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Potassium in PDB 9gkz: Crystal Structure of Acetylpolyamine Amidohydrolase (Apah) From Pseudomonas Sp. M30-35

Protein crystallography data

The structure of Crystal Structure of Acetylpolyamine Amidohydrolase (Apah) From Pseudomonas Sp. M30-35, PDB code: 9gkz was solved by L.G.Graf, S.Schulze, G.J.Palm, M.Lammers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.67 / 2.72
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 147.342, 48.858, 82.249, 90, 90, 90
R / Rfree (%) 15.6 / 23.3

Other elements in 9gkz:

The structure of Crystal Structure of Acetylpolyamine Amidohydrolase (Apah) From Pseudomonas Sp. M30-35 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Chlorine (Cl) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Acetylpolyamine Amidohydrolase (Apah) From Pseudomonas Sp. M30-35 (pdb code 9gkz). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the Crystal Structure of Acetylpolyamine Amidohydrolase (Apah) From Pseudomonas Sp. M30-35, PDB code: 9gkz:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6;

Potassium binding site 1 out of 6 in 9gkz

Go back to Potassium Binding Sites List in 9gkz
Potassium binding site 1 out of 6 in the Crystal Structure of Acetylpolyamine Amidohydrolase (Apah) From Pseudomonas Sp. M30-35


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 Acetylpolyamine Amidohydrolase (Apah) From Pseudomonas Sp. M30-35 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K402

b:27.1
occ:1.00
 O A:ASP195 2.6 25.1 1.0
OD1 A:ASP193 2.7 29.2 1.0
O A:ILE217 2.7 32.0 1.0
O A:HIS197 2.8 33.6 1.0
O A:ASP193 2.8 27.4 1.0
OG A:SER216 2.9 31.6 1.0
CG A:ASP193 3.4 27.2 1.0
C A:ILE217 3.5 25.8 1.0
C A:ASP193 3.6 28.1 1.0
C A:ASP195 3.6 29.1 1.0
N A:ILE217 3.7 23.3 1.0
N A:ASP195 3.7 30.8 1.0
C A:HIS197 3.7 30.4 1.0
CB A:ASP193 3.8 26.1 1.0
CB A:HIS218 3.9 30.7 1.0
CA A:ASP195 4.0 30.3 1.0
CB A:SER216 4.0 31.7 1.0
CB A:ASP195 4.1 22.8 1.0
N A:HIS218 4.1 23.1 1.0
CA A:HIS218 4.1 29.9 1.0
C A:VAL194 4.2 31.3 1.0
OD2 A:ASP193 4.2 24.1 1.0
CA A:ILE217 4.2 21.6 1.0
ND1 A:HIS218 4.2 28.8 1.0
CA A:SER216 4.3 30.1 1.0
N A:VAL194 4.3 25.8 1.0
C A:SER216 4.3 29.5 1.0
CA A:ASP193 4.3 25.2 1.0
N A:HIS197 4.4 26.4 1.0
CA A:HIS198 4.4 31.7 1.0
N A:HIS198 4.5 28.2 1.0
N A:GLY199 4.5 29.6 1.0
CA A:VAL194 4.5 22.9 1.0
CG A:HIS218 4.5 29.2 1.0
O A:HOH504 4.6 26.7 1.0
C A:TYR196 4.6 27.5 1.0
CA A:HIS197 4.7 26.7 1.0
N A:TYR196 4.7 24.2 1.0
C A:HIS198 4.7 26.8 1.0
O A:VAL194 4.9 30.8 1.0
CE1 A:HIS158 4.9 27.1 1.0

Potassium binding site 2 out of 6 in 9gkz

Go back to Potassium Binding Sites List in 9gkz
Potassium binding site 2 out of 6 in the Crystal Structure of Acetylpolyamine Amidohydrolase (Apah) From Pseudomonas Sp. M30-35


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 Acetylpolyamine Amidohydrolase (Apah) From Pseudomonas Sp. M30-35 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K403

