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Potassium in PDB 4zup: Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate Inhibitor

Protein crystallography data

The structure of Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate Inhibitor, PDB code: 4zup was solved by C.Decroos, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.68 / 1.42
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.715, 120.903, 64.146, 90.00, 96.98, 90.00
R / Rfree (%) 13.1 / 15.2

Other elements in 4zup:

The structure of Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate Inhibitor also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate Inhibitor (pdb code 4zup). 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 Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate Inhibitor, PDB code: 4zup:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 4zup

Go back to Potassium Binding Sites List in 4zup
Potassium binding site 1 out of 4 in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate 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 Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K403

b:8.8
occ:1.00
 O A:ASP195 2.6 9.0 1.0
O A:LEU217 2.7 8.8 1.0
OD1 A:ASP193 2.7 8.6 1.0
O A:HIS197 2.7 8.3 1.0
OG A:SER216 2.8 8.8 1.0
O A:ASP193 2.9 8.8 1.0
CG A:ASP193 3.3 8.6 1.0
C A:ASP193 3.5 8.2 1.0
C A:ASP195 3.6 8.0 1.0
C A:HIS197 3.7 7.2 1.0
C A:LEU217 3.7 7.6 1.0
CB A:ASP193 3.8 8.3 1.0
N A:ASP195 3.8 7.8 1.0
CB A:HIS218 3.9 8.4 1.0
N A:LEU217 3.9 8.0 1.0
CB A:SER216 4.0 8.7 1.0
OD2 A:ASP193 4.1 9.0 1.0
CA A:ASP195 4.1 7.6 1.0
N A:VAL194 4.2 7.5 1.0
C A:VAL194 4.2 7.8 1.0
CA A:HIS198 4.2 8.5 1.0
CA A:ASP193 4.2 8.8 1.0
N A:HIS198 4.3 8.1 1.0
ND1 A:HIS218 4.3 8.8 1.0
CB A:ASP195 4.3 7.7 1.0
N A:GLY199 4.3 8.0 1.0
CA A:SER216 4.3 8.3 1.0
CA A:VAL194 4.4 8.1 1.0
CA A:HIS218 4.4 7.8 1.0
N A:HIS197 4.4 7.8 1.0
C A:SER216 4.5 8.3 1.0
CA A:LEU217 4.5 7.6 1.0
N A:HIS218 4.5 7.6 1.0
C A:PHE196 4.5 8.2 1.0
CG A:HIS218 4.5 8.1 1.0
O A:HOH706 4.6 9.3 1.0
C A:HIS198 4.6 8.6 1.0
CA A:HIS197 4.7 7.7 1.0
N A:PHE196 4.7 7.1 1.0
O A:PHE196 4.7 8.5 1.0
CE1 A:HIS158 4.8 8.6 1.0
O A:VAL194 4.8 8.4 1.0
ND1 A:HIS158 4.9 8.4 1.0

Potassium binding site 2 out of 4 in 4zup

Go back to Potassium Binding Sites List in 4zup
Potassium binding site 2 out of 4 in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate 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 Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K404

b:11.4
occ:1.00
 O A:VAL212 2.6 12.1 1.0
O A:ARG209 2.7 12.9 1.0
O A:PHE206 2.8 9.7 1.0
O A:HOH609 2.8 11.2 1.0
OG1 A:THR243 2.8 13.4 1.0
O A:THR243 3.0 10.2 1.0
O A:HOH718 3.6 11.0 1.0
CB A:THR243 3.7 12.6 1.0
C A:THR243 3.7 10.9 1.0
C A:PHE206 3.8 8.9 1.0
C A:VAL212 3.8 10.7 1.0
C A:ARG209 3.9 11.9 1.0
CB A:PHE206 4.0 9.2 1.0
OG1 A:THR244 4.1 10.3 1.0
CA A:THR243 4.3 10.7 1.0
O A:GLY240 4.4 11.5 1.0
N A:PHE214 4.5 9.2 1.0
CA A:GLY240 4.5 13.8 1.0
CA A:PHE213 4.5 9.5 1.0
CA A:PHE206 4.5 8.7 1.0
N A:THR244 4.5 10.6 1.0
N A:ARG209 4.6 13.2 1.0
N A:PHE213 4.6 10.3 1.0
O A:TYR207 4.6 10.4 1.0
N A:TYR207 4.7 9.3 1.0
CA A:TYR207 4.7 10.1 1.0
CA A:ARG209 4.7 13.0 1.0
C A:TYR207 4.7 9.8 1.0
C A:PHE213 4.9 11.0 1.0
CA A:VAL212 4.9 10.7 1.0
N A:GLY210 4.9 13.5 1.0
CB A:ARG209 4.9 13.9 1.0
C A:GLY240 4.9 12.0 1.0
CA A:GLY210 5.0 15.2 1.0
N A:VAL212 5.0 11.9 1.0
CG2 A:THR243 5.0 14.3 1.0

