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Potassium in PDB 3mz4: Crystal Structure of D101L MN2+ HDAC8 Complexed with M344

Enzymatic activity of Crystal Structure of D101L MN2+ HDAC8 Complexed with M344

All present enzymatic activity of Crystal Structure of D101L MN2+ HDAC8 Complexed with M344:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of D101L MN2+ HDAC8 Complexed with M344, PDB code: 3mz4 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) 45.35 / 1.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.353, 91.148, 104.547, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 24.9

Other elements in 3mz4:

The structure of Crystal Structure of D101L MN2+ HDAC8 Complexed with M344 also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of D101L MN2+ HDAC8 Complexed with M344 (pdb code 3mz4). 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 D101L MN2+ HDAC8 Complexed with M344, PDB code: 3mz4:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 3mz4

Go back to Potassium Binding Sites List in 3mz4
Potassium binding site 1 out of 4 in the Crystal Structure of D101L MN2+ 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 D101L MN2+ HDAC8 Complexed with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K391

b:15.7
occ:1.00
 O A:LEU200 2.6 14.2 1.0
O A:ASP178 2.7 12.8 1.0
O A:HIS180 2.8 14.4 1.0
OG A:SER199 2.8 15.4 1.0
OD1 A:ASP176 2.8 13.1 1.0
O A:ASP176 2.9 13.6 1.0
C A:ASP176 3.5 14.2 1.0
CG A:ASP176 3.5 13.9 1.0
N A:ASP178 3.5 12.7 1.0
C A:ASP178 3.6 13.6 1.0
C A:LEU200 3.6 14.8 1.0
C A:HIS180 3.7 15.3 1.0
CB A:HIS201 3.8 12.4 1.0
CB A:ASP176 3.9 13.0 1.0
CA A:ASP178 3.9 12.9 1.0
N A:LEU200 3.9 13.4 1.0
CB A:ASP178 3.9 11.7 1.0
CB A:SER199 4.0 16.0 1.0
C A:LEU177 4.1 12.2 1.0
N A:LEU177 4.1 13.5 1.0
ND1 A:HIS201 4.2 14.8 1.0
CA A:LEU177 4.2 14.4 1.0
CA A:HIS201 4.3 14.1 1.0
N A:GLY182 4.3 14.2 1.0
CA A:SER199 4.3 13.8 1.0
CA A:ASP176 4.3 12.0 1.0
N A:HIS201 4.3 13.6 1.0
OD2 A:ASP176 4.4 11.8 1.0
CA A:HIS181 4.4 15.3 1.0
N A:HIS180 4.4 15.1 1.0
N A:HIS181 4.4 16.9 1.0
C A:SER199 4.4 14.7 1.0
CG A:HIS201 4.4 14.9 1.0
O A:HOH400 4.5 16.2 1.0
CA A:LEU200 4.5 14.3 1.0
C A:LEU179 4.6 15.8 1.0
C A:HIS181 4.7 15.8 1.0
CA A:HIS180 4.7 15.7 1.0
N A:LEU179 4.7 12.5 1.0
O A:LEU177 4.8 14.7 1.0
O A:LEU179 4.9 14.4 1.0
CE1 A:HIS142 5.0 11.0 1.0

Potassium binding site 2 out of 4 in 3mz4

Go back to Potassium Binding Sites List in 3mz4
Potassium binding site 2 out of 4 in the Crystal Structure of D101L MN2+ 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 D101L MN2+ HDAC8 Complexed with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K392

b:19.7
occ:1.00
 O A:VAL195 2.5 20.2 1.0
O A:PHE189 2.7 23.7 1.0
O A:HOH413 2.7 20.9 1.0
O A:HOH397 2.7 15.4 1.0
O A:THR192 2.9 22.7 1.0
O A:TYR225 3.0 17.3 1.0
C A:PHE189 3.6 21.8 1.0
CB A:TYR225 3.6 17.7 1.0
C A:TYR225 3.6 18.0 1.0
C A:VAL195 3.8 19.0 1.0
CB A:PHE189 4.1 19.7 1.0
C A:THR192 4.1 22.7 1.0
OG A:SER226 4.1 17.2 1.0
CA A:TYR225 4.2 19.6 1.0
CA A:MET196 4.4 18.9 1.0
CA A:SER190 4.4 24.2 1.0
N A:SER190 4.4 23.2 1.0
O A:SER190 4.4 24.4 1.0
N A:SER226 4.4 19.4 1.0
CA A:PHE189 4.5 20.7 1.0
C A:SER190 4.5 25.0 1.0
CG2 A:THR192 4.5 24.0 1.0
N A:MET196 4.5 18.8 1.0
N A:THR192 4.6 24.5 1.0
O A:GLY222 4.6 24.5 1.0
N A:THR197 4.7 16.5 1.0
CA A:VAL195 4.8 20.3 1.0
CA A:THR192 4.8 23.6 1.0
CG A:TYR225 4.9 21.7 1.0
C A:MET196 4.9 17.0 1.0
CB A:VAL195 4.9 20.7 1.0
N A:VAL195 5.0 20.0 1.0
CA A:GLY222 5.0 25.8 1.0

