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Potassium in PDB 5g3w: Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65

Protein crystallography data

The structure of Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65, PDB code: 5g3w 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) 125.57 / 1.60
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.270, 130.140, 251.130, 90.00, 90.00, 90.00
R / Rfree (%) 12.5 / 16.7

Other elements in 5g3w:

The structure of Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65 also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65 (pdb code 5g3w). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65, PDB code: 5g3w:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 5g3w

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Potassium binding site 1 out of 8 in the Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K371

b:12.3
occ:0.70
 O A:ASP180 2.6 8.5 1.0
O A:HIS182 2.8 8.9 1.0
OG A:SER201 2.8 10.6 1.0
O A:LEU202 3.0 14.0 1.0
OD1 A:ASP178 3.0 12.9 1.0
CG A:ASP178 3.2 11.5 1.0
O A:ASP178 3.2 11.5 1.0
OD2 A:ASP178 3.5 13.4 1.0
C A:ASP180 3.7 8.2 1.0
C A:ASP178 3.7 9.7 1.0
C A:HIS182 3.8 8.2 1.0
CB A:SER201 3.8 10.6 1.0
CB A:ASP178 3.8 11.2 1.0
C A:LEU202 3.8 12.4 1.0
CB A:HIS203 3.9 10.6 1.0
N A:LEU202 3.9 10.6 1.0
N A:ASP180 4.0 8.1 1.0
N A:GLY184 4.0 8.7 1.0
CA A:SER201 4.0 9.9 1.0
C A:SER201 4.2 10.2 1.0
CA A:ASP180 4.2 8.0 1.0
CA A:HIS183 4.3 8.2 1.0
N A:TRP179 4.3 9.3 1.0
CB A:ASP180 4.4 8.6 1.0
C A:TRP179 4.4 8.7 1.0
CA A:ASP178 4.4 9.3 1.0
CA A:TRP179 4.4 9.5 1.0
C A:HIS183 4.4 8.4 1.0
CE1 A:HIS142 4.5 11.5 1.0
N A:HIS183 4.5 7.7 1.0
ND1 A:HIS142 4.5 10.5 1.0
ND1 A:HIS203 4.5 13.6 1.0
CA A:HIS203 4.5 10.3 1.0
N A:HIS182 4.5 7.8 1.0
CA A:LEU202 4.6 11.6 1.0
N A:HIS203 4.6 10.4 1.0
CG A:HIS203 4.7 10.8 1.0
N A:VAL181 4.7 8.0 1.0
CA A:GLY184 4.8 8.6 1.0
C A:VAL181 4.8 7.4 1.0
CA A:HIS182 4.8 8.3 1.0
O A:HOH2337 4.9 11.0 1.0

Potassium binding site 2 out of 8 in 5g3w

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Potassium binding site 2 out of 8 in the Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K372

b:13.6
occ:1.00
 O A:VAL197 2.7 12.5 1.0
O A:HOH2345 2.7 16.7 1.0
O A:TRP191 2.8 11.4 1.0
O A:HOH2341 2.9 13.2 1.0
O A:ASP194 2.9 15.8 1.0
O A:TYR226 2.9 14.3 1.0
C A:TRP191 3.6 11.8 1.0
CB A:TRP191 3.7 11.9 1.0
C A:TYR226 3.7 13.6 1.0
OG1 A:THR199 3.7 11.7 1.0
C A:VAL197 3.9 11.6 1.0
C A:ASP194 4.0 14.8 1.0
CB A:TYR226 4.1 12.8 1.0
CA A:TRP191 4.3 11.8 1.0
CG2 A:THR199 4.4 12.2 1.0
N A:THR199 4.4 10.1 1.0
N A:ASN227 4.5 13.3 1.0
CA A:TYR226 4.5 13.3 1.0
N A:ASP194 4.6 14.5 1.0
N A:TRP192 4.6 11.3 1.0
CB A:THR199 4.6 11.8 1.0
CA A:LEU198 4.7 10.7 1.0
CA A:ASP194 4.7 14.5 1.0
N A:LEU198 4.7 10.7 1.0
O A:TRP192 4.8 12.5 1.0
CB A:ASN227 4.8 11.4 1.0
CA A:TRP192 4.8 11.9 1.0
CA A:ASN227 4.8 11.5 1.0
CA A:VAL197 4.8 11.8 1.0
C A:TRP192 4.8 12.5 1.0
CB A:ASP194 4.9 14.4 1.0
O A:GLY223 4.9 15.8 1.0
N A:PRO195 4.9 15.0 1.0
CG A:TRP191 4.9 11.8 1.0
N A:VAL197 5.0 11.7 1.0
CB A:VAL197 5.0 12.6 1.0
C A:LEU198 5.0 10.7 1.0

