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Potassium in PDB 2gh6: Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound

Protein crystallography data

The structure of Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound, PDB code: 2gh6 was solved by T.K.Nielsen, C.Hildmann, D.Riester, D.Wegener, A.Schwienhorst, R.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.84 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.507, 94.897, 123.301, 90.00, 104.28, 90.00
R / Rfree (%) 15.8 / 21.4

Other elements in 2gh6:

The structure of Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Zinc (Zn) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound (pdb code 2gh6). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound, PDB code: 2gh6:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 2gh6

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Potassium binding site 1 out of 8 in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound


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 A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K9450

b:23.1
occ:1.00
O A:ASP180 2.5 16.6 1.0
O A:LEU202 2.6 16.6 1.0
O A:HIS182 2.6 15.9 1.0
OG A:SER201 2.8 16.7 1.0
OD2 A:ASP178 2.8 17.9 1.0
O A:ASP178 3.1 17.1 1.0
CG A:ASP178 3.2 18.6 1.0
C A:ASP180 3.6 16.5 1.0
OD1 A:ASP178 3.6 22.0 1.0
C A:LEU202 3.7 17.1 1.0
C A:HIS182 3.7 16.4 1.0
C A:ASP178 3.7 17.7 1.0
N A:ASP180 3.9 16.6 1.0
N A:LEU202 3.9 17.2 1.0
CB A:ASP178 4.0 18.4 1.0
CB A:SER201 4.0 16.5 1.0
CB A:HIS203 4.0 17.4 1.0
N A:GLY184 4.1 17.6 1.0
CA A:ASP180 4.2 16.0 1.0
C A:TRP179 4.2 17.1 1.0
CA A:SER201 4.2 17.3 1.0
N A:TRP179 4.3 17.6 1.0
CA A:TRP179 4.3 17.7 1.0
CB A:ASP180 4.3 15.7 1.0
N A:HIS182 4.3 16.0 1.0
C A:SER201 4.4 17.1 1.0
CA A:HIS183 4.4 16.9 1.0
N A:HIS183 4.4 17.1 1.0
CA A:ASP178 4.4 17.8 1.0
CE1 A:HIS142 4.5 16.3 1.0
ND1 A:HIS203 4.5 14.4 1.0
CA A:LEU202 4.5 17.4 1.0
CA A:HIS203 4.5 17.5 1.0
N A:HIS203 4.5 17.1 1.0
C A:HIS183 4.5 17.2 1.0
ND1 A:HIS142 4.5 16.2 1.0
C A:VAL181 4.6 15.9 1.0
O A:HOH9455 4.6 13.0 1.0
N A:VAL181 4.6 16.5 1.0
CA A:HIS182 4.6 16.5 1.0
CG A:HIS203 4.7 15.8 1.0
CA A:VAL181 4.9 15.4 1.0
OD1 A:ASP180 4.9 16.0 1.0
O A:TRP179 4.9 18.0 1.0
CA A:GLY184 5.0 18.1 1.0

Potassium binding site 2 out of 8 in 2gh6

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Potassium binding site 2 out of 8 in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound


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 A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K9449

b:34.1
occ:1.00
O A:VAL197 2.3 19.3 1.0
O A:HOH9574 2.5 25.6 1.0
O A:ASP194 2.5 22.6 1.0
O A:HOH9476 2.5 12.4 1.0
O A:TRP191 2.5 21.2 1.0
O A:TYR226 3.5 20.9 1.0
C A:TRP191 3.5 20.4 1.0
C A:VAL197 3.6 20.0 1.0
C A:ASP194 3.6 22.8 1.0
CB A:TRP191 3.6 19.5 1.0
CB A:TYR226 4.0 21.1 1.0
C A:TYR226 4.1 21.0 1.0
CA A:TRP191 4.2 20.2 1.0
N A:ASP194 4.3 22.9 1.0
CA A:ASP194 4.4 22.8 1.0
OG1 A:THR199 4.4 18.7 1.0
CA A:VAL197 4.4 20.0 1.0
N A:VAL197 4.5 21.2 1.0
N A:LEU198 4.5 19.1 1.0
CA A:LEU198 4.5 19.1 1.0
N A:PRO195 4.5 22.3 1.0
N A:TRP192 4.6 20.7 1.0
CA A:PRO195 4.6 21.6 1.0
N A:THR199 4.7 18.2 1.0
CB A:ASP194 4.7 23.1 1.0
CB A:VAL197 4.7 19.5 1.0
CA A:TYR226 4.7 21.1 1.0
O A:TRP192 4.7 21.0 1.0
C A:TRP192 4.8 21.5 1.0
O A:GLY223 4.8 22.8 1.0
CA A:TRP192 4.8 20.6 1.0
CG A:TRP191 4.9 20.7 1.0
N A:ASN227 4.9 20.4 1.0
CG2 A:THR199 4.9 17.5 1.0
C A:PRO195 5.0 21.7 1.0
C A:LEU198 5.0 18.7 1.0

