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Potassium in PDB 9gky: Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid

Protein crystallography data

The structure of Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid, PDB code: 9gky was solved by L.G.Graf, S.Schulze, G.J.Palm, M.Lammers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.14 / 1.13
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.11, 51.15, 108.82, 90, 102.22, 90
R / Rfree (%) 15.8 / 17.9

Other elements in 9gky:

The structure of Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid (pdb code 9gky). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 9 binding sites of Potassium where determined in the Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid, PDB code: 9gky:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Potassium binding site 1 out of 9 in 9gky

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Potassium binding site 1 out of 9 in the Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid


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 Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K405

b:17.5
occ:1.00
O A:ILE191 2.6 16.6 1.0
O A:HOH599 2.6 36.6 1.0
O A:ARG188 2.6 21.4 1.0
O A:CYS185 2.7 17.8 1.0
O A:HOH687 2.9 32.0 1.0
O A:HOH529 3.1 31.5 1.0
C A:ARG188 3.6 24.0 1.0
HA A:ASP189 3.7 21.9 1.0
H A:ARG188 3.7 23.6 0.6
H A:ARG188 3.7 24.0 0.4
HA A:ALA186 3.8 17.6 1.0
C A:CYS185 3.8 16.6 1.0
C A:ILE191 3.8 14.3 1.0
HB3 A:CYS185 3.9 16.4 1.0
HA A:ILE192 3.9 13.2 1.0
HB2 A:ARG188 4.0 23.1 0.6
HD13 A:ILE192 4.0 17.4 1.0
H A:ILE191 4.1 14.9 1.0
O A:ALA186 4.1 22.8 1.0
HG A:SER210 4.1 10.2 0.0
OG A:SER210 4.2 14.6 1.0
C A:ALA186 4.2 18.6 1.0
HB2 A:ARG188 4.2 26.7 0.4
N A:ARG188 4.2 24.3 1.0
O A:HOH639 4.3 21.3 1.0
HB A:ILE191 4.3 14.8 1.0
CA A:ALA186 4.3 17.3 1.0
N A:ASP189 4.4 20.8 1.0
CA A:ASP189 4.4 21.1 1.0
CA A:ARG188 4.4 23.0 0.6
CA A:ARG188 4.5 24.7 0.4
N A:ALA186 4.5 16.3 1.0
CB A:CYS185 4.6 16.1 1.0
HG1 A:THR193 4.6 7.6 0.0
HB2 A:CYS185 4.7 16.1 1.0
N A:ILE191 4.7 14.2 1.0
CB A:ARG188 4.7 23.1 0.6
H A:THR193 4.7 11.7 1.0
N A:ILE192 4.7 13.1 1.0
CA A:ILE192 4.7 12.6 1.0
CA A:ILE191 4.7 14.3 1.0
C A:ASP189 4.8 20.8 1.0
CA A:CYS185 4.8 15.4 1.0
N A:GLU187 4.9 19.1 1.0
CB A:ARG188 4.9 27.0 0.4
CD1 A:ILE192 4.9 17.9 1.0
HD11 A:ILE192 5.0 17.6 1.0
CB A:ILE191 5.0 14.6 1.0

Potassium binding site 2 out of 9 in 9gky

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Potassium binding site 2 out of 9 in the Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid


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 Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K406

