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Potassium in PDB 3f0r: Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form

Enzymatic activity of Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form

All present enzymatic activity of Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form, PDB code: 3f0r was solved by D.P.Dowling, S.L.Gantt, S.G.Gattis, C.A.Fierke, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.97 / 2.54
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.895, 90.705, 92.141, 90.00, 94.63, 90.00
R / Rfree (%) 21 / 25.8

Other elements in 3f0r:

The structure of Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form (pdb code 3f0r). 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 Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form, PDB code: 3f0r:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 3f0r

Go back to Potassium Binding Sites List in 3f0r
Potassium binding site 1 out of 6 in the Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K401

b:37.5
occ:1.00
 O A:VAL195 2.5 32.7 1.0
O A:PHE189 2.5 33.9 1.0
O A:HOH436 2.8 36.8 1.0
O A:HOH423 2.9 29.8 1.0
O A:TYR225 3.0 43.3 1.0
O A:THR192 3.1 42.8 1.0
CB A:TYR225 3.5 48.6 1.0
C A:PHE189 3.5 36.0 1.0
C A:TYR225 3.6 45.3 1.0
C A:VAL195 3.7 36.3 1.0
CB A:PHE189 3.8 31.2 1.0
CA A:MET196 4.1 38.8 1.0
C A:THR192 4.1 42.9 1.0
CA A:TYR225 4.2 47.4 1.0
CA A:PHE189 4.3 34.1 1.0
N A:MET196 4.4 38.1 1.0
CG2 A:THR192 4.4 40.8 1.0
N A:THR197 4.4 37.6 1.0
N A:SER190 4.4 38.1 1.0
N A:SER226 4.4 42.9 1.0
OG A:SER226 4.5 45.6 1.0
CA A:SER190 4.6 41.3 1.0
N A:THR192 4.7 44.5 1.0
O A:SER190 4.7 43.8 1.0
C A:SER190 4.7 43.0 1.0
O A:GLY222 4.7 55.0 1.0
C A:MET196 4.7 38.5 1.0
CG2 A:THR197 4.7 39.5 1.0
CG A:TYR225 4.8 47.4 1.0
CA A:VAL195 4.8 36.2 1.0
CA A:SER226 4.9 42.2 1.0
CA A:THR192 4.9 42.8 1.0

Potassium binding site 2 out of 6 in 3f0r

Go back to Potassium Binding Sites List in 3f0r
Potassium binding site 2 out of 6 in the Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K402

b:36.7
occ:1.00
 O A:ASP178 2.5 32.7 1.0
O A:HIS180 2.7 36.6 1.0
O A:LEU200 2.8 39.3 1.0
O A:ASP176 2.8 37.3 1.0
OG A:SER199 2.8 39.7 1.0
OD1 A:ASP176 2.9 46.7 1.0
N A:ASP178 3.3 32.8 1.0
C A:ASP176 3.4 37.5 1.0
C A:ASP178 3.4 33.0 1.0
CG A:ASP176 3.5 46.0 1.0
C A:LEU200 3.6 38.1 1.0
CB A:HIS201 3.7 40.3 1.0
C A:HIS180 3.7 37.5 1.0
CB A:ASP176 3.7 40.5 1.0
CA A:ASP178 3.8 32.1 1.0
C A:LEU177 3.9 32.7 1.0
N A:LEU200 3.9 37.6 1.0
CB A:SER199 4.0 40.8 1.0
CB A:ASP178 4.0 31.6 1.0
N A:LEU177 4.0 35.2 1.0
CA A:LEU177 4.1 34.2 1.0
CA A:ASP176 4.2 37.5 1.0
CA A:HIS201 4.3 40.4 1.0
ND1 A:HIS201 4.3 45.8 1.0
N A:HIS201 4.3 37.4 1.0
N A:GLY182 4.3 38.3 1.0
C A:SER199 4.4 39.0 1.0
O A:HOH410 4.4 45.2 1.0
CA A:HIS181 4.4 37.9 1.0
CA A:SER199 4.4 38.9 1.0
CG A:HIS201 4.4 44.8 1.0
N A:HIS181 4.5 36.3 1.0
OD2 A:ASP176 4.5 47.6 1.0
N A:HIS180 4.5 33.6 1.0
CA A:LEU200 4.5 36.9 1.0
C A:LEU179 4.6 36.3 1.0
N A:LEU179 4.6 37.4 1.0
O A:LEU177 4.7 34.4 1.0
C A:HIS181 4.7 38.2 1.0
CA A:HIS180 4.7 35.3 1.0
O A:LEU179 4.8 35.6 1.0
CE1 A:HIS142 4.9 43.3 1.0

Potassium binding site 3 out of 6 in 3f0r

Go back to Potassium Binding Sites List in 3f0r
Potassium binding site 3 out of 6 in the Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K404

b:46.6
occ:1.00
 O B:VAL195 2.4 49.6 1.0
O B:PHE189 2.5 45.1 1.0
O B:HOH406 2.6 45.2 1.0
O B:THR192 2.9 49.2 1.0
O B:HOH402 3.0 42.1 1.0
O B:TYR225 3.2 41.9 1.0
C B:PHE189 3.5 45.1 1.0
C B:VAL195 3.6 50.1 1.0
CB B:TYR225 3.6 43.0 1.0
C B:TYR225 3.9 43.0 1.0
CB B:PHE189 3.9 45.2 1.0
C B:THR192 4.0 49.2 1.0
OG B:SER226 4.1 46.8 1.0
CA B:MET196 4.2 46.8 1.0
CA B:SER190 4.3 45.8 1.0
N B:SER190 4.3 45.3 1.0
CG2 B:THR192 4.3 48.5 1.0
O B:SER190 4.3 48.4 1.0
N B:MET196 4.4 48.6 1.0
CA B:TYR225 4.4 43.5 1.0
CA B:PHE189 4.4 44.3 1.0
C B:SER190 4.5 47.0 1.0
N B:THR197 4.6 44.2 1.0
CA B:VAL195 4.6 50.8 1.0
O B:GLY222 4.6 50.8 1.0
N B:THR192 4.7 48.4 1.0
CB B:VAL195 4.7 49.6 1.0
N B:SER226 4.8 41.0 1.0
CG2 B:THR197 4.8 37.9 1.0
CG B:TYR225 4.9 46.9 1.0
CA B:THR192 4.9 48.3 1.0
N B:VAL195 4.9 54.0 1.0
C B:MET196 4.9 45.8 1.0
N B:SER193 4.9 50.1 1.0
CA B:SER193 5.0 50.8 1.0
OG1 B:THR197 5.0 42.8 1.0

Potassium binding site 4 out of 6 in 3f0r

Go back to Potassium Binding Sites List in 3f0r
Potassium binding site 4 out of 6 in the Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K405

b:34.2
occ:1.00
 O B:ASP178 2.5 34.9 1.0
O B:LEU200 2.6 35.8 1.0
OD1 B:ASP176 2.7 32.8 1.0
O B:ASP176 2.7 35.0 1.0
O B:HIS180 2.9 29.8 1.0
OG B:SER199 3.1 42.0 1.0
N B:ASP178 3.3 33.3 1.0
C B:ASP178 3.4 34.5 1.0
C B:ASP176 3.4 34.0 1.0
CG B:ASP176 3.5 34.2 1.0
C B:LEU200 3.6 36.2 1.0
CB B:HIS201 3.7 33.6 1.0
CA B:ASP178 3.7 33.1 1.0
N B:LEU200 3.8 37.0 1.0
C B:LEU177 3.8 32.3 1.0
C B:HIS180 3.9 32.5 1.0
CB B:ASP178 3.9 33.2 1.0
CB B:ASP176 4.0 33.1 1.0
ND1 B:HIS201 4.0 36.0 1.0
N B:LEU177 4.1 32.4 1.0
CA B:LEU177 4.1 31.8 1.0
CB B:SER199 4.1 41.2 1.0
CG B:HIS201 4.3 33.7 1.0
C B:SER199 4.3 38.3 1.0
CA B:SER199 4.3 39.8 1.0
CA B:ASP176 4.3 34.2 1.0
CA B:HIS201 4.3 33.6 1.0
N B:HIS201 4.4 34.5 1.0
CA B:LEU200 4.4 37.2 1.0
CA B:HIS181 4.5 32.5 1.0
OD2 B:ASP176 4.5 36.2 1.0
N B:LEU179 4.5 34.9 1.0
N B:HIS180 4.5 32.0 1.0
O B:LEU177 4.5 32.4 1.0
N B:HIS181 4.5 30.8 1.0
N B:GLY182 4.6 32.3 1.0
C B:LEU179 4.6 33.7 1.0
O B:HOH395 4.7 32.7 1.0
CA B:HIS180 4.8 31.7 1.0
C B:HIS181 4.8 32.1 1.0
O B:LEU179 4.9 35.3 1.0
CE1 B:HIS142 5.0 32.4 1.0
CA B:LEU179 5.0 32.1 1.0

