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Potassium in PDB 3mz3: Crystal Structure of CO2+ HDAC8 Complexed with M344

Enzymatic activity of Crystal Structure of CO2+ HDAC8 Complexed with M344

All present enzymatic activity of Crystal Structure of CO2+ HDAC8 Complexed with M344:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of CO2+ HDAC8 Complexed with M344, PDB code: 3mz3 was solved by D.P.Dowling, 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) 50.00 / 3.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.626, 86.143, 94.508, 90.00, 94.07, 90.00
R / Rfree (%) 20.4 / 25.6

Other elements in 3mz3:

The structure of Crystal Structure of CO2+ HDAC8 Complexed with M344 also contains other interesting chemical elements:

Cobalt (Co) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of CO2+ HDAC8 Complexed with M344 (pdb code 3mz3). 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 CO2+ HDAC8 Complexed with M344, PDB code: 3mz3:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 3mz3

Go back to Potassium Binding Sites List in 3mz3
Potassium binding site 1 out of 4 in the Crystal Structure of CO2+ HDAC8 Complexed with M344


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 CO2+ HDAC8 Complexed with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K402

b:53.8
occ:1.00
 OD1 A:ASP176 2.7 63.1 1.0
O A:ASP178 2.7 50.7 1.0
O A:ASP176 2.8 58.8 1.0
O A:LEU200 2.8 57.0 1.0
O A:HIS180 2.9 50.4 1.0
OG A:SER199 3.0 58.0 1.0
CG A:ASP176 3.3 62.9 1.0
C A:ASP176 3.3 58.2 1.0
N A:ASP178 3.4 53.4 1.0
CB A:ASP176 3.5 60.9 1.0
CB A:HIS201 3.6 56.9 1.0
C A:ASP178 3.6 49.9 1.0
C A:LEU200 3.6 56.4 1.0
C A:HIS180 3.9 49.0 1.0
CA A:ASP178 3.9 51.8 1.0
N A:LEU177 3.9 56.9 1.0
C A:LEU177 4.0 54.2 1.0
N A:LEU200 4.0 54.9 1.0
CB A:ASP178 4.1 52.4 1.0
CA A:ASP176 4.1 59.6 1.0
N A:GLY182 4.1 50.8 1.0
CA A:LEU177 4.1 54.9 1.0
CA A:HIS201 4.2 56.7 1.0
CB A:SER199 4.2 58.8 1.0
N A:HIS201 4.2 56.6 1.0
OD2 A:ASP176 4.3 63.6 1.0
ND1 A:HIS201 4.3 58.4 1.0
C A:SER199 4.4 56.1 1.0
CG A:HIS201 4.4 58.1 1.0
CA A:HIS181 4.4 49.6 1.0
CA A:SER199 4.4 57.7 1.0
N A:HIS181 4.5 49.6 1.0
N A:HIS180 4.5 47.1 1.0
CA A:LEU200 4.6 55.7 1.0
C A:HIS181 4.6 50.0 1.0
N A:LEU179 4.7 47.6 1.0
C A:LEU179 4.8 46.5 1.0
O A:LEU177 4.8 53.0 1.0
CA A:HIS180 4.8 48.5 1.0

Potassium binding site 2 out of 4 in 3mz3

Go back to Potassium Binding Sites List in 3mz3
Potassium binding site 2 out of 4 in the Crystal Structure of CO2+ HDAC8 Complexed with M344


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 CO2+ HDAC8 Complexed with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K404

b:67.3
occ:1.00
 O A:PHE189 2.6 76.2 1.0
O A:VAL195 2.6 72.6 1.0
O A:TYR225 2.7 83.4 1.0
O A:THR192 2.8 82.2 1.0
CB A:TYR225 3.5 88.0 1.0
C A:TYR225 3.5 83.7 1.0
C A:PHE189 3.6 75.3 1.0
OG A:SER226 3.7 76.1 1.0
C A:VAL195 3.8 74.2 1.0
C A:THR192 3.9 81.6 1.0
CG2 A:THR192 4.0 81.2 1.0
CA A:TYR225 4.1 85.8 1.0
CA A:SER190 4.2 77.9 1.0
CA A:MET196 4.2 73.4 1.0
O A:GLY222 4.2 93.6 1.0
CB A:PHE189 4.2 72.9 1.0
N A:SER190 4.3 76.3 1.0
N A:SER226 4.4 81.7 1.0
C A:SER190 4.4 79.8 1.0
O A:SER190 4.4 81.2 1.0
N A:THR192 4.5 81.0 1.0
N A:MET196 4.5 73.3 1.0
N A:THR197 4.6 69.2 1.0
CA A:PHE189 4.6 73.9 1.0
CA A:THR192 4.7 81.1 1.0
CA A:SER226 4.7 79.1 1.0
CB A:SER226 4.7 78.2 1.0
CG A:TYR225 4.8 90.2 1.0
CA A:GLY222 4.9 93.2 1.0
C A:MET196 4.9 71.9 1.0
N A:SER193 4.9 81.3 1.0
N A:TYR225 4.9 87.4 1.0
CA A:VAL195 4.9 75.7 1.0