b:9.6
occ:0.90
O A:PHE196 2.6 10.5 1.0
O A:ASP174 2.6 10.2 1.0
O A:HIS176 2.7 10.6 1.0
OD1 A:ASP172 2.8 10.6 1.0
OG A:SER195 2.8 10.7 1.0
O A:ASP172 2.9 10.2 1.0
HG A:SER195 3.2 8.5 0.0
CG A:ASP172 3.2 10.6 1.0
HB3 A:HIS197 3.2 10.2 1.0
HD1 A:HIS197 3.5 7.8 0.0
HA A:HIS177 3.5 10.3 1.0
H A:PHE196 3.5 9.8 1.0
C A:ASP172 3.6 9.9 1.0
HB3 A:ASP174 3.6 10.2 1.0
C A:HIS176 3.6 10.6 1.0
C A:ASP174 3.7 10.2 1.0
OD2 A:ASP172 3.7 12.9 1.0
HB3 A:ASP172 3.7 10.2 1.0
C A:PHE196 3.7 10.9 1.0
H A:ASP174 3.7 9.8 1.0
N A:ASP174 3.8 9.8 1.0
H A:GLY178 3.8 10.6 1.0
CB A:ASP172 3.9 10.1 1.0
HE1 A:HIS136 3.9 11.4 1.0
HA A:SER195 3.9 9.8 1.0
N A:PHE196 3.9 10.1 1.0
CB A:SER195 4.0 10.6 1.0
HA A:SER173 4.0 10.4 0.5
HD1 A:HIS136 4.1 9.8 0.0
CB A:HIS197 4.1 10.4 1.0
HA A:SER173 4.2 10.3 0.5
CA A:ASP174 4.2 9.7 1.0
CA A:HIS177 4.2 10.0 1.0
N A:GLY178 4.2 10.5 1.0
C A:SER173 4.2 9.9 1.0
ND1 A:HIS197 4.3 10.4 1.0
N A:SER173 4.3 10.0 1.0
HA A:HIS197 4.3 10.4 1.0
N A:HIS177 4.3 10.4 1.0
CA A:ASP172 4.3 9.5 1.0
CA A:SER195 4.4 9.9 1.0
HB2 A:SER195 4.4 10.4 1.0
CB A:ASP174 4.4 10.0 1.0
N A:HIS176 4.4 10.1 1.0
H A:HIS176 4.4 10.1 1.0
CA A:SER173 4.4 10.1 0.5
CA A:SER173 4.5 10.1 0.5
C A:HIS177 4.5 10.4 1.0
CA A:PHE196 4.5 9.6 1.0
C A:SER195 4.5 10.0 1.0
CE1 A:HIS136 4.6 11.4 1.0
CA A:HIS197 4.6 10.6 1.0
N A:HIS197 4.6 10.5 1.0
ND1 A:HIS136 4.6 11.5 1.0
CA A:HIS176 4.7 10.4 1.0
CG A:HIS197 4.7 10.0 1.0
C A:VAL175 4.7 10.2 1.0
O A:HOH704 4.7 14.8 1.0
HB2 A:PHE196 4.7 10.0 1.0
N A:VAL175 4.7 9.6 1.0
HB2 A:HIS197 4.8 10.3 1.0
HB3 A:SER195 4.8 10.7 1.0
HB2 A:ASP172 4.8 10.1 1.0
HA3 A:GLY178 4.9 10.5 1.0
HA A:ASP172 4.9 9.4 1.0
H A:SER173 4.9 9.9 0.5
H A:SER173 4.9 9.9 0.5
O A:SER173 5.0 12.4 1.0
HA A:VAL175 5.0 10.1 1.0

Potassium binding site 3 out of 9 in 9gky

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Potassium binding site 3 out of 9 in the Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid


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 Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K407

b:24.9
occ:0.70
O A:HOH794 2.4 36.5 1.0
O A:LEU162 2.5 26.1 1.0
O A:LEU160 2.5 19.3 1.0
O A:VAL165 2.5 19.2 1.0
O A:HOH538 2.6 42.4 1.0
O A:HOH782 2.9 34.8 1.0
OD1 A:ASP166 3.5 30.0 1.0
C A:LEU160 3.5 19.2 1.0
H A:VAL165 3.6 21.1 1.0
C A:VAL165 3.6 17.5 1.0
C A:LEU162 3.7 27.7 1.0
HA A:LEU160 3.7 16.1 1.0
HA A:ASP166 3.8 17.8 1.0
HA A:PRO163 4.0 30.4 1.0
N A:LEU162 4.1 22.6 1.0
H A:LEU162 4.1 22.7 1.0
N A:VAL165 4.2 21.0 1.0
CA A:LEU160 4.2 15.7 1.0
O A:PRO163 4.3 30.3 1.0
HB A:VAL165 4.3 17.6 1.0
C A:SER161 4.3 24.0 1.0
HA A:SER161 4.4 22.8 1.0
CA A:VAL165 4.4 17.5 1.0
C A:PRO163 4.4 27.5 1.0
N A:ASP166 4.5 16.4 1.0
N A:SER161 4.5 20.9 1.0
CA A:PRO163 4.5 30.6 1.0
CG A:ASP166 4.5 26.5 1.0
N A:PRO163 4.5 28.9 1.0
CA A:LEU162 4.6 23.8 1.0
O A:HOH815 4.6 46.0 1.0
CA A:ASP166 4.6 17.8 1.0
HD21 A:LEU160 4.6 17.5 1.0
HB3 A:LEU160 4.6 16.7 1.0
CA A:SER161 4.6 21.9 1.0
O A:SER161 4.8 25.7 1.0
O A:ALA159 4.8 15.6 1.0
CB A:VAL165 4.9 17.4 1.0