Potassium binding site 3 out of 8 in 5g3w

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Potassium binding site 3 out of 8 in the Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K371

b:11.1
occ:0.80
 O B:ASP180 2.5 7.1 1.0
O B:HIS182 2.7 8.9 1.0
OG B:SER201 2.8 9.4 1.0
O B:LEU202 2.8 11.9 1.0
OD1 B:ASP178 2.9 12.1 1.0
O B:ASP178 3.1 9.7 1.0
CG B:ASP178 3.2 9.8 1.0
OD2 B:ASP178 3.5 10.4 1.0
C B:ASP180 3.6 7.0 1.0
C B:ASP178 3.7 7.8 1.0
C B:LEU202 3.8 9.6 1.0
C B:HIS182 3.8 7.9 1.0
CB B:SER201 3.9 9.0 1.0
N B:LEU202 3.9 8.9 1.0
N B:ASP180 3.9 7.1 1.0
CB B:ASP178 3.9 8.9 1.0
CB B:HIS203 4.0 9.2 1.0
N B:GLY184 4.0 7.7 1.0
CA B:SER201 4.1 8.3 1.0
CA B:ASP180 4.2 7.4 1.0
C B:SER201 4.3 8.6 1.0
C B:TRP179 4.3 7.1 1.0
N B:TRP179 4.3 6.9 1.0
CB B:ASP180 4.3 7.8 1.0
CA B:HIS183 4.3 8.3 1.0
CA B:TRP179 4.3 7.2 1.0
CA B:ASP178 4.4 8.3 1.0
ND1 B:HIS203 4.4 11.2 1.0
N B:HIS183 4.5 8.0 1.0
C B:HIS183 4.5 8.6 1.0
CE1 B:HIS142 4.5 10.0 1.0
ND1 B:HIS142 4.5 8.9 1.0
N B:HIS182 4.5 6.8 1.0
CA B:LEU202 4.5 9.5 1.0
CA B:HIS203 4.6 8.6 1.0
N B:HIS203 4.6 7.8 1.0
CG B:HIS203 4.7 9.6 1.0
N B:VAL181 4.7 7.1 1.0
C B:VAL181 4.8 6.7 1.0
CA B:HIS182 4.8 7.6 1.0
O B:HOH2257 4.8 8.8 1.0
CA B:GLY184 4.9 8.1 1.0

Potassium binding site 4 out of 8 in 5g3w

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Potassium binding site 4 out of 8 in the Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K372

b:12.5
occ:1.00
 O B:VAL197 2.7 11.9 1.0
O B:HOH2270 2.7 12.7 1.0
O B:TRP191 2.7 11.2 1.0
O B:ASP194 2.9 14.7 1.0
O B:TYR226 2.9 10.8 1.0
O B:HOH2263 2.9 12.7 1.0
C B:TRP191 3.6 11.2 1.0
CB B:TRP191 3.7 12.6 1.0
OG1 B:THR199 3.7 11.1 1.0
C B:TYR226 3.7 10.3 1.0
C B:VAL197 3.9 11.2 1.0
C B:ASP194 4.0 12.2 1.0
CB B:TYR226 4.1 11.3 1.0
CA B:TRP191 4.3 12.0 1.0
N B:THR199 4.4 9.3 1.0
CG2 B:THR199 4.4 11.8 1.0
N B:ASN227 4.5 9.6 1.0
CA B:TYR226 4.5 10.8 1.0
N B:TRP192 4.6 12.2 1.0
CA B:LEU198 4.6 10.6 1.0
N B:ASP194 4.6 12.6 1.0
CB B:THR199 4.6 10.7 1.0
N B:LEU198 4.7 10.9 1.0
O B:TRP192 4.7 13.1 1.0
CA B:ASP194 4.8 12.5 1.0
CA B:TRP192 4.8 11.9 1.0
CB B:ASN227 4.8 9.1 1.0
CA B:ASN227 4.8 9.3 1.0
C B:TRP192 4.8 12.2 1.0
C B:LEU198 4.9 10.2 1.0
CA B:VAL197 4.9 10.4 1.0
CG B:TRP191 4.9 13.1 1.0
N B:PRO195 4.9 13.6 1.0
O B:GLY223 4.9 14.0 1.0
N B:VAL197 5.0 10.4 1.0
CB B:ASP194 5.0 11.6 1.0
CA B:PRO195 5.0 13.0 1.0