Potassium binding site 3 out of 8 in 2gh6

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Potassium binding site 3 out of 8 in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound


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 A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K9550

b:20.4
occ:1.00
O B:ASP180 2.5 17.3 1.0
O B:LEU202 2.6 16.7 1.0
O B:HIS182 2.6 16.8 1.0
OD2 B:ASP178 2.8 19.6 1.0
OG B:SER201 2.9 16.2 1.0
O B:ASP178 3.2 18.0 1.0
CG B:ASP178 3.2 17.9 1.0
C B:LEU202 3.6 16.4 1.0
C B:ASP180 3.6 17.2 1.0
C B:HIS182 3.7 16.8 1.0
OD1 B:ASP178 3.7 16.1 1.0
C B:ASP178 3.7 17.5 1.0
N B:LEU202 3.8 16.5 1.0
CB B:SER201 3.9 15.9 1.0
CB B:HIS203 3.9 17.5 1.0
N B:ASP180 3.9 16.7 1.0
N B:GLY184 4.0 19.8 1.0
CB B:ASP178 4.1 17.1 1.0
CA B:SER201 4.2 16.7 1.0
ND1 B:HIS203 4.2 16.6 1.0
CA B:ASP180 4.2 17.3 1.0
CA B:HIS183 4.3 18.1 1.0
N B:TRP179 4.3 17.5 1.0
C B:SER201 4.3 16.0 1.0
C B:TRP179 4.3 17.3 1.0
N B:HIS182 4.3 16.9 1.0
CA B:TRP179 4.3 17.4 1.0
CB B:ASP180 4.4 15.3 1.0
N B:HIS183 4.4 17.1 1.0
CA B:LEU202 4.4 16.7 1.0
C B:HIS183 4.4 18.6 1.0
N B:HIS203 4.4 16.4 1.0
CA B:HIS203 4.5 17.0 1.0
CE1 B:HIS142 4.5 13.6 1.0
CA B:ASP178 4.5 17.7 1.0
ND1 B:HIS142 4.5 15.1 1.0
CG B:HIS203 4.6 16.6 1.0
C B:VAL181 4.6 16.9 1.0
CA B:HIS182 4.6 16.6 1.0
N B:VAL181 4.6 17.6 1.0
O B:HOH9554 4.7 18.5 1.0
CA B:GLY184 4.9 19.4 1.0
CA B:VAL181 4.9 16.7 1.0

Potassium binding site 4 out of 8 in 2gh6

Go back to Potassium Binding Sites List in 2gh6
Potassium binding site 4 out of 8 in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound


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 A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K9549

b:42.3
occ:1.00
O B:HOH9643 2.5 25.3 1.0
O B:ASP194 2.5 23.2 1.0
O B:VAL197 2.5 18.6 1.0
O B:TRP191 2.5 18.8 1.0
O B:HOH9759 3.0 31.4 1.0
O B:TYR226 3.4 21.2 1.0
C B:TRP191 3.5 19.8 1.0
C B:ASP194 3.6 23.1 1.0
CB B:TRP191 3.6 19.7 1.0
C B:VAL197 3.7 19.4 1.0
CB B:TYR226 3.9 22.1 1.0
C B:TYR226 4.0 21.5 1.0
CA B:TRP191 4.2 20.4 1.0
N B:ASP194 4.2 23.2 1.0
CA B:ASP194 4.3 22.9 1.0
OG1 B:THR199 4.4 19.7 1.0
N B:TRP192 4.5 20.1 1.0
N B:PRO195 4.5 23.5 1.0
CA B:TYR226 4.5 21.9 1.0
CB B:ASP194 4.6 22.9 1.0
N B:VAL197 4.6 20.8 1.0
CA B:VAL197 4.6 19.5 1.0
N B:LEU198 4.6 20.4 1.0
O B:TRP192 4.6 22.4 1.0
CA B:PRO195 4.6 22.6 1.0
CA B:LEU198 4.6 19.7 1.0
O B:GLY223 4.7 23.6 1.0
C B:TRP192 4.8 22.2 1.0
N B:THR199 4.8 19.2 1.0
CA B:TRP192 4.9 21.1 1.0
N B:ASN227 4.9 20.2 1.0
CB B:VAL197 4.9 19.4 1.0
CG B:TRP191 4.9 20.8 1.0
CA B:GLY223 5.0 23.9 1.0