Potassium binding site 4 out of 9 in 9gky

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Potassium binding site 4 out of 9 in the Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid


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 Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K408

b:15.6
occ:0.80
O A:HOH798 2.7 26.6 1.0
O A:GLY259 2.7 12.1 1.0
O A:LEU261 2.8 13.3 1.0
O A:ASN254 2.8 12.4 1.0
O A:HOH640 2.9 11.9 1.0
O A:HIS253 2.9 10.9 1.0
C A:ASN254 3.4 12.5 1.0
HA A:ASN254 3.4 13.1 1.0
O A:HOH759 3.5 30.4 1.0
HB3 A:ASP256 3.5 11.1 1.0
H A:ASP256 3.5 11.4 1.0
O A:ASP256 3.6 12.2 1.0
C A:GLY259 3.6 11.2 1.0
HA A:TYR260 3.7 13.1 1.0
H A:LEU261 3.8 12.4 1.0
CA A:ASN254 3.8 13.1 1.0
O A:HOH517 3.9 14.6 1.0
N A:ASP256 3.9 11.2 1.0
C A:LEU261 3.9 12.8 1.0
N A:LEU261 3.9 12.6 1.0
C A:HIS253 4.0 10.4 1.0
O A:HOH605 4.0 18.1 1.0
C A:TYR260 4.2 13.7 1.0
CB A:ASP256 4.2 10.7 1.0
N A:TYR260 4.2 11.8 1.0
CA A:TYR260 4.2 12.7 1.0
N A:ASP255 4.2 11.8 1.0
HB2 A:ASP256 4.3 10.9 1.0
N A:ASN254 4.3 11.7 1.0
C A:ASP256 4.4 12.2 1.0
CA A:ASP256 4.4 11.4 1.0
HA3 A:GLY259 4.4 11.0 1.0
O A:HOH722 4.4 22.1 1.0
HA A:SER262 4.5 13.1 1.0
CA A:GLY259 4.5 11.1 1.0
O A:HOH725 4.6 27.3 1.0
CA A:LEU261 4.6 11.9 1.0
C A:ASP255 4.6 12.2 1.0
HA A:ASP255 4.6 12.4 1.0
CA A:ASP255 4.8 11.9 1.0
H A:ASP255 4.8 11.8 1.0
N A:GLY259 4.9 11.3 1.0
H A:GLY259 4.9 11.4 1.0
O A:TYR260 4.9 15.3 1.0
O A:ILE252 4.9 11.0 1.0
H A:TYR260 5.0 11.7 1.0
N A:SER262 5.0 13.2 1.0

Potassium binding site 5 out of 9 in 9gky

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Potassium binding site 5 out of 9 in the Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K409

