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Potassium in PDB 3f06: Crystal Structure Analysis of Human HDAC8 D101A Variant.

Enzymatic activity of Crystal Structure Analysis of Human HDAC8 D101A Variant.

All present enzymatic activity of Crystal Structure Analysis of Human HDAC8 D101A Variant.:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure Analysis of Human HDAC8 D101A Variant., PDB code: 3f06 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) 47.32 / 2.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.989, 85.875, 94.834, 90.00, 93.68, 90.00
R / Rfree (%) 22.8 / 25.9

Other elements in 3f06:

The structure of Crystal Structure Analysis of Human HDAC8 D101A Variant. also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure Analysis of Human HDAC8 D101A Variant. (pdb code 3f06). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure Analysis of Human HDAC8 D101A Variant., PDB code: 3f06:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 3f06

Go back to Potassium Binding Sites List in 3f06
Potassium binding site 1 out of 4 in the Crystal Structure Analysis of Human HDAC8 D101A Variant.


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 D101A Variant. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K405

b:57.0
occ:1.00
 O A:ASP178 2.7 58.0 1.0
O A:ASP176 2.8 63.5 1.0
OG A:SER199 2.8 62.5 1.0
O A:HIS180 2.8 53.5 1.0
O A:LEU200 2.9 63.6 1.0
OD1 A:ASP176 3.0 57.1 1.0
CB A:HIS201 3.5 62.4 1.0
C A:LEU200 3.5 63.2 1.0
N A:ASP178 3.5 60.8 1.0
CG A:ASP176 3.6 60.1 1.0
C A:ASP178 3.6 58.1 1.0
C A:ASP176 3.6 62.8 1.0
C A:HIS180 3.7 51.7 1.0
N A:LEU200 3.9 63.4 1.0
CB A:ASP176 3.9 61.0 1.0
CA A:HIS201 4.0 63.5 1.0
CA A:ASP178 4.0 58.8 1.0
N A:HIS201 4.0 62.8 1.0
CB A:SER199 4.1 64.0 1.0
C A:LEU177 4.1 61.1 1.0
CB A:ASP178 4.2 58.3 1.0
ND1 A:HIS201 4.2 61.4 1.0
CA A:HIS181 4.2 53.7 1.0
CG A:HIS201 4.3 61.3 1.0
N A:HIS181 4.3 52.5 1.0
C A:SER199 4.3 64.3 1.0
N A:LEU177 4.3 61.4 1.0
OD2 A:ASP176 4.3 60.9 1.0
CA A:SER199 4.4 63.8 1.0
CA A:LEU177 4.4 61.5 1.0
N A:GLY182 4.4 57.3 1.0
N A:HIS180 4.4 54.0 1.0
CA A:LEU200 4.4 63.9 1.0
CA A:ASP176 4.4 62.8 1.0
O A:HOH390 4.6 68.6 1.0
CA A:HIS180 4.6 50.9 1.0
C A:HIS181 4.7 56.4 1.0
C A:LEU179 4.7 55.9 1.0
N A:LEU179 4.7 56.8 1.0
O A:LEU177 4.9 63.0 1.0

Potassium binding site 2 out of 4 in 3f06

Go back to Potassium Binding Sites List in 3f06
Potassium binding site 2 out of 4 in the Crystal Structure Analysis of Human HDAC8 D101A Variant.


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 D101A Variant. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K406

b:76.9
occ:1.00
 O A:TYR225 2.6 86.2 1.0
O A:PHE189 2.7 80.8 1.0
O A:VAL195 2.7 76.3 1.0
O A:THR192 2.8 82.0 1.0
C A:PHE189 3.7 79.7 1.0
C A:TYR225 3.7 86.5 1.0
CB A:TYR225 3.7 92.0 1.0
C A:VAL195 3.9 76.5 1.0
OG A:SER226 4.0 79.7 1.0
C A:THR192 4.0 83.1 1.0
CB A:PHE189 4.1 78.0 1.0
CA A:SER190 4.3 82.2 1.0
CA A:MET196 4.3 75.5 1.0
CA A:TYR225 4.3 88.8 1.0
N A:SER190 4.4 81.0 1.0
C A:SER190 4.6 82.5 1.0
CA A:PHE189 4.6 78.8 1.0
N A:MET196 4.6 75.2 1.0
N A:THR192 4.7 83.4 1.0
N A:SER226 4.7 83.8 1.0
N A:THR197 4.7 73.5 1.0
O A:GLY222 4.7 92.7 1.0
O A:SER190 4.8 83.0 1.0
CG2 A:THR192 4.8 83.8 1.0
CA A:THR192 4.9 83.2 1.0
N A:SER193 4.9 83.0 1.0
CA A:SER193 5.0 82.5 1.0
CG A:TYR225 5.0 94.9 1.0
C A:MET196 5.0 75.0 1.0

Potassium binding site 3 out of 4 in 3f06

Go back to Potassium Binding Sites List in 3f06
Potassium binding site 3 out of 4 in the Crystal Structure Analysis of Human HDAC8 D101A Variant.