Potassium binding site 5 out of 6 in 3f0r

Go back to Potassium Binding Sites List in 3f0r
Potassium binding site 5 out of 6 in the Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K407

b:63.6
occ:1.00
 O C:PHE189 2.3 49.5 1.0
O C:HOH392 2.5 49.2 1.0
O C:VAL195 2.7 59.9 1.0
O C:HOH393 3.2 50.5 1.0
O C:THR192 3.2 65.6 1.0
O C:TYR225 3.3 69.3 1.0
C C:PHE189 3.4 52.8 1.0
CB C:TYR225 3.5 71.2 1.0
C C:TYR225 3.9 70.6 1.0
C C:VAL195 3.9 61.5 1.0
CB C:PHE189 4.1 53.2 1.0
OG C:SER226 4.1 67.4 1.0
C C:THR192 4.2 64.6 1.0
CA C:SER190 4.2 56.5 1.0
N C:SER190 4.2 53.6 1.0
O C:SER190 4.3 59.9 1.0
CA C:MET196 4.3 62.6 1.0
CA C:TYR225 4.3 71.5 1.0
O C:GLY222 4.4 77.3 1.0
CG2 C:THR192 4.4 63.8 1.0
CA C:PHE189 4.4 53.3 1.0
C C:SER190 4.4 58.8 1.0
N C:MET196 4.6 62.5 1.0
N C:THR197 4.6 62.5 1.0
OG1 C:THR197 4.6 63.7 1.0
N C:SER226 4.7 70.3 1.0
CG C:TYR225 4.7 72.0 1.0
N C:THR192 4.7 64.5 1.0
CA C:GLY222 4.9 76.0 1.0
CA C:VAL195 4.9 62.4 1.0
C C:MET196 4.9 62.6 1.0
N C:SER193 5.0 64.3 1.0
CA C:SER193 5.0 63.0 1.0
CA C:THR192 5.0 64.7 1.0

Potassium binding site 6 out of 6 in 3f0r

Go back to Potassium Binding Sites List in 3f0r
Potassium binding site 6 out of 6 in the Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure Analysis of Human HDAC8 Complexed with Trichostatin A in A New Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K408

b:57.4
occ:1.00
 O C:ASP176 2.7 47.7 1.0
O C:HIS180 2.7 50.0 1.0
O C:ASP178 2.7 47.9 1.0
O C:LEU200 2.8 61.6 1.0
OD1 C:ASP176 2.9 56.8 1.0
OG C:SER199 3.0 64.8 1.0
C C:ASP176 3.3 49.2 1.0
N C:ASP178 3.4 45.5 1.0
C C:ASP178 3.5 45.4 1.0
CG C:ASP176 3.6 54.1 1.0
CB C:HIS201 3.6 65.8 1.0
CB C:ASP176 3.7 49.6 1.0
C C:HIS180 3.7 52.7 1.0
C C:LEU177 3.8 45.9 1.0
C C:LEU200 3.8 61.7 1.0
CA C:ASP178 3.8 43.6 1.0
N C:LEU177 4.0 48.1 1.0
CB C:ASP178 4.0 37.5 1.0
CA C:LEU177 4.1 47.9 1.0
CA C:ASP176 4.2 49.5 1.0
CB C:SER199 4.2 63.3 1.0
N C:LEU200 4.2 62.4 1.0
CG C:HIS201 4.2 67.3 1.0
ND1 C:HIS201 4.3 67.8 1.0
CA C:HIS201 4.4 63.9 1.0
O C:LEU177 4.5 48.9 1.0
N C:HIS180 4.5 53.0 1.0
CA C:HIS181 4.5 56.4 1.0
N C:GLY182 4.5 55.7 1.0
N C:HIS181 4.5 54.5 1.0
N C:HIS201 4.6 62.3 1.0
OD2 C:ASP176 4.6 56.1 1.0
N C:LEU179 4.6 47.5 1.0
C C:SER199 4.6 62.2 1.0
C C:LEU179 4.6 52.2 1.0
CA C:SER199 4.6 63.0 1.0
CE1 C:HIS142 4.7 62.6 1.0
CA C:HIS180 4.7 53.5 1.0
CA C:LEU200 4.8 61.1 1.0
C C:HIS181 4.9 55.4 1.0
O C:LEU179 4.9 52.1 1.0

Reference:

D.P.Dowling, S.L.Gantt, S.G.Gattis, C.A.Fierke, D.W.Christianson. Structural Studies of Human Histone Deacetylase 8 and Its Site-Specific Variants Complexed with Substrate and Inhibitors. Biochemistry V. 47 13554 2008.
ISSN: ISSN 0006-2960
PubMed: 19053282
DOI: 10.1021/BI801610C
Page generated: Mon Aug 12 08:15:39 2024

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