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Potassium in PDB 3c10: Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 in Complex with Trichostatin A (Tsa)

Protein crystallography data

The structure of Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 in Complex with Trichostatin A (Tsa), PDB code: 3c10 was solved by J.Min, A.Schuetz, P.Loppnau, J.Weigelt, M.Sundstrom, C.H.Arrowsmith, A.M.Edwards, 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) 35.42 / 2.00
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 81.827, 81.827, 148.970, 90.00, 90.00, 120.00
R / Rfree (%) 20.1 / 26.3

Other elements in 3c10:

The structure of Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 in Complex with Trichostatin A (Tsa) 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 in Complex with Trichostatin A (Tsa) (pdb code 3c10). 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 in Complex with Trichostatin A (Tsa), PDB code: 3c10:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 3c10

Go back to Potassium Binding Sites List in 3c10
Potassium binding site 1 out of 6 in the Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 in Complex with Trichostatin A (Tsa)


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 in Complex with Trichostatin A (Tsa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K201

b:28.8
occ:1.00
 O A:ASP707 2.6 21.1 1.0
OG A:SER728 2.7 23.3 1.0
OD1 A:ASP705 2.7 20.6 1.0
O A:LEU729 2.7 23.4 1.0
O A:HIS709 2.7 23.5 1.0
O A:ASP705 2.8 21.6 1.0
CG A:ASP705 3.3 22.4 1.0
C A:ASP705 3.5 22.4 1.0
C A:ASP707 3.6 22.8 1.0
C A:LEU729 3.7 22.6 1.0
C A:HIS709 3.7 21.2 1.0
CB A:ASP705 3.8 20.6 1.0
CB A:HIS730 3.9 20.9 1.0
N A:ASP707 3.9 21.6 1.0
OD2 A:ASP705 4.0 26.0 1.0
CB A:SER728 4.0 21.0 1.0
N A:LEU729 4.0 22.6 1.0
CA A:ASP707 4.1 23.0 1.0
C A:TRP706 4.2 23.0 1.0
CB A:ASP707 4.2 23.2 1.0
N A:TRP706 4.2 20.7 1.0
CA A:HIS710 4.2 20.6 1.0
CA A:ASP705 4.3 21.2 1.0
CA A:TRP706 4.3 23.1 1.0
N A:HIS710 4.3 20.5 1.0
CA A:SER728 4.4 22.0 1.0
CD2 A:HIS730 4.4 18.1 1.0
CA A:HIS730 4.4 23.3 1.0
N A:HIS730 4.4 22.5 1.0
CG A:HIS730 4.5 21.2 1.0
N A:HIS709 4.5 21.4 1.0
N A:GLY711 4.5 21.8 1.0
CA A:LEU729 4.6 22.6 1.0
C A:SER728 4.6 23.4 1.0
CE1 A:HIS669 4.7 20.8 1.0
OH A:TYR726 4.7 17.9 1.0
N A:VAL708 4.7 22.7 1.0
C A:VAL708 4.7 23.2 1.0
C A:HIS710 4.7 20.5 1.0
O A:HOH7 4.7 19.9 1.0
CA A:HIS709 4.7 21.6 1.0
O A:TRP706 4.9 23.7 1.0
ND1 A:HIS669 4.9 19.6 1.0

Potassium binding site 2 out of 6 in 3c10

Go back to Potassium Binding Sites List in 3c10
Potassium binding site 2 out of 6 in the Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 in Complex with Trichostatin A (Tsa)


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 in Complex with Trichostatin A (Tsa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K202

b:36.2
occ:1.00
 O A:VAL724 2.3 20.1 1.0
O A:HOH42 2.4 28.2 1.0
O A:HOH4 2.5 29.5 1.0
O A:ASP721 2.5 32.6 1.0
O A:PHE718 2.6 26.1 1.0
C A:VAL724 3.4 21.9 1.0
C A:ASP721 3.5 31.8 1.0
CB A:PHE755 3.5 26.4 1.0
O A:PHE755 3.6 24.5 1.0
C A:PHE718 3.7 24.4 1.0
CB A:PHE718 4.0 23.3 1.0
CA A:VAL724 4.2 23.1 1.0
N A:VAL724 4.2 24.9 1.0
C A:PHE755 4.2 24.9 1.0
N A:ASP721 4.2 30.9 1.0
CB A:VAL724 4.2 23.9 1.0
CA A:ASP721 4.2 30.6 1.0
O A:HOH34 4.4 23.6 1.0
CB A:ASP721 4.4 30.7 1.0
N A:PRO722 4.4 31.6 1.0
CA A:PHE718 4.4 25.1 1.0
CA A:PHE755 4.5 25.3 1.0
N A:LEU725 4.5 21.9 1.0
CA A:PRO722 4.6 30.9 1.0
CG A:PHE755 4.6 25.8 1.0
CA A:LEU725 4.6 22.1 1.0
O A:GLY752 4.7 31.7 1.0
N A:TYR719 4.7 25.1 1.0
O A:TYR719 4.7 24.6 1.0
C A:TYR719 4.8 26.0 1.0
C A:PRO722 4.8 29.7 1.0
CG1 A:VAL724 4.8 21.2 1.0
CA A:TYR719 4.9 24.4 1.0
CA A:GLY752 4.9 33.0 1.0
N A:TYR726 4.9 21.1 1.0

Potassium binding site 3 out of 6 in 3c10

Go back to Potassium Binding Sites List in 3c10
Potassium binding site 3 out of 6 in the Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 in Complex with Trichostatin A (Tsa)


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 in Complex with Trichostatin A (Tsa) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K201

b:30.2
occ:1.00
 O B:ASP707 2.6 27.3 1.0
OG B:SER728 2.6 29.7 1.0
O B:LEU729 2.6 25.6 1.0
O B:HIS709 2.7 27.7 1.0
OD1 B:ASP705 2.7 25.0 1.0
O B:ASP705 2.7 24.5 1.0
CG B:ASP705 3.3 24.2 1.0
C B:ASP705 3.5 22.9 1.0
C B:LEU729 3.6 25.7 1.0
C B:ASP707 3.6 27.1 1.0
N B:ASP707 3.6 25.2 1.0
C B:HIS709 3.7 25.8 1.0
CB B:HIS730 3.8 23.4 1.0
CB B:ASP705 3.9 22.3 1.0
CB B:SER728 4.0 24.9 1.0
N B:LEU729 4.0 25.9 1.0
OD2 B:ASP705 4.0 26.3 1.0
CA B:ASP707 4.1 25.1 1.0
C B:TRP706 4.1 26.1 1.0
N B:TRP706 4.2 23.4 1.0
CA B:HIS710 4.2 25.6 1.0
CA B:TRP706 4.3 24.7 1.0
N B:HIS710 4.3 26.2 1.0
CB B:ASP707 4.3 25.3 1.0
CA B:ASP705 4.3 23.5 1.0
N B:HIS730 4.3 26.1 1.0
CD2 B:HIS730 4.3 21.3 1.0
CA B:HIS730 4.3 26.1 1.0
CA B:SER728 4.3 25.8 1.0
CG B:HIS730 4.4 24.3 1.0
N B:GLY711 4.4 23.8 1.0
CA B:LEU729 4.5 26.4 1.0
N B:HIS709 4.5 26.0 1.0
C B:SER728 4.5 25.6 1.0
O B:HOH920 4.6 26.8 1.0
C B:VAL708 4.7 27.0 1.0
C B:HIS710 4.7 25.4 1.0
N B:VAL708 4.7 28.2 1.0
CE1 B:HIS669 4.7 25.0 1.0
CA B:HIS709 4.7 26.7 1.0
OH B:TYR726 4.8 23.4 1.0
ND1 B:HIS669 5.0 27.4 1.0

Potassium binding site 4 out of 6 in 3c10

Go back to Potassium Binding Sites List in 3c10
Potassium binding site 4 out of 6 in the Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 in Complex with Trichostatin A (Tsa)


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 in Complex with Trichostatin A (Tsa) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K202

b:32.5
occ:1.00
 O B:ASP721 2.5 28.3 1.0
O B:HOH907 2.5 27.8 1.0
O B:HOH913 2.5 29.6 1.0
O B:VAL724 2.5 25.6 1.0
O B:PHE718 2.5 23.8 1.0
C B:ASP721 3.4 27.8 1.0
C B:PHE718 3.6 23.4 1.0
C B:VAL724 3.6 23.0 1.0
O B:PHE755 3.6 24.3 1.0
CB B:PHE755 3.7 24.7 1.0
N B:ASP721 3.9 27.3 1.0
CB B:PHE718 4.0 20.9 1.0
CA B:ASP721 4.0 27.2 1.0
O B:HOH906 4.1 19.6 1.0
CB B:VAL724 4.2 22.0 1.0
C B:PHE755 4.2 23.8 1.0
CA B:VAL724 4.3 22.6 1.0
CB B:ASP721 4.3 27.4 1.0
N B:VAL724 4.4 22.5 1.0
CA B:PHE718 4.4 23.1 1.0
N B:PRO722 4.5 26.9 1.0
O B:TYR719 4.5 25.0 1.0
N B:TYR719 4.6 22.9 1.0
CA B:PHE755 4.6 24.5 1.0
C B:TYR719 4.6 26.2 1.0
N B:LEU725 4.6 23.1 1.0
CG1 B:VAL724 4.6 23.9 1.0
CA B:PRO722 4.7 26.8 1.0
O B:GLY752 4.7 28.9 1.0
CA B:TYR719 4.7 25.1 1.0
CA B:LEU725 4.8 22.0 1.0
CG B:PHE755 4.9 25.8 1.0
CA B:GLY752 4.9 30.2 1.0
N B:ASN756 5.0 22.4 1.0

