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Potassium in PDB 5li3: Crystal Structure of Hdac-Like Protein From P. Aeruginosa in Complex with A Photo-Switchable Inhibitor.

Protein crystallography data

The structure of Crystal Structure of Hdac-Like Protein From P. Aeruginosa in Complex with A Photo-Switchable Inhibitor., PDB code: 5li3 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) 32.00 / 2.40
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 82.190, 82.190, 217.030, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 27

Other elements in 5li3:

The structure of Crystal Structure of Hdac-Like Protein From P. Aeruginosa in Complex with A Photo-Switchable Inhibitor. also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Hdac-Like Protein From P. Aeruginosa in Complex with A Photo-Switchable Inhibitor. (pdb code 5li3). 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 Hdac-Like Protein From P. Aeruginosa in Complex with A Photo-Switchable Inhibitor., PDB code: 5li3:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 5li3

Go back to Potassium Binding Sites List in 5li3
Potassium binding site 1 out of 4 in the Crystal Structure of Hdac-Like Protein From P. Aeruginosa in Complex with A Photo-Switchable Inhibitor.


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 Hdac-Like Protein From P. Aeruginosa in Complex with A Photo-Switchable Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K402

b:33.5
occ:1.00
 O A:HIS183 2.6 25.5 1.0
O A:LEU203 2.6 27.6 1.0
O A:ASP181 2.6 27.0 1.0
OD1 A:ASP179 2.7 35.6 1.0
OG A:SER202 3.0 26.9 1.0
O A:ASP179 3.1 27.2 1.0
CG A:ASP179 3.4 34.1 1.0
C A:HIS183 3.6 27.9 1.0
C A:LEU203 3.6 28.5 1.0
C A:ASP181 3.7 26.6 1.0
C A:ASP179 3.8 28.1 1.0
CB A:SER202 4.0 28.3 1.0
N A:LEU203 4.0 29.1 1.0
CB A:ASP179 4.1 31.4 1.0
CB A:HIS204 4.1 28.2 1.0
N A:GLY185 4.1 33.7 1.0
OD2 A:ASP179 4.1 38.0 1.0
N A:ASP181 4.1 27.5 1.0
CA A:HIS184 4.2 30.6 1.0
CA A:SER202 4.2 28.7 1.0
N A:HIS183 4.3 28.6 1.0
N A:HIS184 4.3 29.0 1.0
CA A:ASP181 4.3 27.2 1.0
N A:TRP180 4.4 27.9 1.0
N A:HIS204 4.4 29.0 1.0
C A:SER202 4.4 29.0 1.0
C A:TRP180 4.4 27.4 1.0
CA A:HIS204 4.4 27.8 1.0
CA A:TRP180 4.5 27.9 1.0
CB A:ASP181 4.5 29.1 1.0
O A:HOH517 4.5 22.6 1.0
CA A:LEU203 4.5 29.3 1.0
CA A:ASP179 4.5 29.4 1.0
C A:HIS184 4.5 32.5 1.0
C A:VAL182 4.5 27.6 1.0
ND1 A:HIS204 4.6 27.6 1.0
CA A:HIS183 4.6 28.3 1.0
N A:VAL182 4.7 27.1 1.0
CE1 A:HIS143 4.8 32.4 1.0
CG A:HIS204 4.8 28.4 1.0
OD1 A:ASP181 4.9 32.5 1.0
ND1 A:HIS143 4.9 32.4 1.0
CA A:VAL182 4.9 27.6 1.0
CA A:GLY185 5.0 34.3 1.0
O A:VAL182 5.0 27.6 1.0

Potassium binding site 2 out of 4 in 5li3

Go back to Potassium Binding Sites List in 5li3
Potassium binding site 2 out of 4 in the Crystal Structure of Hdac-Like Protein From P. Aeruginosa in Complex with A Photo-Switchable Inhibitor.


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 Hdac-Like Protein From P. Aeruginosa in Complex with A Photo-Switchable Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K403

b:37.0
occ:1.00
 O A:TYR192 2.5 33.2 1.0
O A:PHE227 2.7 31.2 1.0
O A:HOH527 2.7 32.4 1.0
O A:VAL198 2.7 38.1 1.0
O A:HOH503 2.9 31.8 1.0
O A:ARG195 3.0 35.3 1.0
C A:TYR192 3.6 34.7 1.0
C A:PHE227 3.6 34.0 1.0
OG A:SER200 3.7 38.6 1.0
C A:VAL198 3.9 35.1 1.0
CB A:TYR192 4.0 35.0 1.0
CB A:PHE227 4.0 33.9 1.0
C A:ARG195 4.2 36.0 1.0
N A:SER200 4.3 31.9 1.0
CA A:PHE227 4.4 34.6 1.0
CA A:TYR192 4.4 33.6 1.0
N A:ASN228 4.5 33.5 1.0
N A:TYR193 4.5 33.9 1.0
CA A:TYR193 4.5 35.8 1.0
O A:TYR193 4.5 37.4 1.0
C A:TYR193 4.6 37.1 1.0
N A:ARG195 4.6 39.1 1.0
CB A:ASN228 4.6 33.1 1.0
CB A:SER200 4.7 34.5 1.0
CA A:LEU199 4.7 31.6 1.0
N A:LEU199 4.8 35.0 1.0
CA A:ASN228 4.8 33.9 1.0
CA A:ARG195 4.8 37.4 1.0
CB A:ARG195 4.8 38.2 1.0
O A:GLY224 4.8 39.6 1.0
CA A:VAL198 4.9 36.1 1.0
C A:LEU199 4.9 32.5 1.0
CB A:VAL198 5.0 36.6 1.0
CA A:GLY224 5.0 43.1 1.0

Potassium binding site 3 out of 4 in 5li3

Go back to Potassium Binding Sites List in 5li3
Potassium binding site 3 out of 4 in the Crystal Structure of Hdac-Like Protein From P. Aeruginosa in Complex with A Photo-Switchable Inhibitor.