b:22.0
occ:0.80
O A:SER22 2.7 15.1 1.0
O A:LEU24 2.8 22.5 1.0
O A:HOH786 2.8 39.5 1.0
OD1 A:ASN35 2.9 17.0 1.0
HG22 A:ILE34 3.3 14.0 1.0
HG21 A:ILE34 3.4 14.1 1.0
HA A:ASP25 3.8 28.1 1.0
CG2 A:ILE34 3.8 14.1 1.0
C A:LEU24 3.8 22.6 1.0
C A:SER22 3.9 14.8 1.0
CG A:ASN35 3.9 14.9 1.0
HD21 A:ASN35 3.9 17.5 1.0
HG13 A:ILE34 3.9 15.4 1.0
O A:HOH582 3.9 19.4 0.5
HB3 A:SER22 4.1 12.0 1.0
HG12 A:ILE34 4.2 15.7 1.0
HH12 A:ARG38 4.2 18.9 0.5
ND2 A:ASN35 4.2 18.3 1.0
HA A:GLN23 4.3 17.9 1.0
C A:GLN23 4.3 21.1 1.0
N A:LEU24 4.4 18.5 1.0
H A:LEU26 4.4 24.1 1.0
CG1 A:ILE34 4.4 15.4 1.0
O A:GLN23 4.5 24.2 1.0
HG23 A:ILE34 4.5 14.0 1.0
CA A:ASP25 4.6 28.5 1.0
N A:ASP25 4.6 24.6 1.0
H A:LEU24 4.6 19.2 1.0
CA A:GLN23 4.7 17.1 1.0
CB A:ILE34 4.7 13.2 1.0
HA A:SER22 4.7 12.1 1.0
HA A:ASN35 4.7 11.6 1.0
N A:GLN23 4.7 15.0 1.0
HH11 A:ARG38 4.7 18.9 0.5
CA A:LEU24 4.8 20.8 1.0
CA A:SER22 4.8 11.9 1.0
NH1 A:ARG38 4.8 18.4 0.5
O A:HOH744 4.8 28.3 1.0
CB A:SER22 4.9 11.8 1.0
HD22 A:ASN35 5.0 17.1 1.0
OD1 A:ASP25 5.0 42.2 1.0

Potassium binding site 6 out of 9 in 9gky

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Potassium binding site 6 out of 9 in the Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K406

b:10.8
occ:0.90
O B:PHE196 2.6 10.6 1.0
O B:ASP174 2.6 11.5 1.0
O B:HIS176 2.7 11.6 1.0
OD1 B:ASP172 2.8 12.1 1.0
OG B:SER195 2.8 10.9 1.0
O B:ASP172 2.9 11.1 1.0
HG B:SER195 3.1 7.2 0.0
HB3 B:HIS197 3.2 10.8 1.0
CG B:ASP172 3.2 12.2 1.0
HA B:HIS177 3.5 11.3 1.0
HD1 B:HIS197 3.6 7.5 0.0
H B:PHE196 3.6 10.1 1.0
C B:ASP172 3.6 10.9 1.0
C B:HIS176 3.6 10.4 1.0
OD2 B:ASP172 3.6 13.5 1.0
C B:ASP174 3.7 11.2 1.0
HB3 B:ASP172 3.7 12.0 1.0
HB3 B:ASP174 3.7 11.4 1.0
C B:PHE196 3.7 10.9 1.0
H B:ASP174 3.7 10.9 1.0
H B:GLY178 3.7 11.8 1.0
N B:ASP174 3.8 10.9 1.0
HE1 B:HIS136 3.8 12.6 1.0
CB B:ASP172 3.9 12.0 1.0
HA B:SER195 3.9 10.6 1.0
N B:PHE196 4.0 10.0 1.0
CB B:SER195 4.0 11.7 1.0
HA B:SER173 4.0 11.1 0.5
CB B:HIS197 4.1 11.1 1.0
HD1 B:HIS136 4.1 9.5 0.0
HA B:SER173 4.2 11.2 0.5
CA B:ASP174 4.2 10.7 1.0
N B:GLY178 4.2 12.0 1.0
CA B:HIS177 4.2 11.2 1.0
HA B:HIS197 4.2 10.6 1.0
C B:SER173 4.2 11.0 1.0
N B:SER173 4.3 10.0 1.0
N B:HIS177 4.3 11.2 1.0
ND1 B:HIS197 4.3 11.5 1.0
HB2 B:SER195 4.3 11.4 1.0
CA B:ASP172 4.4 10.9 1.0
CA B:SER195 4.4 10.7 1.0
CB B:ASP174 4.4 11.4 1.0
N B:HIS176 4.4 10.2 1.0
CA B:SER173 4.4 11.1 0.5
CA B:SER173 4.5 11.2 0.5
H B:HIS176 4.5 10.4 1.0
C B:HIS177 4.5 11.6 1.0
CA B:PHE196 4.5 10.4 1.0
CE1 B:HIS136 4.5 12.6 1.0
CA B:HIS197 4.5 10.9 1.0
C B:SER195 4.5 10.9 1.0
N B:HIS197 4.6 10.5 1.0
ND1 B:HIS136 4.6 12.7 1.0
C B:VAL175 4.6 10.9 1.0
CA B:HIS176 4.7 11.3 1.0
HB2 B:PHE196 4.7 10.4 1.0
HB2 B:HIS197 4.7 11.0 1.0
CG B:HIS197 4.7 10.7 1.0
O B:HOH740 4.7 14.4 1.0
N B:VAL175 4.7 10.8 1.0
HB2 B:ASP172 4.8 11.9 1.0
HB3 B:SER195 4.8 11.6 1.0
HA3 B:GLY178 4.9 11.7 1.0
HA B:ASP172 4.9 10.9 1.0
H B:SER173 4.9 10.3 0.5
H B:SER173 4.9 10.3 0.5
O B:SER173 5.0 12.4 1.0
HA B:VAL175 5.0 10.8 1.0