Potassium binding site 5 out of 8 in 5g3w

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Potassium binding site 5 out of 8 in the Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K371

b:12.3
occ:0.80
 O C:ASP180 2.6 8.2 1.0
O C:HIS182 2.8 10.2 1.0
OG C:SER201 2.8 10.2 1.0
O C:LEU202 2.9 15.9 1.0
OD1 C:ASP178 3.0 11.8 1.0
CG C:ASP178 3.2 11.8 1.0
O C:ASP178 3.2 10.6 1.0
OD2 C:ASP178 3.4 13.5 1.0
C C:ASP180 3.6 9.1 1.0
C C:ASP178 3.7 9.1 1.0
C C:LEU202 3.8 12.3 1.0
C C:HIS182 3.8 9.5 1.0
CB C:SER201 3.9 10.1 1.0
N C:ASP180 3.9 9.2 1.0
N C:LEU202 3.9 10.9 1.0
CB C:ASP178 3.9 10.3 1.0
CB C:HIS203 4.0 11.3 1.0
N C:GLY184 4.0 10.1 1.0
CA C:SER201 4.1 10.1 1.0
CA C:ASP180 4.2 9.5 1.0
C C:SER201 4.3 10.1 1.0
CA C:HIS183 4.3 10.1 1.0
C C:TRP179 4.3 8.7 1.0
CB C:ASP180 4.3 10.1 1.0
N C:TRP179 4.4 8.3 1.0
CA C:TRP179 4.4 8.5 1.0
CA C:ASP178 4.5 9.2 1.0
N C:HIS183 4.5 9.7 1.0
C C:HIS183 4.5 10.2 1.0
ND1 C:HIS142 4.5 11.6 1.0
N C:HIS182 4.5 7.9 1.0
CE1 C:HIS142 4.5 12.2 1.0
ND1 C:HIS203 4.5 12.3 1.0
CA C:HIS203 4.5 10.7 1.0
CA C:LEU202 4.5 11.2 1.0
N C:HIS203 4.6 11.4 1.0
N C:VAL181 4.7 8.4 1.0
CG C:HIS203 4.7 11.6 1.0
C C:VAL181 4.7 8.0 1.0
CA C:HIS182 4.8 8.8 1.0
CA C:GLY184 4.9 11.1 1.0
O C:HOH2308 4.9 10.8 1.0

Potassium binding site 6 out of 8 in 5g3w

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Potassium binding site 6 out of 8 in the Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K372

b:12.5
occ:1.00
 O C:HOH2317 2.7 13.0 1.0
O C:VAL197 2.7 11.8 1.0
O C:TRP191 2.8 12.1 1.0
O C:ASP194 2.8 15.1 1.0
O C:HOH2314 2.9 12.1 1.0
O C:TYR226 2.9 11.0 1.0
C C:TRP191 3.6 11.6 1.0
CB C:TRP191 3.6 11.0 1.0
C C:TYR226 3.7 10.8 1.0
OG1 C:THR199 3.7 10.4 1.0
C C:VAL197 3.9 11.3 1.0
C C:ASP194 4.0 13.8 1.0
CB C:TYR226 4.1 11.7 1.0
CA C:TRP191 4.3 11.2 1.0
N C:THR199 4.4 10.3 1.0
CG2 C:THR199 4.4 12.1 1.0
N C:ASN227 4.4 10.4 1.0
CA C:TYR226 4.4 11.8 1.0
N C:TRP192 4.5 12.2 1.0
CB C:THR199 4.6 11.4 1.0
CA C:LEU198 4.6 10.7 1.0
N C:ASP194 4.6 15.0 1.0
N C:LEU198 4.7 10.6 1.0
CA C:ASP194 4.8 14.4 1.0
CA C:ASN227 4.8 11.0 1.0
CA C:TRP192 4.8 12.6 1.0
O C:TRP192 4.8 13.6 1.0
CB C:ASN227 4.8 11.1 1.0
C C:TRP192 4.9 13.2 1.0
C C:LEU198 4.9 10.1 1.0
CG C:TRP191 4.9 10.7 1.0
CA C:VAL197 4.9 11.1 1.0
N C:PRO195 4.9 13.0 1.0
O C:GLY223 5.0 14.3 1.0
CA C:PRO195 5.0 12.7 1.0
N C:VAL197 5.0 10.6 1.0