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 D101A Variant. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K402

b:59.6
occ:1.00
 O B:ASP178 2.6 58.8 1.0
O B:ASP176 2.7 62.6 1.0
O B:LEU200 2.9 64.4 1.0
OD1 B:ASP176 2.9 59.4 1.0
O B:HIS180 2.9 57.8 1.0
OG B:SER199 3.0 63.9 1.0
N B:ASP178 3.3 58.3 1.0
C B:ASP176 3.5 61.9 1.0
CG B:ASP176 3.5 62.1 1.0
C B:ASP178 3.5 58.5 1.0
C B:LEU200 3.6 64.1 1.0
CB B:HIS201 3.6 65.5 1.0
C B:HIS180 3.8 55.0 1.0
CA B:ASP178 3.8 57.5 1.0
CB B:ASP176 3.9 60.9 1.0
N B:LEU200 3.9 63.6 1.0
C B:LEU177 3.9 59.4 1.0
CB B:ASP178 4.0 58.3 1.0
CA B:HIS201 4.1 65.7 1.0
N B:LEU177 4.1 60.8 1.0
N B:HIS201 4.1 64.4 1.0
CB B:SER199 4.2 64.8 1.0
CA B:LEU177 4.2 59.9 1.0
OD2 B:ASP176 4.3 62.2 1.0
CA B:ASP176 4.3 61.5 1.0
C B:SER199 4.4 64.3 1.0
ND1 B:HIS201 4.4 65.5 1.0
CA B:SER199 4.4 64.4 1.0
O B:HOH396 4.4 70.4 1.0
CA B:HIS181 4.4 56.0 1.0
N B:HIS180 4.5 54.8 1.0
N B:HIS181 4.5 56.0 1.0
CA B:LEU200 4.5 63.7 1.0
CG B:HIS201 4.5 65.9 1.0
N B:GLY182 4.5 58.1 1.0
N B:LEU179 4.6 58.0 1.0
O B:LEU177 4.7 61.3 1.0
C B:LEU179 4.7 57.2 1.0
CA B:HIS180 4.7 53.3 1.0
C B:HIS181 4.8 57.1 1.0

Potassium binding site 4 out of 4 in 3f06

Go back to Potassium Binding Sites List in 3f06
Potassium binding site 4 out of 4 in the Crystal Structure Analysis of Human HDAC8 D101A Variant.


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 D101A Variant. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K403

b:76.0
occ:1.00
 O B:PHE189 2.6 81.1 1.0
O B:TYR225 2.7 87.8 1.0
O B:VAL195 2.7 78.1 1.0
O B:HOH395 2.8 86.8 1.0
O B:THR192 2.9 84.3 1.0
C B:PHE189 3.5 80.7 1.0
C B:TYR225 3.7 87.2 1.0
CB B:TYR225 3.9 92.2 1.0
OG B:SER226 3.9 79.4 1.0
C B:VAL195 3.9 78.5 1.0
CB B:PHE189 4.0 77.9 1.0
C B:THR192 4.1 84.1 1.0
CA B:SER190 4.2 83.1 1.0
N B:SER190 4.3 81.4 1.0
CA B:MET196 4.3 77.5 1.0
CA B:TYR225 4.5 89.3 1.0
CA B:PHE189 4.5 79.1 1.0
C B:SER190 4.5 83.4 1.0
N B:THR197 4.6 74.5 1.0
N B:MET196 4.6 77.4 1.0
N B:THR192 4.7 84.6 1.0
N B:SER226 4.7 83.9 1.0
O B:SER190 4.7 83.7 1.0
O B:GLY222 4.8 93.2 1.0
CG2 B:THR192 4.8 85.0 1.0
CA B:THR192 5.0 84.5 1.0
OG1 B:THR197 5.0 72.3 1.0
CB B:SER226 5.0 80.0 1.0
C B:MET196 5.0 76.8 1.0
CA B:SER226 5.0 80.9 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 08:13:55 2024

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