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Potassium in PDB 3f07: Crystal Structure Analysis of Human HDAC8 Complexed with Apha in A New Monoclinic Crystal Form

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

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

Protein crystallography data

The structure of Crystal Structure Analysis of Human HDAC8 Complexed with Apha in A New Monoclinic Crystal Form, PDB code: 3f07 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) 31.50 / 3.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 88.381, 90.171, 92.267, 90.00, 94.74, 90.00
R / Rfree (%) 21.6 / 26

Other elements in 3f07:

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

Zinc (Zn) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure Analysis of Human HDAC8 Complexed with Apha in A New Monoclinic Crystal Form (pdb code 3f07). 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 Apha in A New Monoclinic Crystal Form, PDB code: 3f07:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 3f07

Go back to Potassium Binding Sites List in 3f07
Potassium binding site 1 out of 6 in the Crystal Structure Analysis of Human HDAC8 Complexed with Apha 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 Apha in A New Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K401

b:35.1
occ:1.00
 O A:HIS180 2.6 43.5 1.0
O A:LEU200 2.7 44.5 1.0
O A:ASP176 2.8 37.7 1.0
O A:ASP178 2.9 36.7 1.0
OG A:SER199 3.2 42.4 1.0
CG A:ASP176 3.2 40.8 1.0
N A:ASP178 3.3 37.3 1.0
OD2 A:ASP176 3.3 41.5 1.0
C A:ASP176 3.3 38.7 1.0
CB A:ASP176 3.6 40.6 1.0
C A:ASP178 3.6 36.8 1.0
OD1 A:ASP176 3.7 41.9 1.0
C A:HIS180 3.7 42.8 1.0
C A:LEU200 3.8 44.0 1.0
CA A:ASP178 3.8 36.8 1.0
CB A:ASP178 3.9 37.1 1.0
C A:LEU177 3.9 37.4 1.0
N A:LEU177 3.9 37.6 1.0
CB A:HIS201 4.0 46.4 1.0
N A:LEU200 4.0 41.9 1.0
CA A:ASP176 4.1 40.1 1.0
CA A:LEU177 4.1 37.1 1.0
N A:GLY182 4.2 46.3 1.0
CA A:HIS181 4.2 43.8 1.0
CB A:SER199 4.2 42.8 1.0
ND1 A:HIS201 4.3 46.6 1.0
N A:HIS181 4.4 42.5 1.0
CA A:SER199 4.4 42.0 1.0
C A:SER199 4.5 41.9 1.0
C A:HIS181 4.5 45.7 1.0
CG A:HIS201 4.6 46.5 1.0
CA A:LEU200 4.6 42.6 1.0
CA A:HIS201 4.6 46.6 1.0
N A:HIS201 4.6 45.6 1.0
N A:HIS180 4.7 41.4 1.0
C A:LEU179 4.7 40.1 1.0
N A:LEU179 4.7 37.9 1.0
CE1 A:HIS142 4.7 50.9 1.0
CA A:HIS180 4.8 42.9 1.0
O A:HOH800 4.8 28.5 1.0
O A:LEU179 4.8 41.0 1.0
O A:LEU177 4.8 37.0 1.0
ND1 A:HIS142 4.9 50.7 1.0

Potassium binding site 2 out of 6 in 3f07

Go back to Potassium Binding Sites List in 3f07
Potassium binding site 2 out of 6 in the Crystal Structure Analysis of Human HDAC8 Complexed with Apha 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 Apha in A New Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K402

b:45.3
occ:1.00
 O A:PHE189 2.3 48.9 1.0
O A:TYR225 2.7 62.8 1.0
O A:VAL195 2.8 46.4 1.0
O A:THR192 3.1 52.0 1.0
C A:PHE189 3.4 49.0 1.0
CB A:TYR225 3.5 63.3 1.0
C A:TYR225 3.5 62.6 1.0
OG A:SER226 3.6 60.4 1.0
C A:VAL195 4.0 46.3 1.0
CA A:SER190 4.1 50.3 1.0
CA A:TYR225 4.1 62.9 1.0
CB A:PHE189 4.1 47.8 1.0
N A:SER190 4.2 49.8 1.0
O A:SER190 4.2 51.8 1.0
O A:GLY222 4.2 65.1 1.0
C A:SER190 4.2 50.9 1.0
C A:THR192 4.2 52.0 1.0
N A:SER226 4.4 61.8 1.0
CA A:PHE189 4.4 48.3 1.0
CA A:MET196 4.5 45.1 1.0
CG2 A:THR192 4.6 51.7 1.0
N A:THR192 4.6 52.3 1.0
N A:MET196 4.7 46.1 1.0
N A:THR197 4.7 44.1 1.0
CG A:TYR225 4.7 63.7 1.0
CB A:SER226 4.8 60.4 1.0
CA A:SER226 4.8 60.6 1.0
CA A:GLY222 4.8 64.2 1.0
CG2 A:THR197 4.8 42.4 1.0
OG1 A:THR197 4.9 45.5 1.0
CA A:THR192 4.9 52.1 1.0
N A:PHE191 5.0 51.7 1.0
C A:GLY222 5.0 64.9 1.0