Potassium binding site 7 out of 8 in 5g3w

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Potassium binding site 7 out of 8 in the Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K371

b:14.5
occ:1.00
 O D:HOH2236 2.6 14.9 1.0
O D:VAL197 2.7 14.3 1.0
O D:TRP191 2.7 12.9 1.0
O D:HOH2230 2.9 13.4 1.0
O D:ASP194 2.9 15.3 1.0
O D:TYR226 2.9 13.4 1.0
C D:TRP191 3.6 13.2 1.0
OG1 D:THR199 3.7 12.3 1.0
CB D:TRP191 3.7 13.5 1.0
C D:TYR226 3.7 13.6 1.0
C D:VAL197 3.9 13.8 1.0
C D:ASP194 4.0 14.5 1.0
CB D:TYR226 4.1 13.0 1.0
CA D:TRP191 4.3 13.0 1.0
N D:THR199 4.4 12.5 1.0
CG2 D:THR199 4.4 14.4 1.0
N D:ASN227 4.5 13.3 1.0
CA D:TYR226 4.5 12.9 1.0
N D:TRP192 4.5 12.5 1.0
CB D:THR199 4.6 12.8 1.0
CA D:LEU198 4.6 13.5 1.0
N D:ASP194 4.6 13.4 1.0
N D:LEU198 4.7 13.3 1.0
O D:TRP192 4.8 13.9 1.0
CA D:TRP192 4.8 12.9 1.0
CA D:ASP194 4.8 12.5 1.0
C D:TRP192 4.8 14.3 1.0
CA D:ASN227 4.9 12.3 1.0
CB D:ASN227 4.9 11.8 1.0
C D:LEU198 4.9 13.2 1.0
CA D:VAL197 4.9 15.0 1.0
O D:GLY223 5.0 16.3 1.0
N D:PRO195 5.0 16.1 1.0
CG D:TRP191 5.0 13.9 1.0
N D:VAL197 5.0 16.6 1.0
CA D:PRO195 5.0 16.1 1.0

Potassium binding site 8 out of 8 in 5g3w

Go back to Potassium Binding Sites List in 5g3w
Potassium binding site 8 out of 8 in the Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Structure of Hdac Like Protein From Bordetella Alcaligenes in Complex with the Photoswitchable Inhibitor CEW65 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K372

b:12.7
occ:0.80
 O D:ASP180 2.6 9.7 1.0
O D:HIS182 2.7 10.4 1.0
OG D:SER201 2.8 10.5 1.0
O D:LEU202 2.8 14.4 1.0
OD1 D:ASP178 2.9 13.9 1.0
O D:ASP178 3.1 11.7 1.0
CG D:ASP178 3.2 12.5 1.0
OD2 D:ASP178 3.5 13.7 1.0
C D:ASP180 3.6 8.3 1.0
C D:ASP178 3.7 10.7 1.0
C D:LEU202 3.8 11.3 1.0
C D:HIS182 3.8 9.3 1.0
CB D:SER201 3.9 10.6 1.0
N D:ASP180 3.9 9.7 1.0
CB D:ASP178 3.9 11.6 1.0
N D:LEU202 3.9 10.4 1.0
N D:GLY184 4.0 9.1 1.0
CB D:HIS203 4.1 11.0 1.0
CA D:SER201 4.1 10.9 1.0
CA D:ASP180 4.2 9.5 1.0
C D:SER201 4.3 11.0 1.0
CA D:HIS183 4.3 8.7 1.0
N D:TRP179 4.3 9.5 1.0
C D:TRP179 4.3 9.6 1.0
CB D:ASP180 4.4 10.0 1.0
CA D:TRP179 4.4 10.5 1.0
CA D:ASP178 4.4 11.3 1.0
C D:HIS183 4.4 8.9 1.0
N D:HIS183 4.4 8.8 1.0
N D:HIS182 4.5 8.4 1.0
ND1 D:HIS203 4.5 12.8 1.0
ND1 D:HIS142 4.5 10.9 1.0
CE1 D:HIS142 4.5 11.6 1.0
CA D:LEU202 4.5 11.9 1.0
N D:HIS203 4.6 9.9 1.0
CA D:HIS203 4.6 10.3 1.0
N D:VAL181 4.7 7.8 1.0
C D:VAL181 4.7 8.1 1.0
CG D:HIS203 4.7 11.9 1.0
CA D:HIS182 4.8 8.8 1.0
O D:HOH2224 4.8 12.2 1.0
CA D:GLY184 4.8 9.8 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 13:45:34 2024

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