b:57.9
occ:1.00
 N A:TYR170 2.7 28.4 1.0
N A:LEU171 3.0 31.9 1.0
O A:PRO156 3.0 27.5 1.0
O A:HOH521 3.1 29.7 1.0
CA A:TYR170 3.3 26.5 1.0
CB A:TYR170 3.4 28.2 1.0
CG A:PRO155 3.4 37.0 1.0
O A:LEU171 3.4 20.5 1.0
C A:TYR170 3.6 25.6 1.0
CD2 A:TYR170 3.6 30.9 1.0
CB A:PRO155 3.8 35.4 1.0
C A:CYS169 3.8 31.2 1.0
CA A:CYS169 4.0 32.5 1.0
CG A:TYR170 4.0 28.3 1.0
O A:PRO155 4.0 24.4 1.0
CA A:LEU171 4.0 28.6 1.0
C A:PRO156 4.0 32.3 1.0
C A:LEU171 4.1 23.1 1.0
C A:PRO155 4.2 29.5 1.0
CB A:ALA128 4.3 27.6 1.0
O A:TYR168 4.5 29.6 1.0
CB A:LEU171 4.5 28.2 1.0
CA A:GLY157 4.5 24.7 1.0
CA A:PRO155 4.5 33.8 1.0
CD A:PRO155 4.6 27.1 1.0
CA A:ALA128 4.6 33.0 1.0
N A:GLY157 4.8 31.4 1.0
N A:PRO156 4.8 35.0 1.0
CE2 A:TYR170 4.8 31.4 1.0
CB A:CYS169 4.8 28.1 1.0
ND2 A:ASN173 4.8 29.9 1.0
O A:TYR170 4.8 26.8 1.0
OD1 A:ASN173 4.9 28.2 1.0
O A:CYS169 4.9 30.9 1.0
CG A:LEU171 4.9 24.5 1.0
N A:CYS169 5.0 33.7 1.0

Potassium binding site 3 out of 6 in 9gkz

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Potassium binding site 3 out of 6 in the Crystal Structure of Acetylpolyamine Amidohydrolase (Apah) From Pseudomonas Sp. M30-35


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 Acetylpolyamine Amidohydrolase (Apah) From Pseudomonas Sp. M30-35 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K404

b:36.7
occ:1.00
 O A:PHE206 2.5 32.0 1.0
O A:VAL212 2.7 33.2 1.0
O A:HOH519 2.8 32.4 1.0
O A:ARG209 2.8 34.7 1.0
O A:PHE243 3.1 34.8 1.0
O A:HOH526 3.4 24.3 1.0
C A:PHE206 3.5 34.6 1.0
CB A:PHE206 3.8 26.4 1.0
C A:PHE243 3.9 34.8 1.0
C A:ARG209 3.9 35.2 1.0
C A:VAL212 3.9 32.5 1.0
CB A:PHE243 4.0 29.6 1.0
N A:ARG209 4.3 35.2 1.0
CA A:PHE206 4.3 30.2 1.0
N A:TYR207 4.4 29.1 1.0
C A:TYR207 4.5 36.3 1.0
CA A:TYR207 4.5 25.9 1.0
CA A:ARG209 4.5 38.2 1.0
O A:TYR207 4.6 36.1 1.0
CA A:PHE243 4.6 36.8 1.0
CA A:LEU213 4.6 34.4 1.0
O A:GLY240 4.6 32.7 1.0
N A:PHE214 4.6 33.5 1.0
N A:ASN244 4.7 31.3 1.0
N A:LEU213 4.7 35.1 1.0
CB A:ARG209 4.7 33.4 1.0
CA A:VAL212 4.9 34.4 1.0
CA A:GLY240 4.9 34.9 1.0
N A:SER210 4.9 33.6 1.0
N A:SER208 5.0 40.5 1.0
C A:LEU213 5.0 33.7 1.0

Potassium binding site 4 out of 6 in 9gkz

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Potassium binding site 4 out of 6 in the Crystal Structure of Acetylpolyamine Amidohydrolase (Apah) From Pseudomonas Sp. M30-35


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 Acetylpolyamine Amidohydrolase (Apah) From Pseudomonas Sp. M30-35 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K403

b:26.1
occ:1.00
 OD1 B:ASP193 2.6 25.5 1.0
O B:ASP195 2.7 29.2 1.0
O B:ASP193 2.7 35.0 1.0
O B:HIS197 2.7 26.3 1.0
OG B:SER216 2.7 24.8 1.0
O B:ILE217 2.8 31.6 1.0
CG B:ASP193 3.3 27.5 1.0
C B:ASP193 3.4 31.3 1.0
C B:ASP195 3.6 27.7 1.0
C B:HIS197 3.6 26.6 1.0
CB B:ASP193 3.7 30.1 1.0
C B:ILE217 3.7 28.7 1.0
N B:ASP195 3.7 31.5 1.0
CB B:HIS218 3.9 28.6 1.0
N B:ILE217 3.9 29.8 1.0
CA B:ASP195 4.0 23.1 1.0
CB B:SER216 4.0 29.5 1.0
C B:VAL194 4.1 33.8 1.0
CB B:ASP195 4.1 26.1 1.0
OD2 B:ASP193 4.1 29.0 1.0
N B:VAL194 4.2 25.9 1.0
ND1 B:HIS218 4.2 31.3 1.0
CA B:ASP193 4.2 28.5 1.0
CA B:HIS198 4.2 28.0 1.0
N B:HIS198 4.3 24.1 1.0
CA B:SER216 4.4 30.3 1.0
N B:HIS197 4.4 29.0 1.0
CA B:VAL194 4.4 29.7 1.0
N B:GLY199 4.4 27.7 1.0
CA B:ILE217 4.5 30.8 1.0
C B:SER216 4.5 30.6 1.0
CG B:HIS218 4.5 29.1 1.0
CA B:HIS218 4.5 31.0 1.0
N B:HIS218 4.6 27.4 1.0
C B:TYR196 4.6 28.5 1.0
CA B:HIS197 4.6 25.3 1.0
C B:HIS198 4.7 28.2 1.0
O B:VAL194 4.7 29.8 1.0
N B:TYR196 4.7 29.0 1.0
O B:HOH538 4.7 28.1 1.0
O B:TYR196 4.9 27.6 1.0

Potassium binding site 5 out of 6 in 9gkz

Go back to Potassium Binding Sites List in 9gkz
Potassium binding site 5 out of 6 in the Crystal Structure of Acetylpolyamine Amidohydrolase (Apah) From Pseudomonas Sp. M30-35


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 Acetylpolyamine Amidohydrolase (Apah) From Pseudomonas Sp. M30-35 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K404

b:37.6
occ:1.00
 O B:PHE206 2.5 38.7 1.0
O B:HOH529 2.6 36.7 1.0
O B:ARG209 2.8 42.1 1.0
O B:VAL212 2.8 34.6 1.0
O B:PHE243 3.1 37.2 1.0
O B:HOH509 3.2 31.1 1.0
C B:PHE206 3.7 35.6 1.0
C B:ARG209 3.8 42.6 1.0
C B:PHE243 3.9 39.4 1.0
CB B:PHE206 4.0 29.9 1.0
C B:VAL212 4.0 35.4 1.0
CB B:PHE243 4.0 41.4 1.0
N B:PHE214 4.3 32.2 1.0
N B:ARG209 4.4 39.2 1.0
O B:TYR207 4.5 34.1 1.0
CA B:PHE206 4.5 34.3 1.0
CA B:TYR207 4.5 32.7 1.0
CA B:LEU213 4.5 34.5 1.0
C B:TYR207 4.5 38.0 1.0
N B:TYR207 4.5 36.7 1.0
CA B:ARG209 4.6 39.3 1.0
N B:ASN244 4.6 43.2 1.0
CA B:PHE243 4.6 41.8 1.0
CB B:ASN244 4.7 29.8 1.0
O B:GLY240 4.7 42.2 1.0
N B:LEU213 4.7 35.3 1.0
OD1 B:ASN244 4.8 38.4 1.0
CA B:ASN244 4.8 36.1 1.0
CB B:PHE214 4.8 29.9 1.0
CB B:ARG209 4.8 31.2 1.0
C B:LEU213 4.8 33.9 1.0
N B:SER210 4.8 37.6 1.0
CA B:SER210 5.0 44.4 1.0

Potassium binding site 6 out of 6 in 9gkz

Go back to Potassium Binding Sites List in 9gkz
Potassium binding site 6 out of 6 in the Crystal Structure of Acetylpolyamine Amidohydrolase (Apah) From Pseudomonas Sp. M30-35


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 Acetylpolyamine Amidohydrolase (Apah) From Pseudomonas Sp. M30-35 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K405

b:57.0
occ:1.00
 OD2 B:ASP193 2.7 29.0 1.0
OG1 B:THR202 3.0 32.3 1.0
OG B:SER280 3.0 28.8 1.0
CB B:HIS158 3.3 30.9 1.0
CB B:SER280 3.4 26.8 1.0
CB B:THR202 3.4 32.5 1.0
CG B:ASP193 3.6 27.5 1.0
CE1 B:PHE214 3.6 29.6 1.0
CG2 B:THR202 3.6 26.9 1.0
CB B:ASP193 3.9 30.1 1.0
CG2 B:ILE191 3.9 31.3 1.0
OE2 B:GLU320 4.2 33.2 1.0
CG B:HIS158 4.3 35.0 1.0
ND1 B:HIS158 4.3 35.2 1.0
CA B:HIS158 4.3 27.7 1.0
CZ B:PHE214 4.3 29.6 1.0
CA B:GLY199 4.5 31.4 1.0
CB B:ALA174 4.6 25.7 1.0
CD1 B:PHE214 4.6 33.0 1.0
OD1 B:ASP193 4.6 25.5 1.0
CA B:ASP193 4.7 28.5 1.0
O B:HOH533 4.8 30.6 1.0
CA B:SER280 4.9 30.6 1.0
CA B:THR202 4.9 32.0 1.0
O B:GLY199 4.9 32.9 1.0

Reference:

L.G.Graf, C.Moreno-Yruela, C.Qin, S.Schulze, G.J.Palm, O.Schmoeker, N.Wang, D.Hocking, L.Jebeli, B.Girbardt, L.Berndt, D.M.Weis, M.Janetzky, D.Zuehlke, S.Sievers, R.A.Strugnell, C.A.Olsen, K.Hofmann, M.Lammers. Distribution and Diversity of Classical Deacylases in Bacteria Nature Communications 2024.
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