Potassium binding site 7 out of 9 in 9gky

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Potassium binding site 7 out of 9 in the Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K407

b:20.9
occ:0.80
O B:CYS185 2.4 20.8 1.0
O B:HOH818 2.5 26.9 1.0
O B:ILE191 2.6 19.0 1.0
O B:ARG188 2.6 29.2 1.0
O B:HOH646 2.7 29.2 1.0
HB3 B:CYS185 3.5 17.9 1.0
C B:CYS185 3.6 17.9 1.0
H B:ARG188 3.7 30.7 1.0
C B:ARG188 3.7 31.0 1.0
O B:HOH575 3.8 22.9 1.0
HB2 B:ARG188 3.8 32.8 1.0
C B:ILE191 3.8 16.5 1.0
HA B:ASP189 3.8 28.2 1.0
HA B:ILE192 3.9 14.8 1.0
O B:HOH791 3.9 45.9 1.0
HA B:ALA186 3.9 21.4 1.0
HD13 B:ILE192 4.0 19.9 1.0
H B:ILE191 4.1 18.2 1.0
HG B:SER210 4.2 8.8 0.0
O B:HOH577 4.2 19.6 0.5
O B:ALA186 4.2 26.9 1.0
N B:ARG188 4.2 31.5 1.0
OG B:SER210 4.2 15.2 1.0
C B:ALA186 4.3 24.8 1.0
CB B:CYS185 4.3 17.7 1.0
HB B:ILE191 4.4 16.7 1.0
CA B:ALA186 4.4 21.0 1.0
CA B:ARG188 4.4 31.1 1.0
HB2 B:CYS185 4.5 17.6 1.0
N B:ALA186 4.5 20.0 1.0
CA B:CYS185 4.5 17.5 1.0
N B:ASP189 4.5 28.1 1.0
CA B:ASP189 4.6 27.4 1.0
CB B:ARG188 4.6 33.4 1.0
HG1 B:THR193 4.6 7.6 0.0
CA B:ILE192 4.7 14.3 1.0
N B:ILE192 4.7 14.7 1.0
H B:THR193 4.7 13.1 1.0
N B:ILE191 4.7 17.5 1.0
HA B:CYS185 4.8 17.7 1.0
CA B:ILE191 4.8 16.6 1.0
N B:GLU187 4.8 25.0 1.0
HG22 B:THR193 4.9 13.5 1.0
CD1 B:ILE192 4.9 20.7 1.0
HB3 B:ARG188 4.9 33.3 1.0
C B:ASP189 5.0 26.4 1.0
O B:HOH537 5.0 18.8 0.5
O A:HOH671 5.0 21.9 1.0

Potassium binding site 8 out of 9 in 9gky

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Potassium binding site 8 out of 9 in the Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K408

