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Potassium in PDB 5g10: Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide

Protein crystallography data

The structure of Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide, PDB code: 5g10 was solved by A.Kraemer, F.J.Meyer-Almes, O.Yildiz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.94 / 1.71
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 81.740, 81.740, 205.210, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 19.4

Other elements in 5g10:

The structure of Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide (pdb code 5g10). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide, PDB code: 5g10:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 5g10

Go back to Potassium Binding Sites List in 5g10
Potassium binding site 1 out of 4 in the Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1373

b:13.5
occ:1.00
 O A:ASP181 2.6 12.2 1.0
O A:LEU203 2.6 12.6 1.0
OD1 A:ASP179 2.6 13.2 1.0
O A:HIS183 2.6 12.5 1.0
OG A:SER202 2.7 13.8 1.0
O A:ASP179 2.7 12.3 1.0
CG A:ASP179 3.2 12.3 1.0
C A:ASP179 3.5 11.3 1.0
C A:LEU203 3.6 11.7 1.0
C A:ASP181 3.6 11.8 1.0
C A:HIS183 3.7 11.7 1.0
CB A:ASP179 3.8 12.2 1.0
CB A:SER202 3.8 12.8 1.0
N A:LEU203 3.9 12.8 1.0
OD2 A:ASP179 4.0 13.1 1.0
N A:ASP181 4.0 11.4 1.0
CB A:HIS204 4.1 11.9 1.0
N A:GLY185 4.1 12.5 1.0
CA A:SER202 4.1 12.2 1.0
N A:TRP180 4.2 11.5 1.0
CA A:ASP179 4.2 11.8 1.0
CA A:ASP181 4.3 11.0 1.0
C A:SER202 4.3 13.1 1.0
C A:TRP180 4.3 11.7 1.0
CA A:HIS184 4.4 11.9 1.0
CA A:TRP180 4.4 11.7 1.0
N A:HIS204 4.4 10.6 1.0
CB A:ASP181 4.4 11.4 1.0
CA A:LEU203 4.4 12.7 1.0
N A:HIS183 4.4 11.4 1.0
CA A:HIS204 4.5 11.5 1.0
N A:HIS184 4.5 11.6 1.0
C A:HIS184 4.5 12.2 1.0
O A:HOH2181 4.6 13.9 1.0
ND1 A:HIS204 4.6 13.6 1.0
C A:VAL182 4.6 11.4 1.0
N A:VAL182 4.7 10.7 1.0
CA A:HIS183 4.7 11.7 1.0
CE1 A:HIS143 4.8 16.7 1.0
CG A:HIS204 4.8 13.4 1.0
ND1 A:HIS143 4.9 16.2 1.0
CA A:VAL182 5.0 11.7 1.0
CA A:GLY185 5.0 12.5 1.0

Potassium binding site 2 out of 4 in 5g10

Go back to Potassium Binding Sites List in 5g10
Potassium binding site 2 out of 4 in the Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1374

b:14.2
occ:1.00
 O A:VAL198 2.6 16.8 1.0
O A:TYR192 2.6 15.0 1.0
O A:HOH2193 2.6 13.6 1.0
O A:PHE227 2.7 14.5 1.0
O A:HOH2188 2.7 16.0 1.0
O A:ARG195 2.8 13.6 1.0
C A:PHE227 3.5 15.4 1.0
C A:TYR192 3.6 14.7 1.0
CB A:PHE227 3.7 16.6 1.0
OG A:SER200 3.8 13.5 1.0
C A:VAL198 3.8 16.0 1.0
CB A:TYR192 3.9 14.2 1.0
C A:ARG195 4.0 15.7 1.0
CA A:PHE227 4.2 16.1 1.0
N A:SER200 4.3 13.1 1.0
N A:ASN228 4.3 14.8 1.0
CA A:TYR192 4.3 14.5 1.0
N A:ARG195 4.5 16.1 1.0
N A:TYR193 4.5 14.5 1.0
CA A:TYR193 4.5 15.2 1.0
CA A:LEU199 4.5 14.8 1.0
CA A:ARG195 4.6 16.4 1.0
N A:LEU199 4.6 14.4 1.0
C A:TYR193 4.6 15.7 1.0
O A:TYR193 4.6 15.3 1.0
CB A:ASN228 4.7 14.7 1.0
CA A:ASN228 4.7 14.7 1.0
CB A:SER200 4.8 14.2 1.0
CB A:ARG195 4.8 16.6 1.0
CA A:VAL198 4.9 15.7 1.0
O A:GLY224 4.9 14.9 1.0
C A:LEU199 4.9 14.4 1.0
CB A:VAL198 5.0 15.7 1.0