Potassium binding site 3 out of 6 in 3f07

Go back to Potassium Binding Sites List in 3f07
Potassium binding site 3 out of 6 in the Crystal Structure Analysis of Human HDAC8 Complexed with Apha 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 Apha in A New Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K404

b:35.2
occ:1.00
 O B:HIS180 2.6 42.5 1.0
O B:LEU200 2.7 44.3 1.0
O B:ASP176 2.8 37.5 1.0
O B:ASP178 2.8 37.9 1.0
OG B:SER199 3.2 45.6 1.0
N B:ASP178 3.3 35.0 1.0
CG B:ASP176 3.3 40.9 1.0
C B:ASP176 3.3 38.3 1.0
OD2 B:ASP176 3.4 43.4 1.0
C B:ASP178 3.6 38.1 1.0
CB B:ASP176 3.6 40.4 1.0
C B:HIS180 3.7 43.2 1.0
OD1 B:ASP176 3.7 39.9 1.0
C B:LEU200 3.7 44.0 1.0
CA B:ASP178 3.8 36.8 1.0
C B:LEU177 3.9 34.7 1.0
CB B:ASP178 3.9 36.7 1.0
CB B:HIS201 3.9 47.5 1.0
N B:LEU177 3.9 36.4 1.0
N B:LEU200 4.0 42.2 1.0
CA B:ASP176 4.1 39.9 1.0
CA B:LEU177 4.1 35.4 1.0
N B:GLY182 4.2 46.4 1.0
CA B:HIS181 4.2 44.6 1.0
CB B:SER199 4.3 43.8 1.0
ND1 B:HIS201 4.3 47.1 1.0
N B:HIS181 4.4 43.5 1.0
C B:SER199 4.5 42.2 1.0
CA B:SER199 4.5 42.3 1.0
C B:HIS181 4.5 45.7 1.0
CG B:HIS201 4.6 47.3 1.0
CA B:HIS201 4.6 47.0 1.0
CA B:LEU200 4.6 42.8 1.0
N B:HIS201 4.6 45.5 1.0
N B:HIS180 4.6 41.4 1.0
C B:LEU179 4.7 40.3 1.0
N B:LEU179 4.7 39.4 1.0
O B:LEU179 4.7 40.5 1.0
CE1 B:HIS142 4.8 51.1 1.0
O B:LEU177 4.8 34.3 1.0
CA B:HIS180 4.8 43.1 1.0
O B:HOH804 4.9 37.1 1.0
ND1 B:HIS142 4.9 50.8 1.0

Potassium binding site 4 out of 6 in 3f07

Go back to Potassium Binding Sites List in 3f07
Potassium binding site 4 out of 6 in the Crystal Structure Analysis of Human HDAC8 Complexed with Apha 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 Apha in A New Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K405

b:47.6
occ:1.00
 O B:PHE189 2.3 48.2 1.0
O B:TYR225 2.7 61.9 1.0
O B:VAL195 2.8 45.4 1.0
O B:THR192 3.1 51.6 1.0
C B:PHE189 3.4 48.7 1.0
CB B:TYR225 3.5 63.0 1.0
C B:TYR225 3.5 61.8 1.0
OG B:SER226 3.6 61.7 1.0
C B:VAL195 4.0 46.4 1.0
CA B:SER190 4.1 50.2 1.0
CA B:TYR225 4.1 62.5 1.0
CB B:PHE189 4.1 46.9 1.0
N B:SER190 4.2 49.8 1.0
O B:SER190 4.2 50.5 1.0
C B:SER190 4.2 50.1 1.0
O B:GLY222 4.2 64.4 1.0
C B:THR192 4.2 51.1 1.0
N B:SER226 4.4 60.8 1.0
CA B:PHE189 4.4 47.8 1.0
CA B:MET196 4.5 45.7 1.0
N B:THR192 4.6 50.9 1.0
CG2 B:THR192 4.6 53.9 1.0
N B:THR197 4.7 43.5 1.0
N B:MET196 4.7 46.0 1.0
CG B:TYR225 4.7 62.1 1.0
CB B:SER226 4.7 60.5 1.0
CA B:SER226 4.8 59.5 1.0
CA B:GLY222 4.8 64.9 1.0
CG2 B:THR197 4.8 43.3 1.0
OG1 B:THR197 4.9 45.6 1.0
N B:PHE191 5.0 50.5 1.0
CA B:THR192 5.0 51.4 1.0
C B:GLY222 5.0 64.9 1.0

