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Potassium in PDB 5dc8: Crystal Structure of H142A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate

Enzymatic activity of Crystal Structure of H142A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate

All present enzymatic activity of Crystal Structure of H142A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of H142A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 5dc8 was solved by C.Decroos, M.S.Lee, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.00 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.800, 97.887, 104.612, 90.00, 90.00, 90.00
R / Rfree (%) 12.8 / 14.9

Other elements in 5dc8:

The structure of Crystal Structure of H142A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of H142A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate (pdb code 5dc8). 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 of H142A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate, PDB code: 5dc8:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 5dc8

Go back to Potassium Binding Sites List in 5dc8
Potassium binding site 1 out of 4 in the Crystal Structure of H142A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate


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 H142A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K402

b:8.9
occ:1.00
 OD1 A:ASP176 2.7 10.3 1.0
O A:LEU200 2.7 9.6 1.0
O A:ASP178 2.7 8.8 1.0
O A:ASP176 2.8 9.2 1.0
O A:HIS180 2.8 8.7 1.0
OG A:SER199 2.9 10.3 1.0
CG A:ASP176 3.4 10.3 1.0
C A:ASP176 3.4 8.4 1.0
N A:ASP178 3.5 8.9 1.0
C A:ASP178 3.6 7.6 1.0
C A:LEU200 3.6 9.4 1.0
C A:HIS180 3.8 7.9 1.0
CB A:HIS201 3.8 8.4 1.0
CB A:ASP176 3.9 10.7 1.0
N A:LEU200 3.9 9.0 1.0
CA A:ASP178 3.9 9.5 1.0
C A:LEU177 4.0 9.2 1.0
CB A:ASP178 4.0 10.1 1.0
N A:LEU177 4.0 8.6 1.0
CB A:SER199 4.1 10.5 1.0
CA A:LEU177 4.2 9.1 1.0
CA A:ASP176 4.3 8.6 1.0
OD2 A:ASP176 4.3 12.4 1.0
ND1 A:HIS201 4.3 10.3 1.0
N A:GLY182 4.3 10.6 1.0
CA A:HIS201 4.3 8.6 1.0
CA A:SER199 4.3 9.2 1.0
CA A:HIS181 4.4 8.3 1.0
N A:HIS201 4.4 9.1 1.0
N A:HIS180 4.4 7.8 1.0
N A:HIS181 4.4 8.0 1.0
C A:SER199 4.5 9.4 1.0
O A:HOH704 4.5 14.6 1.0
CA A:LEU200 4.5 9.8 1.0
CG A:HIS201 4.5 8.8 1.0
O A:HOH578 4.6 10.4 1.0
C A:HIS181 4.7 9.1 1.0
C A:LEU179 4.7 7.5 1.0
N A:LEU179 4.7 7.7 1.0
O A:LEU177 4.7 9.7 1.0
CA A:HIS180 4.8 8.0 1.0

Potassium binding site 2 out of 4 in 5dc8

Go back to Potassium Binding Sites List in 5dc8
Potassium binding site 2 out of 4 in the Crystal Structure of H142A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate


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 H142A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K403

b:12.0
occ:1.00
 O A:VAL195 2.6 13.0 1.0
O A:PHE189 2.6 13.1 1.0
O A:HOH577 2.7 13.0 1.0
O A:THR192 2.8 15.8 1.0
O A:HOH739 2.8 13.1 1.0
O A:TYR225 3.0 12.4 1.0
C A:PHE189 3.6 12.0 1.0
CB A:TYR225 3.6 13.5 1.0
C A:TYR225 3.7 12.2 1.0
C A:VAL195 3.8 11.5 1.0
C A:THR192 4.0 14.6 1.0
CB A:PHE189 4.0 11.7 1.0
OG A:SER226 4.1 13.8 1.0
CA A:TYR225 4.3 12.9 1.0
N A:SER190 4.4 13.0 0.2
CA A:PHE189 4.4 11.1 1.0
CA A:SER190 4.4 14.0 0.2
CA A:MET196 4.4 11.6 0.7
O A:SER190 4.4 15.3 0.8
N A:SER190 4.4 12.4 0.8
CA A:SER190 4.5 13.3 0.8
C A:SER190 4.5 14.2 0.8
CA A:MET196 4.5 12.0 0.3
N A:SER226 4.5 12.0 1.0
N A:THR192 4.5 16.0 1.0
C A:SER190 4.6 14.3 0.2
CG2 A:THR192 4.6 20.6 1.0
N A:MET196 4.6 11.4 0.7
N A:MET196 4.6 11.7 0.3
O A:SER190 4.6 14.8 0.2
O A:GLY222 4.7 16.1 1.0
N A:THR197 4.7 11.1 1.0
CA A:THR192 4.8 15.8 1.0
CA A:VAL195 4.8 12.3 1.0
CG A:TYR225 4.9 14.0 1.0
CB A:VAL195 4.9 11.5 1.0
N A:SER193 4.9 14.0 1.0
OG1 A:THR197 4.9 14.3 1.0
N A:VAL195 5.0 12.2 1.0
C A:MET196 5.0 10.4 0.7