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 Hdac-Like Protein From P. Aeruginosa in Complex with A Photo-Switchable Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K402

b:44.2
occ:1.00
 O B:LEU203 2.5 42.3 1.0
O B:ASP181 2.6 39.1 1.0
OD1 B:ASP179 2.6 47.4 1.0
O B:HIS183 2.7 35.2 1.0
OG B:SER202 3.0 44.1 1.0
O B:ASP179 3.0 46.6 1.0
CG B:ASP179 3.4 48.3 1.0
C B:LEU203 3.6 45.2 1.0
C B:ASP179 3.7 46.5 1.0
C B:ASP181 3.7 38.8 1.0
C B:HIS183 3.7 39.4 1.0
N B:LEU203 4.0 48.6 1.0
CB B:SER202 4.0 45.6 1.0
CB B:ASP179 4.0 47.1 1.0
N B:ASP181 4.1 36.3 1.0
CB B:HIS204 4.1 46.9 1.0
OD2 B:ASP179 4.2 48.2 1.0
N B:GLY185 4.2 43.6 1.0
CA B:SER202 4.2 48.8 1.0
N B:TRP180 4.3 44.8 1.0
C B:TRP180 4.3 39.5 1.0
CA B:ASP181 4.3 37.2 1.0
C B:SER202 4.3 48.2 1.0
CA B:HIS184 4.3 42.2 1.0
CA B:TRP180 4.4 41.2 1.0
N B:HIS204 4.4 46.6 1.0
CA B:LEU203 4.4 47.0 1.0
N B:HIS183 4.4 36.6 1.0
CA B:HIS204 4.4 46.1 1.0
CA B:ASP179 4.4 47.8 1.0
N B:HIS184 4.4 40.1 1.0
CB B:ASP181 4.5 36.7 1.0
O B:HOH505 4.5 40.6 1.0
C B:VAL182 4.6 37.0 1.0
ND1 B:HIS204 4.6 54.0 1.0
C B:HIS184 4.6 41.9 1.0
N B:VAL182 4.7 39.9 1.0
CA B:HIS183 4.7 39.1 1.0
CG B:HIS204 4.8 52.4 1.0
CE1 B:HIS143 4.9 45.9 1.0
CA B:VAL182 5.0 38.6 1.0
OD1 B:ASP181 5.0 38.0 1.0
O B:TRP180 5.0 42.4 1.0

Potassium binding site 4 out of 4 in 5li3

Go back to Potassium Binding Sites List in 5li3
Potassium binding site 4 out of 4 in the Crystal Structure of Hdac-Like Protein From P. Aeruginosa in Complex with A Photo-Switchable Inhibitor.


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 Hdac-Like Protein From P. Aeruginosa in Complex with A Photo-Switchable Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K403

b:49.0
occ:1.00
 O B:HOH538 2.5 42.6 1.0
O B:PHE227 2.6 54.3 1.0
O B:TYR192 2.6 42.6 1.0
O B:VAL198 2.7 50.9 1.0
O B:HOH553 3.0 39.3 1.0
O B:ARG195 3.1 56.1 1.0
C B:PHE227 3.5 55.0 1.0
C B:TYR192 3.7 51.9 1.0
C B:VAL198 3.9 50.8 1.0
CB B:PHE227 3.9 60.4 1.0
CB B:TYR192 4.0 60.9 1.0
N B:SER200 4.2 50.4 1.0
C B:ARG195 4.2 55.1 1.0
CA B:PHE227 4.3 57.2 1.0
N B:ASN228 4.4 52.4 1.0
CB B:SER200 4.4 49.8 1.0
CA B:TYR192 4.5 55.5 1.0
CB B:ASN228 4.5 49.6 1.0
O B:TYR193 4.6 51.3 1.0
N B:TYR193 4.6 53.7 1.0
CA B:TYR193 4.6 53.4 1.0
CA B:LEU199 4.6 48.3 1.0
CA B:ASN228 4.6 51.2 1.0
N B:LEU199 4.7 48.4 1.0
C B:TYR193 4.7 53.8 1.0
N B:ARG195 4.7 55.9 1.0
O B:GLY224 4.8 55.7 1.0
C B:LEU199 4.8 50.1 1.0
CA B:ARG195 4.9 55.8 1.0
CA B:VAL198 4.9 53.8 1.0
CB B:ARG195 4.9 58.1 1.0
CB B:VAL198 5.0 53.0 1.0
CA B:SER200 5.0 51.5 1.0
CA B:GLY224 5.0 57.3 1.0

Reference:

C.E.Weston, A.Kramer, F.Colin, O.Yildiz, M.G.Baud, F.J.Meyer-Almes, M.J.Fuchter. Toward Photopharmacological Antimicrobial Chemotherapy Using Photoswitchable Amidohydrolase Inhibitors. Acs Infect Dis V. 3 152 2017.
ISSN: ESSN 2373-8227
PubMed: 27756124
DOI: 10.1021/ACSINFECDIS.6B00148
Page generated: Mon Aug 12 14:13:15 2024

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