b:16.4
occ:0.90
O B:HOH797 2.5 31.3 1.0
O B:GLY259 2.7 13.0 1.0
O B:ASN254 2.8 13.1 1.0
O B:LEU261 2.9 13.8 1.0
O B:HOH663 2.9 11.9 1.0
O B:HIS253 3.0 11.1 1.0
O B:HOH678 3.2 41.4 1.0
O B:ASP256 3.3 13.1 1.0
HB3 B:ASP256 3.3 11.5 1.0
H B:ASP256 3.4 11.1 1.0
C B:ASN254 3.4 11.9 1.0
HA B:ASN254 3.6 12.8 1.0
C B:GLY259 3.6 11.7 1.0
HA B:TYR260 3.7 13.6 1.0
N B:ASP256 3.8 10.9 1.0
H B:LEU261 3.8 12.3 1.0
O B:HOH517 3.9 21.2 1.0
CA B:ASN254 4.0 12.8 1.0
C B:HIS253 4.0 10.4 1.0
C B:LEU261 4.0 13.4 1.0
O B:HOH554 4.0 30.9 1.0
CB B:ASP256 4.0 11.3 1.0
N B:LEU261 4.1 12.3 1.0
C B:ASP256 4.1 12.3 1.0
CA B:ASP256 4.2 11.5 1.0
HB2 B:ASP256 4.2 11.2 1.0
N B:ASP255 4.3 11.3 1.0
N B:TYR260 4.3 12.5 1.0
CA B:TYR260 4.3 13.2 1.0
C B:TYR260 4.3 13.7 1.0
HA3 B:GLY259 4.4 11.4 1.0
N B:ASN254 4.4 11.0 1.0
C B:ASP255 4.4 11.8 1.0
CA B:GLY259 4.5 11.6 1.0
HA B:ASP255 4.5 12.6 1.0
HA B:SER262 4.6 13.2 1.0
CA B:ASP255 4.7 12.3 1.0
CA B:LEU261 4.7 11.9 1.0
H B:GLY259 4.8 12.1 1.0
N B:GLY259 4.8 12.1 1.0
H B:ASP255 4.9 11.4 1.0
O B:HOH755 4.9 29.7 1.0
O B:ILE252 5.0 10.3 1.0
O B:ASP251 5.0 10.6 1.0

Potassium binding site 9 out of 9 in 9gky

Go back to Potassium Binding Sites List in 9gky
Potassium binding site 9 out of 9 in the Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Crystal Structure of Histone Deacetylase (Hdah) From Vibrio Cholerae in Complex with Decanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K409

b:28.3
occ:0.80
O B:LEU160 2.6 23.0 1.0
O B:HOH525 2.6 38.1 1.0
O B:VAL165 2.6 22.8 1.0
O B:HOH796 2.6 38.4 1.0
O B:LEU162 2.8 29.1 1.0
O B:HOH808 3.0 42.6 1.0
C B:LEU160 3.6 21.7 1.0
OD1 B:ASP166 3.6 33.4 1.0
C B:VAL165 3.6 20.4 1.0
H B:VAL165 3.6 25.9 1.0
C B:LEU162 3.7 32.8 1.0
HA B:PRO163 3.8 34.1 1.0
HA B:LEU160 3.8 19.9 1.0
HA B:ASP166 3.9 21.9 1.0
H B:LEU162 4.1 25.9 1.0
N B:LEU162 4.1 25.5 1.0
N B:VAL165 4.2 25.6 1.0
CA B:LEU160 4.3 19.8 1.0
O B:PRO163 4.3 36.8 1.0
HB B:VAL165 4.3 20.6 1.0
C B:SER161 4.4 27.1 1.0
CA B:PRO163 4.4 34.0 1.0
C B:PRO163 4.4 32.6 1.0
HA B:SER161 4.4 25.1 1.0
CA B:VAL165 4.4 20.9 1.0
N B:ASP166 4.5 20.3 1.0
N B:PRO163 4.5 31.8 1.0
N B:SER161 4.5 21.8 1.0
HB3 B:LEU160 4.5 20.6 1.0
CA B:LEU162 4.5 28.2 1.0
CG B:ASP166 4.5 29.8 1.0
CA B:ASP166 4.6 21.5 1.0
CA B:SER161 4.7 24.5 1.0
HD21 B:LEU160 4.7 20.1 1.0
O B:SER161 4.9 29.0 1.0
O B:ALA159 4.9 19.1 1.0
CB B:VAL165 4.9 20.4 1.0

Reference:

L.G.Graf, C.Moreno-Yruela, C.Qin, S.Schulze, G.J.Palm, O.Schmoeker, N.Wang, D.Hocking, L.Jebeli, B.Girbardt, L.Berndt, D.M.Weis, M.Janetzky, D.Zuehlke, S.Sievers, R.A.Strugnell, C.A.Olsen, K.Hofmann, M.Lammers. Distribution and Diversity of Classical Deacylases in Bacteria Nature Communications 2024.
Page generated: Sat Aug 9 19:07:11 2025

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