Potassium binding site 3 out of 4 in 5dc8

Go back to Potassium Binding Sites List in 5dc8
Potassium binding site 3 out of 4 in the Crystal Structure of H142A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate


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 H142A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K401

b:9.6
occ:1.00
 OD1 B:ASP176 2.6 11.3 1.0
O B:LEU200 2.7 9.8 1.0
O B:ASP178 2.7 9.3 1.0
O B:ASP176 2.8 9.5 1.0
O B:HIS180 2.8 9.6 1.0
OG B:SER199 2.9 10.8 1.0
CG B:ASP176 3.4 11.7 1.0
C B:ASP176 3.4 9.0 1.0
N B:ASP178 3.5 9.5 1.0
C B:ASP178 3.6 8.3 1.0
C B:LEU200 3.6 9.0 1.0
CB B:HIS201 3.8 9.5 1.0
C B:HIS180 3.8 8.9 1.0
CB B:ASP176 3.9 10.6 1.0
N B:LEU200 3.9 10.2 1.0
CA B:ASP178 3.9 9.2 1.0
CB B:ASP178 4.0 10.6 1.0
C B:LEU177 4.0 9.5 1.0
N B:LEU177 4.0 9.6 1.0
CB B:SER199 4.1 10.6 1.0
CA B:LEU177 4.2 9.5 1.0
N B:GLY182 4.3 11.0 1.0
CA B:ASP176 4.3 9.3 1.0
OD2 B:ASP176 4.3 13.6 1.0
ND1 B:HIS201 4.3 10.8 1.0
CA B:SER199 4.3 10.3 1.0
CA B:HIS201 4.3 8.6 1.0
CA B:HIS181 4.4 9.2 1.0
O B:HOH665 4.4 16.8 1.0
N B:HIS201 4.4 9.5 1.0
C B:SER199 4.4 10.0 1.0
N B:HIS181 4.5 8.8 1.0
CA B:LEU200 4.5 9.9 1.0
N B:HIS180 4.5 8.1 1.0
CG B:HIS201 4.5 9.6 1.0
O B:HOH579 4.6 10.8 1.0
C B:HIS181 4.7 10.2 1.0
C B:LEU179 4.7 8.3 1.0
N B:LEU179 4.7 8.0 1.0
O B:LEU177 4.7 10.2 1.0
CA B:HIS180 4.8 8.3 1.0

Potassium binding site 4 out of 4 in 5dc8

Go back to Potassium Binding Sites List in 5dc8
Potassium binding site 4 out of 4 in the Crystal Structure of H142A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate


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 H142A-Y306F HDAC8 in Complex with A Tetrapeptide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K403

b:13.0
occ:1.00
 O B:VAL195 2.6 14.7 1.0
O B:PHE189 2.6 12.8 1.0
O B:HOH582 2.7 13.3 1.0
O B:THR192 2.8 14.3 1.0
O B:HOH726 2.8 14.4 1.0
O B:TYR225 3.0 13.6 1.0
C B:PHE189 3.6 12.6 1.0
CB B:TYR225 3.6 14.1 1.0
C B:TYR225 3.7 13.1 1.0
C B:VAL195 3.8 12.8 1.0
C B:THR192 4.0 13.8 1.0
CB B:PHE189 4.1 13.5 1.0
OG B:SER226 4.1 15.6 1.0
CA B:TYR225 4.3 13.7 1.0
O B:SER190 4.4 14.3 0.8
CA B:MET196 4.4 12.4 0.7
CA B:SER190 4.4 14.6 0.2
N B:SER190 4.4 13.6 0.2
N B:SER190 4.4 12.6 0.8
CA B:SER190 4.4 13.5 0.8
CA B:PHE189 4.4 12.7 1.0
C B:SER190 4.5 13.4 0.8
CA B:MET196 4.5 14.2 0.3
N B:THR192 4.5 14.6 1.0
CG2 B:THR192 4.5 15.4 1.0
N B:SER226 4.5 12.9 1.0
C B:SER190 4.6 14.5 0.2
N B:MET196 4.6 12.7 0.7
N B:MET196 4.6 13.6 0.3
O B:GLY222 4.7 15.6 1.0
N B:THR197 4.7 11.8 1.0
O B:SER190 4.7 15.1 0.2
CA B:THR192 4.7 14.1 1.0
CA B:VAL195 4.8 13.2 1.0
CA B:GLY222 4.9 17.8 1.0
CG B:TYR225 4.9 15.5 1.0
OG1 B:THR197 4.9 15.4 1.0
C B:MET196 4.9 11.5 0.7
N B:VAL195 5.0 13.1 1.0
CB B:VAL195 5.0 13.6 1.0

Reference:

S.M.Gantt, C.Decroos, M.S.Lee, L.E.Gullett, C.M.Bowman, D.W.Christianson, C.A.Fierke. General Base-General Acid Catalysis in Human Histone Deacetylase 8. Biochemistry V. 55 820 2016.
ISSN: ISSN 0006-2960
PubMed: 26806311
DOI: 10.1021/ACS.BIOCHEM.5B01327
Page generated: Mon Aug 12 13:13:39 2024

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