Potassium binding site 3 out of 4 in 3mz3

Go back to Potassium Binding Sites List in 3mz3
Potassium binding site 3 out of 4 in the Crystal Structure of CO2+ HDAC8 Complexed with M344


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 CO2+ HDAC8 Complexed with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K403

b:53.8
occ:1.00
 O B:ASP178 2.7 51.4 1.0
O B:LEU200 2.7 58.0 1.0
OD1 B:ASP176 2.8 57.0 1.0
O B:ASP176 2.9 57.2 1.0
O B:HIS180 2.9 46.6 1.0
OG B:SER199 3.0 57.7 1.0
CB B:HIS201 3.4 55.7 1.0
CG B:ASP176 3.4 58.0 1.0
C B:ASP176 3.5 57.9 1.0
N B:ASP178 3.5 54.9 1.0
C B:LEU200 3.5 57.6 1.0
C B:ASP178 3.6 50.7 1.0
CB B:ASP176 3.7 58.7 1.0
C B:HIS180 3.8 47.3 1.0
N B:LEU200 4.0 57.4 1.0
CA B:ASP178 4.0 53.1 1.0
CA B:HIS201 4.0 55.1 1.0
C B:LEU177 4.0 55.4 1.0
N B:LEU177 4.1 56.9 1.0
N B:HIS201 4.1 56.6 1.0
N B:GLY182 4.1 54.2 1.0
CB B:SER199 4.1 60.6 1.0
CB B:ASP178 4.2 53.7 1.0
ND1 B:HIS201 4.2 56.2 1.0
CA B:ASP176 4.2 59.0 1.0
CG B:HIS201 4.2 56.1 1.0
CA B:LEU177 4.2 56.0 1.0
C B:SER199 4.3 57.9 1.0
CA B:HIS181 4.3 50.0 1.0
OD2 B:ASP176 4.4 58.7 1.0
CA B:SER199 4.4 59.3 1.0
N B:HIS181 4.4 48.0 1.0
N B:HIS180 4.5 46.0 1.0
O B:HOH409 4.5 54.2 1.0
CA B:LEU200 4.5 57.4 1.0
C B:HIS181 4.6 52.5 1.0
C B:LEU179 4.7 44.8 1.0
N B:LEU179 4.7 46.8 1.0
CA B:HIS180 4.7 46.8 1.0
O B:LEU177 4.9 55.0 1.0

Potassium binding site 4 out of 4 in 3mz3

Go back to Potassium Binding Sites List in 3mz3
Potassium binding site 4 out of 4 in the Crystal Structure of CO2+ HDAC8 Complexed with M344


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 CO2+ HDAC8 Complexed with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K405

b:72.2
occ:1.00
 O B:PHE189 2.5 75.4 1.0
O B:HOH393 2.6 61.4 1.0
O B:VAL195 2.6 72.5 1.0
O B:TYR225 2.7 82.2 1.0
O B:HOH395 2.8 54.6 1.0
O B:THR192 3.0 78.3 1.0
C B:PHE189 3.5 74.5 1.0
C B:TYR225 3.5 82.7 1.0
OG B:SER226 3.6 76.7 1.0
CB B:TYR225 3.7 86.5 1.0
C B:VAL195 3.8 73.0 1.0
CA B:SER190 4.1 76.4 1.0
CB B:PHE189 4.1 71.0 1.0
CG2 B:THR192 4.1 81.6 1.0
C B:THR192 4.1 79.2 1.0
N B:SER190 4.2 75.7 1.0
CA B:MET196 4.2 71.8 1.0
CA B:TYR225 4.2 84.5 1.0
N B:SER226 4.3 80.7 1.0
C B:SER190 4.4 77.2 1.0
O B:GLY222 4.4 94.0 1.0
O B:SER190 4.4 77.5 1.0
N B:THR197 4.4 68.7 1.0
CA B:PHE189 4.5 72.7 1.0
N B:MET196 4.5 72.0 1.0
N B:THR192 4.6 79.5 1.0
CB B:SER226 4.6 77.3 1.0
CA B:SER226 4.7 78.5 1.0
CA B:THR192 4.8 79.7 1.0
OG1 B:THR197 4.8 63.1 1.0
C B:MET196 4.8 71.1 1.0
CA B:VAL195 5.0 73.4 1.0

Reference:

D.P.Dowling, S.G.Gattis, C.A.Fierke, D.W.Christianson. Structures of Metal-Substituted Human Histone Deacetylase 8 Provide Mechanistic Inferences on Biological Function. Biochemistry V. 49 5048 2010.
ISSN: ISSN 0006-2960
PubMed: 20545365
DOI: 10.1021/BI1005046
Page generated: Mon Aug 12 08:47:20 2024

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