Atomistry » Potassium » PDB 3du0-3f2t » 3f07
Atomistry »
  Potassium »
    PDB 3du0-3f2t »
      3f07 »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy