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Potassium in PDB 5g12: Pseudomonas Aeruginosa Hdah (Y313F) Unliganded.

Protein crystallography data

The structure of Pseudomonas Aeruginosa Hdah (Y313F) Unliganded., PDB code: 5g12 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) 75.79 / 2.02
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 81.560, 81.560, 205.150, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 22.4

Other elements in 5g12:

The structure of Pseudomonas Aeruginosa Hdah (Y313F) Unliganded. also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Pseudomonas Aeruginosa Hdah (Y313F) Unliganded. (pdb code 5g12). 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 (Y313F) Unliganded., PDB code: 5g12:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 5g12

Go back to Potassium Binding Sites List in 5g12
Potassium binding site 1 out of 4 in the Pseudomonas Aeruginosa Hdah (Y313F) Unliganded.


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 (Y313F) Unliganded. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1373

b:14.1
occ:1.00
 O A:ASP181 2.6 12.5 1.0
OD1 A:ASP179 2.6 14.3 1.0
O A:LEU203 2.6 14.4 1.0
OG A:SER202 2.6 14.5 1.0
O A:HIS183 2.6 13.4 1.0
O A:ASP179 2.7 14.1 1.0
CG A:ASP179 3.2 15.0 1.0
C A:ASP179 3.4 13.6 1.0
C A:LEU203 3.6 14.4 1.0
C A:ASP181 3.6 12.9 1.0
C A:HIS183 3.8 14.1 1.0
CB A:SER202 3.8 14.6 1.0
CB A:ASP179 3.8 14.3 1.0
N A:LEU203 3.8 15.4 1.0
OD2 A:ASP179 3.9 15.4 1.0
N A:ASP181 4.0 13.1 1.0
CA A:SER202 4.1 14.7 1.0
N A:GLY185 4.1 14.1 1.0
CB A:HIS204 4.1 14.2 1.0
N A:TRP180 4.2 13.3 1.0
CA A:ASP179 4.2 14.0 1.0
C A:SER202 4.3 15.3 1.0
CA A:ASP181 4.3 13.1 1.0
C A:TRP180 4.3 13.4 1.0
CA A:HIS184 4.3 14.2 1.0
CA A:TRP180 4.4 13.4 1.0
CA A:LEU203 4.4 15.6 1.0
N A:HIS204 4.4 13.7 1.0
CB A:ASP181 4.4 13.8 1.0
N A:HIS184 4.5 14.2 1.0
N A:HIS183 4.5 13.6 1.0
CA A:HIS204 4.5 13.5 1.0
C A:HIS184 4.5 13.9 1.0
O A:HOH2092 4.6 13.3 1.0
ND1 A:HIS204 4.7 16.5 1.0
N A:VAL182 4.7 12.8 1.0
C A:VAL182 4.7 13.0 1.0
CE1 A:HIS143 4.8 21.5 1.0
CA A:HIS183 4.8 13.5 1.0
CG A:HIS204 4.9 15.5 1.0
ND1 A:HIS143 4.9 21.0 1.0
CA A:GLY185 4.9 14.6 1.0

Potassium binding site 2 out of 4 in 5g12

Go back to Potassium Binding Sites List in 5g12
Potassium binding site 2 out of 4 in the Pseudomonas Aeruginosa Hdah (Y313F) Unliganded.


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 (Y313F) Unliganded. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1374

b:15.2
occ:1.00
 O A:TYR192 2.6 14.2 1.0
O A:VAL198 2.6 15.5 1.0
O A:HOH2104 2.6 13.5 1.0
O A:HOH2099 2.7 18.0 1.0
O A:PHE227 2.7 14.6 1.0
O A:ARG195 2.7 17.8 1.0
C A:PHE227 3.5 14.7 1.0
C A:TYR192 3.5 14.2 1.0
CB A:PHE227 3.7 17.2 1.0
OG A:SER200 3.8 15.9 1.0
C A:VAL198 3.8 15.4 1.0
C A:ARG195 3.9 19.2 1.0
CB A:TYR192 3.9 14.7 1.0
CA A:PHE227 4.2 15.8 1.0
N A:SER200 4.3 15.4 1.0
N A:ASN228 4.3 14.6 1.0
CA A:TYR192 4.3 14.5 1.0
N A:TYR193 4.4 14.3 1.0
N A:ARG195 4.4 19.3 1.0
CA A:TYR193 4.5 15.2 1.0
CA A:ARG195 4.5 19.8 1.0
CA A:LEU199 4.6 15.3 1.0
C A:TYR193 4.6 15.5 1.0
O A:TYR193 4.6 15.8 1.0
N A:LEU199 4.6 15.2 1.0
CB A:ARG195 4.7 20.5 1.0
CB A:SER200 4.7 15.6 1.0
CA A:ASN228 4.7 14.8 1.0
CB A:ASN228 4.8 14.1 1.0
O A:GLY224 4.8 18.9 1.0
CA A:VAL198 4.8 17.0 1.0
C A:LEU199 4.9 15.3 1.0
CB A:VAL198 5.0 17.6 1.0
N A:ASP196 5.0 20.4 1.0

Potassium binding site 3 out of 4 in 5g12

Go back to Potassium Binding Sites List in 5g12
Potassium binding site 3 out of 4 in the Pseudomonas Aeruginosa Hdah (Y313F) Unliganded.


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 (Y313F) Unliganded. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1378

b:13.7
occ:1.00
 O B:TYR192 2.6 15.1 1.0
O B:VAL198 2.6 14.0 1.0
O B:HOH2091 2.6 13.7 1.0
O B:HOH2086 2.7 16.2 1.0
O B:PHE227 2.7 13.7 1.0
O B:ARG195 2.7 17.5 1.0
C B:PHE227 3.4 14.8 1.0
C B:TYR192 3.6 14.8 1.0
CB B:PHE227 3.7 16.2 1.0
OG B:SER200 3.8 15.4 1.0
C B:VAL198 3.8 14.5 1.0
CB B:TYR192 3.9 16.1 1.0
C B:ARG195 3.9 18.7 1.0
CA B:PHE227 4.2 15.4 1.0
N B:ASN228 4.2 14.7 1.0
N B:SER200 4.3 13.6 1.0
CA B:TYR192 4.3 15.8 1.0
N B:ARG195 4.4 18.6 1.0
N B:TYR193 4.5 14.6 1.0
CA B:LEU199 4.5 14.4 1.0
CA B:ARG195 4.6 19.5 1.0
CA B:TYR193 4.6 14.7 1.0
CA B:ASN228 4.6 14.6 1.0
N B:LEU199 4.6 14.5 1.0
CB B:ASN228 4.6 14.2 1.0
C B:TYR193 4.7 15.2 1.0
O B:TYR193 4.7 14.9 1.0
CB B:ARG195 4.7 22.1 1.0
CB B:SER200 4.8 14.2 1.0
O B:GLY224 4.8 16.4 1.0
C B:LEU199 4.8 14.2 1.0
CA B:VAL198 4.9 15.4 1.0
CB B:VAL198 5.0 16.3 1.0
N B:ASP196 5.0 19.1 1.0

Potassium binding site 4 out of 4 in 5g12

Go back to Potassium Binding Sites List in 5g12
Potassium binding site 4 out of 4 in the Pseudomonas Aeruginosa Hdah (Y313F) Unliganded.


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 (Y313F) Unliganded. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1380

b:14.2
occ:1.00
 O B:LEU203 2.6 12.7 1.0
O B:ASP181 2.6 14.2 1.0
OD1 B:ASP179 2.6 15.8 1.0
O B:HIS183 2.6 13.7 1.0
OG B:SER202 2.6 15.0 1.0
O B:ASP179 2.7 13.4 1.0
CG B:ASP179 3.2 16.0 1.0
C B:ASP179 3.5 13.7 1.0
C B:LEU203 3.6 12.8 1.0
C B:ASP181 3.7 14.2 1.0
C B:HIS183 3.7 13.9 1.0
CB B:SER202 3.8 14.5 1.0
CB B:ASP179 3.9 15.1 1.0
N B:LEU203 3.9 13.0 1.0
OD2 B:ASP179 3.9 16.6 1.0
N B:ASP181 4.0 14.1 1.0
N B:GLY185 4.1 14.8 1.0
CA B:SER202 4.1 14.2 1.0
CB B:HIS204 4.1 13.4 1.0
N B:TRP180 4.2 13.0 1.0
CA B:ASP179 4.3 14.1 1.0
CA B:ASP181 4.3 14.2 1.0
C B:SER202 4.3 13.5 1.0
CA B:HIS184 4.3 14.4 1.0
C B:TRP180 4.3 13.3 1.0
CA B:TRP180 4.4 13.7 1.0
CB B:ASP181 4.4 14.6 1.0
N B:HIS204 4.4 12.7 1.0
N B:HIS184 4.4 13.8 1.0
CA B:LEU203 4.4 13.1 1.0
N B:HIS183 4.5 14.2 1.0
CA B:HIS204 4.5 13.3 1.0
C B:HIS184 4.5 14.4 1.0
O B:HOH2080 4.6 16.3 1.0
ND1 B:HIS204 4.6 15.0 1.0
C B:VAL182 4.7 13.7 1.0
N B:VAL182 4.7 14.2 1.0
CA B:HIS183 4.7 14.1 1.0
CE1 B:HIS143 4.7 20.7 1.0
CG B:HIS204 4.9 14.4 1.0
ND1 B:HIS143 4.9 21.3 1.0
CA B:GLY185 5.0 14.9 1.0
CA B:VAL182 5.0 14.3 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: Sat Aug 9 09:08:37 2025

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