Potassium binding site 5 out of 6 in 3c10

Go back to Potassium Binding Sites List in 3c10
Potassium binding site 5 out of 6 in the Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 in Complex with Trichostatin A (Tsa)


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 in Complex with Trichostatin A (Tsa) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K201

b:34.0
occ:1.00
 OG C:SER728 2.6 30.2 1.0
O C:ASP707 2.6 32.1 1.0
OD1 C:ASP705 2.6 27.5 1.0
O C:LEU729 2.6 31.2 1.0
O C:HIS709 2.7 32.8 1.0
O C:ASP705 2.7 30.3 1.0
CG C:ASP705 3.2 26.9 1.0
C C:ASP705 3.5 28.6 1.0
C C:LEU729 3.7 30.8 1.0
C C:ASP707 3.7 30.8 1.0
C C:HIS709 3.7 30.4 1.0
CB C:ASP705 3.7 26.9 1.0
CB C:SER728 3.9 27.1 1.0
N C:ASP707 3.9 29.5 1.0
N C:LEU729 3.9 29.1 1.0
OD2 C:ASP705 3.9 30.4 1.0
CB C:HIS730 3.9 29.5 1.0
CA C:ASP707 4.2 31.0 1.0
CA C:ASP705 4.2 27.9 1.0
N C:TRP706 4.2 28.4 1.0
CB C:ASP707 4.3 30.8 1.0
CA C:HIS710 4.3 28.8 1.0
C C:TRP706 4.3 29.2 1.0
CA C:SER728 4.3 28.0 1.0
N C:HIS710 4.3 28.6 1.0
CA C:TRP706 4.4 29.1 1.0
C C:SER728 4.4 27.8 1.0
CA C:LEU729 4.5 29.4 1.0
N C:HIS730 4.5 30.4 1.0
CD2 C:HIS730 4.5 26.2 1.0
N C:HIS709 4.5 30.4 1.0
N C:GLY711 4.5 29.6 1.0
CA C:HIS730 4.5 29.8 1.0
O C:HOH920 4.6 31.0 1.0
CG C:HIS730 4.6 28.4 1.0
OH C:TYR726 4.6 34.9 1.0
CA C:HIS709 4.7 30.7 1.0
C C:VAL708 4.8 31.1 1.0
C C:HIS710 4.8 29.9 1.0
CE1 C:HIS669 4.8 26.5 1.0
N C:VAL708 4.8 30.9 1.0
ND1 C:HIS669 4.9 26.6 1.0

Potassium binding site 6 out of 6 in 3c10

Go back to Potassium Binding Sites List in 3c10
Potassium binding site 6 out of 6 in the Crystal Structure of Catalytic Domain of Human Histone Deacetylase HDAC7 in Complex with Trichostatin A (Tsa)


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 in Complex with Trichostatin A (Tsa) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K202

b:40.4
occ:1.00
 O C:HOH906 2.1 24.0 1.0
O C:VAL724 2.5 34.5 1.0
O C:ASP721 2.5 37.5 1.0
O C:HOH913 2.5 36.3 1.0
O C:PHE718 2.5 35.1 1.0
O C:PHE755 3.5 29.7 1.0
C C:VAL724 3.6 32.4 1.0
C C:ASP721 3.6 37.5 1.0
C C:PHE718 3.6 32.8 1.0
CB C:PHE755 3.8 29.0 1.0
CB C:PHE718 3.9 30.8 1.0
N C:ASP721 4.0 37.2 1.0
O C:HOH907 4.1 30.1 1.0
CA C:ASP721 4.2 37.8 1.0
CB C:ASP721 4.2 37.9 1.0
C C:PHE755 4.2 29.3 1.0
CB C:VAL724 4.2 32.6 1.0
CA C:VAL724 4.2 33.8 1.0
CA C:PHE718 4.3 32.1 1.0
N C:VAL724 4.4 34.5 1.0
N C:LEU725 4.6 31.6 1.0
CA C:PHE755 4.6 29.5 1.0
N C:TYR719 4.6 32.7 1.0
O C:TYR719 4.7 33.5 1.0
C C:TYR719 4.7 34.0 1.0
N C:PRO722 4.7 37.0 1.0
CG1 C:VAL724 4.7 32.0 1.0
CA C:LEU725 4.8 30.2 1.0
CA C:TYR719 4.8 33.5 1.0
N C:TYR726 4.8 30.5 1.0
CG C:PHE755 4.9 30.5 1.0
O C:GLY752 4.9 30.2 1.0
CA C:PRO722 4.9 36.3 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 07:53:06 2024

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