Potassium binding site 5 out of 6 in 3f07

Go back to Potassium Binding Sites List in 3f07
Potassium binding site 5 out of 6 in the Crystal Structure Analysis of Human HDAC8 Complexed with Apha 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 Apha in A New Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K407

b:38.6
occ:1.00
 O C:HIS180 2.6 45.5 1.0
O C:ASP176 2.8 39.5 1.0
O C:LEU200 2.8 45.6 1.0
O C:ASP178 2.9 41.6 1.0
OG C:SER199 3.2 45.3 1.0
CG C:ASP176 3.2 42.1 1.0
N C:ASP178 3.3 39.9 1.0
OD2 C:ASP176 3.3 42.0 1.0
C C:ASP176 3.3 41.1 1.0
CB C:ASP176 3.5 41.8 1.0
OD1 C:ASP176 3.6 42.9 1.0
C C:ASP178 3.6 41.2 1.0
C C:HIS180 3.7 45.9 1.0
C C:LEU200 3.8 45.5 1.0
CA C:ASP178 3.8 40.2 1.0
CB C:ASP178 3.9 39.9 1.0
N C:LEU177 3.9 39.9 1.0
C C:LEU177 4.0 39.4 1.0
CB C:HIS201 4.0 49.9 1.0
N C:LEU200 4.0 45.0 1.0
CA C:ASP176 4.1 42.4 1.0
N C:GLY182 4.1 49.7 1.0
CA C:LEU177 4.2 38.9 1.0
CA C:HIS181 4.2 47.6 1.0
CB C:SER199 4.2 44.8 1.0
ND1 C:HIS201 4.3 50.6 1.0
N C:HIS181 4.4 46.5 1.0
CA C:SER199 4.5 44.9 1.0
C C:HIS181 4.5 48.9 1.0
C C:SER199 4.5 44.8 1.0
CG C:HIS201 4.6 50.4 1.0
CA C:HIS201 4.6 50.3 1.0
CA C:LEU200 4.6 44.1 1.0
N C:HIS201 4.7 47.6 1.0
N C:HIS180 4.7 44.2 1.0
CE1 C:HIS142 4.7 55.9 1.0
C C:LEU179 4.7 43.5 1.0
N C:LEU179 4.8 41.5 1.0
O C:LEU179 4.8 42.6 1.0
CA C:HIS180 4.8 45.5 1.0
O C:LEU177 4.8 40.0 1.0
ND1 C:HIS142 4.9 56.9 1.0

Potassium binding site 6 out of 6 in 3f07

Go back to Potassium Binding Sites List in 3f07
Potassium binding site 6 out of 6 in the Crystal Structure Analysis of Human HDAC8 Complexed with Apha 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 Apha in A New Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K408

b:51.7
occ:1.00
 O C:PHE189 2.3 51.5 1.0
O C:TYR225 2.7 62.1 1.0
O C:VAL195 2.9 48.5 1.0
O C:THR192 3.1 55.1 1.0
CB C:TYR225 3.4 64.2 1.0
C C:TYR225 3.4 63.0 1.0
C C:PHE189 3.4 51.7 1.0
OG C:SER226 3.5 61.4 1.0
O C:HOH810 3.5 40.4 1.0
CA C:TYR225 4.0 63.9 1.0
CA C:SER190 4.0 54.5 1.0
C C:VAL195 4.1 48.7 1.0
O C:GLY222 4.1 67.1 1.0
O C:SER190 4.2 54.5 1.0
N C:SER190 4.2 52.7 1.0
C C:SER190 4.2 55.1 1.0
CB C:PHE189 4.2 50.0 1.0
C C:THR192 4.3 53.8 1.0
N C:SER226 4.3 62.5 1.0
CA C:PHE189 4.5 50.8 1.0
CA C:MET196 4.5 48.5 1.0
N C:THR192 4.6 53.4 1.0
CG2 C:THR192 4.6 53.0 1.0
CG C:TYR225 4.7 64.9 1.0
CB C:SER226 4.7 60.5 1.0
CA C:SER226 4.7 61.3 1.0
CA C:GLY222 4.7 66.5 1.0
N C:THR197 4.8 47.2 1.0
N C:MET196 4.8 48.5 1.0
C C:GLY222 4.9 66.9 1.0
CG2 C:THR197 4.9 45.4 1.0
N C:TYR225 4.9 65.3 1.0
OG1 C:THR197 4.9 47.9 1.0
N C:PHE191 5.0 55.1 1.0
CA C:THR192 5.0 53.6 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 08:14:09 2024

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