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Potassium in PDB 6j6t: Crystal Structure of HDA15 Hd Domain

Enzymatic activity of Crystal Structure of HDA15 Hd Domain

All present enzymatic activity of Crystal Structure of HDA15 Hd Domain:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of HDA15 Hd Domain, PDB code: 6j6t was solved by Y.S.Cheng, J.C.Hsu, H.C.Hung, T.C.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.52 / 2.36
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.809, 78.833, 176.794, 90.00, 94.22, 90.00
R / Rfree (%) 16.7 / 21.8

Other elements in 6j6t:

The structure of Crystal Structure of HDA15 Hd Domain also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of HDA15 Hd Domain (pdb code 6j6t). 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 HDA15 Hd Domain, PDB code: 6j6t:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6j6t

Go back to Potassium Binding Sites List in 6j6t
Potassium binding site 1 out of 4 in the Crystal Structure of HDA15 Hd Domain


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 HDA15 Hd Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K602

b:17.5
occ:1.00
 O A:ASP313 2.6 11.6 1.0
O A:HIS315 2.8 13.9 1.0
O A:LEU335 2.8 13.0 1.0
O A:ASP311 2.9 12.3 1.0
OD1 A:ASP311 2.9 15.3 1.0
OG A:SER334 3.0 13.9 1.0
CG A:ASP311 3.2 15.2 1.0
C A:ASP311 3.6 11.2 1.0
C A:ASP313 3.6 12.7 1.0
C A:HIS315 3.7 12.8 1.0
C A:LEU335 3.8 12.4 1.0
OD2 A:ASP311 3.8 18.5 1.0
CB A:ASP311 3.8 14.3 1.0
N A:ASP313 3.8 12.9 1.0
CB A:HIS336 3.9 11.7 1.0
N A:LEU335 4.0 13.1 1.0
CB A:SER334 4.0 14.9 1.0
CA A:ASP313 4.0 13.0 1.0
CB A:ASP313 4.1 11.6 1.0
C A:TRP312 4.2 14.9 1.0
N A:TRP312 4.2 13.2 1.0
CA A:HIS316 4.2 13.9 1.0
ND1 A:HIS336 4.2 12.6 1.0
N A:HIS316 4.3 10.9 1.0
CA A:ASP311 4.3 11.5 1.0
CA A:SER334 4.3 13.4 1.0
CA A:TRP312 4.4 17.5 1.0
N A:HIS315 4.4 12.7 1.0
C A:SER334 4.5 13.4 1.0
CG A:HIS336 4.5 13.0 1.0
N A:GLY317 4.6 12.8 1.0
CA A:HIS336 4.6 14.9 1.0
CA A:LEU335 4.6 12.8 1.0
N A:HIS336 4.6 13.3 1.0
CE1 A:HIS276 4.7 13.8 1.0
N A:VAL314 4.7 13.1 1.0
C A:VAL314 4.7 14.3 1.0
CA A:HIS315 4.7 13.1 1.0
O A:HOH712 4.7 11.3 1.0
C A:HIS316 4.8 13.6 1.0
ND1 A:HIS276 4.8 15.8 1.0
O A:TRP312 4.9 13.0 1.0
OH A:TYR332 5.0 15.6 1.0

Potassium binding site 2 out of 4 in 6j6t

Go back to Potassium Binding Sites List in 6j6t
Potassium binding site 2 out of 4 in the Crystal Structure of HDA15 Hd Domain


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 HDA15 Hd Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K602

b:17.1
occ:1.00
 O B:ASP313 2.5 11.5 1.0
O B:HIS315 2.7 13.7 1.0
O B:LEU335 2.8 12.3 1.0
OD1 B:ASP311 2.8 18.5 1.0
O B:ASP311 2.8 14.8 1.0
OG B:SER334 3.0 17.5 1.0
CG B:ASP311 3.2 19.9 1.0
C B:ASP313 3.5 13.7 1.0
C B:ASP311 3.5 14.3 1.0
N B:ASP313 3.7 16.3 1.0
C B:LEU335 3.7 12.5 1.0
C B:HIS315 3.8 14.0 1.0
OD2 B:ASP311 3.8 21.9 1.0
CB B:ASP311 3.9 14.0 1.0
CB B:HIS336 3.9 13.0 1.0
CA B:ASP313 4.0 14.0 1.0
N B:LEU335 4.0 11.5 1.0
CB B:SER334 4.0 18.3 1.0
C B:TRP312 4.1 14.2 1.0
CB B:ASP313 4.1 12.8 1.0
N B:TRP312 4.2 14.1 1.0
CA B:TRP312 4.2 13.5 1.0
CA B:HIS316 4.3 15.8 1.0
CA B:ASP311 4.3 17.2 1.0
CA B:SER334 4.4 12.9 1.0
ND1 B:HIS336 4.4 15.1 1.0
N B:HIS316 4.4 12.9 1.0
C B:SER334 4.5 15.8 1.0
CA B:HIS336 4.5 16.1 1.0
N B:HIS336 4.5 13.6 1.0
N B:HIS315 4.5 13.5 1.0
CA B:LEU335 4.5 12.6 1.0
N B:GLY317 4.6 17.0 1.0
CG B:HIS336 4.6 15.8 1.0
O B:HOH704 4.6 13.1 1.0
N B:VAL314 4.6 12.9 1.0
C B:VAL314 4.7 14.9 1.0
O B:TRP312 4.7 15.9 1.0
CE1 B:HIS276 4.8 20.1 1.0
OH B:TYR332 4.8 18.4 1.0
CA B:HIS315 4.8 14.1 1.0
C B:HIS316 4.8 19.4 1.0
ND1 B:HIS276 4.9 17.2 1.0