Potassium binding site 3 out of 4 in 3mz4

Go back to Potassium Binding Sites List in 3mz4
Potassium binding site 3 out of 4 in the Crystal Structure of D101L MN2+ 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 D101L MN2+ HDAC8 Complexed with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K391

b:14.3
occ:1.00
 O B:LEU200 2.6 15.3 1.0
OD1 B:ASP176 2.7 9.9 1.0
O B:ASP178 2.7 15.5 1.0
O B:HIS180 2.7 12.7 1.0
OG B:SER199 2.8 13.4 1.0
O B:ASP176 2.8 15.8 1.0
C B:ASP176 3.4 12.6 1.0
CG B:ASP176 3.5 15.8 1.0
N B:ASP178 3.5 12.8 1.0
C B:LEU200 3.6 12.6 1.0
C B:ASP178 3.7 14.9 1.0
C B:HIS180 3.7 13.2 1.0
CB B:ASP176 3.9 14.0 1.0
CB B:HIS201 3.9 12.6 1.0
N B:LEU200 3.9 12.2 1.0
CA B:ASP178 4.0 12.7 1.0
CB B:ASP178 4.0 11.3 1.0
CB B:SER199 4.0 11.7 1.0
C B:LEU177 4.0 13.6 1.0
N B:LEU177 4.1 13.7 1.0
N B:GLY182 4.2 14.4 1.0
CA B:LEU177 4.2 13.1 1.0
CA B:ASP176 4.3 14.7 1.0
ND1 B:HIS201 4.3 13.8 1.0
CA B:HIS181 4.3 15.1 1.0
CA B:SER199 4.3 13.8 1.0
CA B:HIS201 4.4 13.4 1.0
OD2 B:ASP176 4.4 14.0 1.0
N B:HIS181 4.4 12.5 1.0
N B:HIS201 4.4 13.8 1.0
C B:SER199 4.4 12.2 1.0
CA B:LEU200 4.5 12.8 1.0
N B:HIS180 4.5 15.2 1.0
O B:HOH394 4.5 17.0 1.0
C B:HIS181 4.6 14.2 1.0
CG B:HIS201 4.6 14.5 1.0
C B:LEU179 4.7 15.3 1.0
CA B:HIS180 4.8 15.0 1.0
O B:LEU177 4.8 13.1 1.0
N B:LEU179 4.8 13.1 1.0
CE1 B:HIS142 4.9 13.3 1.0

Potassium binding site 4 out of 4 in 3mz4

Go back to Potassium Binding Sites List in 3mz4
Potassium binding site 4 out of 4 in the Crystal Structure of D101L MN2+ 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 D101L MN2+ HDAC8 Complexed with M344 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K392

b:20.2
occ:1.00
 O B:VAL195 2.6 22.4 1.0
O B:HOH393 2.7 16.9 1.0
O B:PHE189 2.7 20.3 1.0
O B:HOH401 2.8 17.1 1.0
O B:THR192 2.8 20.8 1.0
O B:TYR225 3.0 18.5 1.0
CB B:TYR225 3.6 18.9 1.0
C B:PHE189 3.7 17.9 1.0
C B:TYR225 3.7 18.1 1.0
C B:VAL195 3.8 19.6 1.0
CB B:PHE189 4.0 18.8 1.0
C B:THR192 4.0 23.2 1.0
OG B:SER226 4.1 19.6 1.0
CA B:TYR225 4.3 18.6 1.0
CA B:SER190 4.4 20.9 1.0
O B:SER190 4.4 23.1 1.0
CA B:MET196 4.4 18.3 1.0
CA B:PHE189 4.5 17.8 1.0
C B:SER190 4.5 22.7 1.0
N B:SER190 4.5 18.1 1.0
N B:THR192 4.5 24.1 1.0
N B:SER226 4.5 17.9 1.0
CG2 B:THR192 4.6 21.3 1.0
N B:THR197 4.6 17.9 1.0
N B:MET196 4.6 19.0 1.0
O B:GLY222 4.6 23.4 1.0
CA B:THR192 4.7 23.4 1.0
CA B:VAL195 4.8 20.9 1.0
CG B:TYR225 4.9 17.9 1.0
OG1 B:THR197 4.9 19.5 1.0
CA B:GLY222 4.9 25.4 1.0
C B:MET196 5.0 19.5 1.0
N B:VAL195 5.0 21.4 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 08:47:33 2024

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