Potassium binding site 3 out of 4 in 5g10

Go back to Potassium Binding Sites List in 5g10
Potassium binding site 3 out of 4 in the Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1379

b:13.6
occ:1.00
 O B:VAL198 2.6 14.8 1.0
O B:HOH2169 2.6 14.0 1.0
O B:TYR192 2.6 14.6 1.0
O B:HOH2164 2.7 15.5 1.0
O B:PHE227 2.7 13.2 1.0
O B:ARG195 2.7 15.7 1.0
C B:PHE227 3.5 13.9 1.0
C B:TYR192 3.5 14.7 1.0
CB B:PHE227 3.7 15.4 1.0
CB B:TYR192 3.8 15.1 1.0
C B:VAL198 3.8 15.2 1.0
OG B:SER200 3.9 13.7 1.0
C B:ARG195 3.9 16.8 1.0
CA B:PHE227 4.2 14.9 1.0
CA B:TYR192 4.3 15.0 1.0
N B:SER200 4.4 13.9 1.0
N B:ASN228 4.4 13.5 1.0
N B:TYR193 4.4 14.3 1.0
N B:ARG195 4.5 16.9 1.0
CA B:TYR193 4.5 15.7 1.0
CA B:LEU199 4.6 14.2 1.0
CA B:ARG195 4.6 17.4 1.0
C B:TYR193 4.6 16.0 1.0
O B:TYR193 4.6 14.8 1.0
N B:LEU199 4.7 14.1 1.0
CB B:ASN228 4.7 14.1 1.0
CB B:ARG195 4.8 17.1 1.0
CA B:ASN228 4.8 13.8 1.0
CB B:SER200 4.8 14.3 1.0
O B:GLY224 4.8 14.3 1.0
CA B:VAL198 4.8 15.3 1.0
C B:LEU199 4.9 13.9 1.0
CB B:VAL198 4.9 15.8 1.0

Potassium binding site 4 out of 4 in 5g10

Go back to Potassium Binding Sites List in 5g10
Potassium binding site 4 out of 4 in the Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Pseudomonas Aeruginosa Hdah Bound to 9,9,9 Trifluoro-8,8-Dihydroy-N- Phenylnonanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1380

b:13.2
occ:1.00
 O B:ASP181 2.6 12.2 1.0
O B:LEU203 2.6 11.9 1.0
OD1 B:ASP179 2.6 13.3 1.0
O B:HIS183 2.6 13.4 1.0
OG B:SER202 2.7 13.5 1.0
O B:ASP179 2.7 12.1 1.0
CG B:ASP179 3.2 13.6 1.0
C B:ASP179 3.5 11.7 1.0
C B:LEU203 3.6 11.7 1.0
C B:ASP181 3.6 11.6 1.0
C B:HIS183 3.7 12.2 1.0
CB B:ASP179 3.8 12.9 1.0
CB B:SER202 3.8 13.0 1.0
N B:LEU203 3.9 10.9 1.0
OD2 B:ASP179 4.0 13.3 1.0
N B:ASP181 4.1 11.7 1.0
CB B:HIS204 4.1 12.2 1.0
CA B:SER202 4.1 12.2 1.0
N B:GLY185 4.1 12.9 1.0
N B:TRP180 4.2 11.3 1.0
CA B:ASP179 4.2 11.5 1.0
C B:SER202 4.3 12.7 1.0
CA B:ASP181 4.3 11.9 1.0
C B:TRP180 4.3 11.9 1.0
CA B:HIS184 4.3 12.9 1.0
CA B:TRP180 4.4 11.5 1.0
N B:HIS183 4.4 11.9 1.0
CA B:LEU203 4.4 11.7 1.0
CB B:ASP181 4.4 12.2 1.0
N B:HIS204 4.4 11.1 1.0
CA B:HIS204 4.5 11.8 1.0
N B:HIS184 4.5 12.2 1.0
C B:HIS184 4.5 13.1 1.0
O B:HOH2158 4.5 13.3 1.0
ND1 B:HIS204 4.6 13.9 1.0
C B:VAL182 4.6 12.3 1.0
N B:VAL182 4.7 11.6 1.0
CA B:HIS183 4.7 12.2 1.0
CE1 B:HIS143 4.8 17.0 1.0
CG B:HIS204 4.8 13.0 1.0
ND1 B:HIS143 4.9 15.8 1.0
CA B:VAL182 4.9 12.1 1.0
CA B:GLY185 5.0 13.3 1.0

Reference:

A.Kramer, T.Wagner, O.Yildiz, F.J.Meyer-Almes. Crystal Structure of A Histone Deacetylase Homologue From Pseudomonas Aeruginosa. Biochemistry V. 55 6858 2016.
ISSN: ISSN 1520-4995
PubMed: 27951649
DOI: 10.1021/ACS.BIOCHEM.6B00613
Page generated: Mon Aug 12 13:42:21 2024

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