP705 3.5 36.3 1.0
C C:HIS709 3.7 36.9 1.0
C C:ASP707 3.7 37.5 1.0
C C:LEU729 3.7 36.3 1.0
CB C:ASP705 3.8 35.8 1.0
N C:LEU729 3.8 35.1 1.0
OD2 C:ASP705 3.8 37.5 1.0
N C:ASP707 3.9 37.2 1.0
CB C:SER728 4.0 33.5 1.0
CB C:HIS730 4.0 34.9 1.0
CA C:ASP707 4.2 37.8 1.0
CB C:ASP707 4.2 37.7 1.0
CA C:HIS710 4.2 34.9 1.0
CA C:ASP705 4.2 36.0 1.0
C C:TRP706 4.3 37.0 1.0
N C:TRP706 4.3 36.6 1.0
N C:HIS710 4.3 34.3 1.0
CA C:SER728 4.4 33.9 1.0
CA C:TRP706 4.4 37.1 1.0
C C:SER728 4.4 34.0 1.0
N C:GLY711 4.5 35.3 1.0
CA C:LEU729 4.5 35.7 1.0
N C:HIS709 4.5 37.0 1.0
OH C:TYR726 4.5 42.8 1.0
N C:HIS730 4.6 35.7 1.0
CA C:HIS730 4.6 35.6 1.0
CD2 C:HIS730 4.7 35.1 1.0
CG C:HIS730 4.7 37.0 1.0
CE1 C:HIS669 4.7 36.6 1.0
CA C:HIS709 4.7 36.9 1.0
C C:VAL708 4.8 37.2 1.0
C C:HIS710 4.8 35.6 1.0
N C:VAL708 4.8 37.4 1.0
O C:HOH112 4.9 41.1 1.0
ND1 C:HIS669 4.9 36.7 1.0

Potassium binding site 6 out of 6 in 3c0y

Go back to Potassium Binding Sites List in 3c0y
Potassium binding site 6 out of 6 in the Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K905

b:61.0
occ:1.00
 O C:VAL724 2.2 38.9 1.0
O C:HOH45 2.2 32.8 1.0
O C:ASP721 2.4 44.7 1.0
O C:PHE718 2.5 42.6 1.0
O C:HOH190 2.5 39.2 1.0
C C:VAL724 3.4 38.5 1.0
O C:PHE755 3.5 36.0 1.0
C C:ASP721 3.6 44.4 1.0
C C:PHE718 3.6 41.6 1.0
CB C:PHE755 3.8 36.5 1.0
CB C:PHE718 3.8 39.7 1.0
O C:HOH63 4.0 36.0 1.0
CA C:VAL724 4.1 39.1 1.0
N C:ASP721 4.1 45.8 1.0
C C:PHE755 4.2 36.1 1.0
CB C:VAL724 4.2 39.4 1.0
CA C:ASP721 4.2 45.6 1.0
CA C:PHE718 4.3 40.6 1.0
CB C:ASP721 4.3 46.2 1.0
N C:VAL724 4.4 40.2 1.0
N C:LEU725 4.4 37.3 1.0
CA C:LEU725 4.6 36.7 1.0
CA C:PHE755 4.6 36.9 1.0
N C:TYR719 4.6 42.1 1.0
N C:PRO722 4.6 43.1 1.0
CG1 C:VAL724 4.7 37.9 1.0
N C:TYR726 4.8 37.2 1.0
CA C:TYR719 4.8 43.6 1.0
C C:TYR719 4.8 44.2 1.0
O C:GLY752 4.9 40.5 1.0
CG C:PHE755 4.9 38.8 1.0
CA C:PRO722 4.9 41.5 1.0
O C:TYR719 4.9 43.8 1.0

Reference:

A.Schuetz, J.Min, A.Allali-Hassani, M.Schapira, M.Shuen, P.Loppnau, R.Mazitschek, N.P.Kwiatkowski, T.A.Lewis, R.L.Maglathin, T.H.Mclean, A.Bochkarev, A.N.Plotnikov, M.Vedadi, C.H.Arrowsmith. Human HDAC7 Harbors A Class Iia Histone Deacetylase-Specific Zinc Binding Motif and Cryptic Deacetylase Activity. J.Biol.Chem. V. 283 11355 2008.
ISSN: ISSN 0021-9258
PubMed: 18285338
DOI: 10.1074/JBC.M707362200
Page generated: Mon Aug 12 07:52:35 2024

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