Potassium binding site 3 out of 4 in 6j6t

Go back to Potassium Binding Sites List in 6j6t
Potassium binding site 3 out of 4 in the Crystal Structure of HDA15 Hd Domain


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 HDA15 Hd Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K602

b:33.2
occ:1.00
 O C:ASP313 2.7 29.7 1.0
OD1 C:ASP311 2.8 35.0 1.0
O C:HIS315 2.8 28.2 1.0
O C:ASP311 2.8 29.2 1.0
O C:LEU335 2.9 33.2 1.0
OG C:SER334 3.0 33.5 1.0
CG C:ASP311 3.1 39.0 1.0
C C:ASP311 3.5 27.7 1.0
OD2 C:ASP311 3.6 34.7 1.0
C C:ASP313 3.7 28.7 1.0
C C:LEU335 3.7 36.6 1.0
C C:HIS315 3.7 28.4 1.0
N C:ASP313 3.7 34.4 1.0
CB C:ASP311 3.8 33.4 1.0
CB C:HIS336 3.8 31.5 1.0
N C:LEU335 3.9 30.1 1.0
CA C:ASP313 4.1 31.0 1.0
C C:TRP312 4.1 36.4 1.0
CB C:SER334 4.1 33.4 1.0
N C:TRP312 4.2 23.6 1.0
CA C:HIS316 4.2 31.5 1.0
CB C:ASP313 4.2 29.8 1.0
CA C:TRP312 4.2 35.4 1.0
CA C:ASP311 4.3 28.9 1.0
N C:HIS316 4.3 23.6 1.0
ND1 C:HIS336 4.3 27.0 1.0
CA C:SER334 4.4 33.9 1.0
CA C:HIS336 4.4 38.1 1.0
N C:GLY317 4.4 32.7 1.0
O C:HOH701 4.4 30.4 1.0
N C:HIS336 4.4 32.6 1.0
C C:SER334 4.5 32.0 1.0
CA C:LEU335 4.5 35.4 1.0
CG C:HIS336 4.5 35.9 1.0
N C:HIS315 4.6 28.8 1.0
C C:HIS316 4.7 32.1 1.0
OH C:TYR332 4.7 34.9 1.0
CA C:HIS315 4.8 29.7 1.0
C C:VAL314 4.8 29.7 1.0
N C:VAL314 4.9 30.8 1.0
O C:TRP312 4.9 35.0 1.0
ND1 C:HIS276 5.0 28.3 1.0

Potassium binding site 4 out of 4 in 6j6t

Go back to Potassium Binding Sites List in 6j6t
Potassium binding site 4 out of 4 in the Crystal Structure of HDA15 Hd Domain


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 HDA15 Hd Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K602

b:20.4
occ:1.00
 O D:ASP313 2.6 17.7 1.0
OD1 D:ASP311 2.8 20.0 1.0
O D:ASP311 2.8 14.8 1.0
OG D:SER334 2.8 18.0 1.0
O D:LEU335 2.9 16.8 1.0
O D:HIS315 3.0 19.0 1.0
CG D:ASP311 3.3 20.7 1.0
C D:ASP311 3.5 16.0 1.0
C D:ASP313 3.6 16.6 1.0
N D:ASP313 3.7 18.9 1.0
CB D:ASP311 3.7 14.4 1.0
C D:LEU335 3.8 21.7 1.0
CB D:SER334 3.9 15.0 1.0
CB D:HIS336 3.9 17.4 1.0
C D:HIS315 3.9 18.6 1.0
N D:LEU335 3.9 16.1 1.0
CA D:ASP313 4.0 17.8 1.0
OD2 D:ASP311 4.0 20.2 1.0
CB D:ASP313 4.1 16.3 1.0
C D:TRP312 4.2 15.9 1.0
CA D:ASP311 4.2 17.3 1.0
N D:TRP312 4.2 15.7 1.0
CA D:SER334 4.3 14.1 1.0
CA D:TRP312 4.3 16.7 1.0
ND1 D:HIS336 4.4 18.5 1.0
CA D:HIS316 4.4 19.2 1.0
C D:SER334 4.4 19.1 1.0
N D:GLY317 4.5 15.1 1.0
CA D:LEU335 4.5 16.2 1.0
CA D:HIS336 4.5 21.9 1.0
N D:HIS316 4.5 17.3 1.0
N D:HIS315 4.6 16.3 1.0
N D:HIS336 4.6 18.3 1.0
CG D:HIS336 4.6 20.0 1.0
CE1 D:HIS276 4.7 17.9 1.0
OH D:TYR332 4.7 20.1 1.0
O D:HOH719 4.8 19.6 1.0
N D:VAL314 4.8 16.9 1.0
C D:HIS316 4.8 17.8 1.0
C D:VAL314 4.8 18.8 1.0
CA D:HIS315 4.9 15.5 1.0
ND1 D:HIS276 4.9 18.4 1.0
O D:TRP312 4.9 15.3 1.0

Reference:

Y.S.Cheng, Y.S.Cheng, J.C.Hsu, H.C.Hung, T.C.Liu. N/A N/A.
Page generated: Mon Aug 12 16:41:24 2024

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