Potassium binding site 5 out of 8 in 2gh6

Go back to Potassium Binding Sites List in 2gh6
Potassium binding site 5 out of 8 in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound


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 A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K9650

b:22.7
occ:1.00
O C:ASP180 2.5 15.8 1.0
O C:LEU202 2.6 19.4 1.0
OD2 C:ASP178 2.7 22.5 1.0
O C:HIS182 2.7 18.1 1.0
OG C:SER201 2.8 19.6 1.0
O C:ASP178 3.0 18.4 1.0
CG C:ASP178 3.2 21.5 1.0
C C:ASP180 3.5 17.4 1.0
OD1 C:ASP178 3.6 20.9 1.0
C C:LEU202 3.6 19.3 1.0
C C:ASP178 3.7 19.0 1.0
C C:HIS182 3.8 18.8 1.0
N C:LEU202 3.8 19.2 1.0
N C:ASP180 4.0 16.8 1.0
CB C:SER201 4.0 18.9 1.0
CB C:ASP178 4.0 19.4 1.0
CB C:HIS203 4.1 19.4 1.0
N C:GLY184 4.2 19.4 1.0
CA C:ASP180 4.2 17.3 1.0
CA C:SER201 4.2 19.1 1.0
C C:SER201 4.3 19.1 1.0
N C:TRP179 4.3 18.6 1.0
CB C:ASP180 4.3 17.1 1.0
N C:HIS182 4.3 18.7 1.0
C C:TRP179 4.4 18.4 1.0
ND1 C:HIS203 4.4 19.8 1.0
CA C:TRP179 4.4 18.8 1.0
CA C:HIS183 4.4 19.1 1.0
CA C:LEU202 4.4 20.0 1.0
O C:HOH9654 4.4 14.9 1.0
N C:HIS183 4.5 18.5 1.0
CA C:ASP178 4.5 19.3 1.0
CE1 C:HIS142 4.5 16.2 1.0
ND1 C:HIS142 4.5 14.8 1.0
N C:HIS203 4.5 19.1 1.0
CA C:HIS203 4.5 19.4 1.0
C C:HIS183 4.5 18.9 1.0
N C:VAL181 4.6 17.7 1.0
C C:VAL181 4.6 18.5 1.0
CG C:HIS203 4.7 20.3 1.0
CA C:HIS182 4.7 18.1 1.0
CA C:VAL181 4.9 18.0 1.0
CA C:GLY184 5.0 19.2 1.0

Potassium binding site 6 out of 8 in 2gh6

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Potassium binding site 6 out of 8 in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound


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 A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K9649

b:46.1
occ:1.00
O C:HOH9715 2.5 20.3 1.0
O C:TRP191 2.5 23.0 1.0
O C:VAL197 2.5 20.7 1.0
O C:ASP194 2.6 24.9 1.0
O C:HOH9724 2.7 27.4 1.0
O C:TYR226 3.3 22.3 1.0
C C:TRP191 3.5 22.6 1.0
CB C:TRP191 3.6 23.4 1.0
C C:ASP194 3.6 23.8 1.0
C C:VAL197 3.7 20.6 1.0
CB C:TYR226 3.9 23.4 1.0
C C:TYR226 4.0 22.2 1.0
CA C:TRP191 4.2 23.2 1.0
N C:ASP194 4.3 24.0 1.0
CA C:ASP194 4.4 24.0 1.0
OG1 C:THR199 4.5 24.0 1.0
N C:TRP192 4.5 23.0 1.0
CA C:TYR226 4.5 22.5 1.0
N C:PRO195 4.6 23.3 1.0
CA C:LEU198 4.6 19.1 1.0
CA C:VAL197 4.6 21.4 1.0
N C:THR199 4.6 18.8 1.0
N C:LEU198 4.7 20.5 1.0
N C:VAL197 4.7 22.3 1.0
CA C:PRO195 4.7 23.1 1.0
O C:TRP192 4.7 23.4 1.0
CB C:ASP194 4.7 23.4 1.0
N C:ASN227 4.8 21.2 1.0
C C:TRP192 4.8 24.4 1.0
O C:GLY223 4.8 21.8 1.0
CA C:TRP192 4.8 23.9 1.0
CB C:VAL197 4.9 21.3 1.0
CG2 C:THR199 4.9 20.8 1.0
CG C:TRP191 4.9 24.8 1.0

Potassium binding site 7 out of 8 in 2gh6

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Potassium binding site 7 out of 8 in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound


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 A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K9750

b:22.9
occ:1.00
O D:LEU202 2.5 18.4 1.0
O D:ASP180 2.6 19.0 1.0
O D:HIS182 2.6 17.1 1.0
OG D:SER201 2.7 20.6 1.0
OD2 D:ASP178 3.0 25.9 1.0
O D:ASP178 3.0 22.2 1.0
CG D:ASP178 3.2 25.0 1.0
OD1 D:ASP178 3.5 25.8 1.0
C D:LEU202 3.6 19.5 1.0
C D:ASP178 3.6 21.9 1.0
C D:ASP180 3.7 19.2 1.0
C D:HIS182 3.7 18.1 1.0
CB D:SER201 3.9 19.7 1.0
N D:LEU202 3.9 20.2 1.0
N D:ASP180 3.9 19.6 1.0
CB D:HIS203 4.0 19.2 1.0
CB D:ASP178 4.0 22.2 1.0
CA D:SER201 4.1 20.6 1.0
N D:GLY184 4.2 20.0 1.0
ND1 D:HIS203 4.2 21.0 1.0
N D:TRP179 4.2 21.3 1.0
C D:TRP179 4.3 20.2 1.0
C D:SER201 4.3 20.8 1.0
CA D:TRP179 4.3 20.8 1.0
N D:HIS182 4.3 17.4 1.0
CA D:ASP180 4.3 19.4 1.0
CA D:LEU202 4.4 19.7 1.0
CA D:HIS183 4.4 19.4 1.0
N D:HIS183 4.4 19.2 1.0
CA D:ASP178 4.4 22.3 1.0
N D:HIS203 4.5 19.4 1.0
CA D:HIS203 4.5 19.6 1.0
CB D:ASP180 4.5 18.8 1.0
O D:HOH9753 4.5 24.1 1.0
ND1 D:HIS142 4.6 19.2 1.0
CE1 D:HIS142 4.6 18.1 1.0
CG D:HIS203 4.6 20.2 1.0
C D:HIS183 4.6 19.9 1.0
C D:VAL181 4.6 17.3 1.0
CA D:HIS182 4.7 17.6 1.0
N D:VAL181 4.7 18.3 1.0
CA D:VAL181 5.0 16.9 1.0

Potassium binding site 8 out of 8 in 2gh6

Go back to Potassium Binding Sites List in 2gh6
Potassium binding site 8 out of 8 in the Crystal Structure of A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound


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 A Hdac-Like Protein with 9,9,9-Trifluoro-8-Oxo-N- Phenylnonan Amide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K9749

b:55.9
occ:1.00
O D:HOH9849 2.5 21.7 1.0
O D:TRP191 2.5 23.9 1.0
O D:VAL197 2.6 23.3 1.0
O D:ASP194 2.6 28.6 1.0
O D:TYR226 3.3 24.3 1.0
C D:TRP191 3.5 24.5 1.0
CB D:TRP191 3.5 24.7 1.0
C D:ASP194 3.6 28.1 1.0
C D:VAL197 3.8 22.9 1.0
CB D:TYR226 4.0 25.6 1.0
C D:TYR226 4.0 24.5 1.0
CA D:TRP191 4.1 24.7 1.0
N D:ASP194 4.3 28.2 1.0
CA D:ASP194 4.4 27.8 1.0
N D:TRP192 4.5 25.1 1.0
O D:GLY223 4.6 27.7 1.0
N D:PRO195 4.6 28.0 1.0
O D:TRP192 4.6 26.9 1.0
OG1 D:THR199 4.6 25.6 1.0
CA D:TYR226 4.6 24.9 1.0
N D:LEU198 4.6 22.2 1.0
CA D:LEU198 4.7 22.4 1.0
C D:TRP192 4.7 26.6 1.0
CA D:VAL197 4.7 23.6 1.0
CA D:PRO195 4.7 26.8 1.0
CB D:ASP194 4.7 28.4 1.0
N D:VAL197 4.7 24.6 1.0
N D:THR199 4.8 22.5 1.0
CA D:TRP192 4.8 26.4 1.0
N D:ASN227 4.9 23.5 1.0
CG D:TRP191 4.9 25.0 1.0
CG2 D:THR199 5.0 23.6 1.0
CA D:GLY223 5.0 27.6 1.0

Reference:

T.K.Nielsen, C.Hildmann, D.Riester, D.Wegener, A.Schwienhorst, R.Ficner. Complex Structure of A Bacterial Class 2 Histone Deacetylase Homologue with A Trifluoromethylketone Inhibitor. Acta Crystallogr.,Sect.F V. 63 270 2007.
ISSN: ESSN 1744-3091
PubMed: 17401192
DOI: 10.1107/S1744309107012377
Page generated: Sun Dec 13 23:09:58 2020

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