Potassium binding site 3 out of 4 in 4zup

Go back to Potassium Binding Sites List in 4zup
Potassium binding site 3 out of 4 in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate 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 Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K403

b:8.2
occ:1.00
 O B:ASP195 2.6 8.7 1.0
O B:LEU217 2.6 8.2 1.0
OD1 B:ASP193 2.7 7.3 1.0
O B:HIS197 2.7 7.9 1.0
OG B:SER216 2.8 8.2 1.0
O B:ASP193 2.8 8.8 1.0
CG B:ASP193 3.3 9.4 1.0
C B:ASP193 3.5 9.0 1.0
C B:ASP195 3.6 6.9 1.0
C B:LEU217 3.7 7.7 1.0
C B:HIS197 3.7 6.7 1.0
N B:ASP195 3.8 8.1 1.0
CB B:ASP193 3.8 8.2 1.0
CB B:HIS218 3.9 8.4 1.0
N B:LEU217 3.9 7.9 1.0
CB B:SER216 4.0 8.4 1.0
OD2 B:ASP193 4.1 8.6 1.0
CA B:ASP195 4.1 7.5 1.0
N B:VAL194 4.1 7.7 1.0
C B:VAL194 4.2 7.2 1.0
CA B:HIS198 4.2 7.4 1.0
CA B:ASP193 4.2 8.3 1.0
N B:GLY199 4.3 6.8 1.0
N B:HIS198 4.3 7.6 1.0
ND1 B:HIS218 4.3 7.7 1.0
CB B:ASP195 4.3 7.7 1.0
CA B:SER216 4.4 7.4 1.0
CA B:VAL194 4.4 7.4 1.0
N B:HIS197 4.4 7.3 1.0
CA B:HIS218 4.4 8.3 1.0
CA B:LEU217 4.5 8.3 1.0
C B:SER216 4.5 8.0 1.0
C B:PHE196 4.5 8.0 1.0
N B:HIS218 4.5 7.7 1.0
C B:HIS198 4.5 7.6 1.0
O B:HOH684 4.5 8.4 1.0
CG B:HIS218 4.6 7.0 1.0
CA B:HIS197 4.7 7.0 1.0
N B:PHE196 4.7 6.7 1.0
O B:PHE196 4.7 8.4 1.0
CE1 B:HIS158 4.8 8.5 1.0
O B:VAL194 4.9 8.8 1.0
ND1 B:HIS158 4.9 8.2 1.0

Potassium binding site 4 out of 4 in 4zup

Go back to Potassium Binding Sites List in 4zup
Potassium binding site 4 out of 4 in the Crystal Structure of Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate 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 Acetylpolyamine Amidohydrolase From Mycoplana Ramosa in Complex with A Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K404

b:10.8
occ:1.00
 O B:VAL212 2.6 12.1 1.0
O B:HOH610 2.8 9.8 1.0
O B:ARG209 2.8 11.5 1.0
O B:PHE206 2.8 9.2 1.0
OG1 B:THR243 2.8 12.1 1.0
O B:THR243 3.0 9.1 1.0
CB B:THR243 3.6 10.8 1.0
O B:HOH698 3.7 10.6 1.0
C B:THR243 3.7 9.6 1.0
C B:PHE206 3.8 8.9 1.0
C B:VAL212 3.9 10.7 1.0
C B:ARG209 4.0 9.8 1.0
CB B:PHE206 4.0 10.1 1.0
OG1 B:THR244 4.1 10.4 1.0
CA B:THR243 4.2 9.9 1.0
CA B:GLY240 4.4 10.1 1.0
O B:GLY240 4.4 10.1 1.0
N B:PHE214 4.5 9.0 1.0
CA B:PHE213 4.5 10.0 1.0
N B:THR244 4.5 10.1 1.0
CA B:PHE206 4.5 8.9 1.0
N B:ARG209 4.6 10.6 1.0
O B:TYR207 4.6 9.5 1.0
N B:PHE213 4.6 10.1 1.0
CA B:TYR207 4.7 9.0 1.0
N B:TYR207 4.7 8.7 1.0
C B:TYR207 4.7 8.9 1.0
CA B:ARG209 4.7 10.5 1.0
CA B:VAL212 4.9 10.0 1.0
N B:GLY210 4.9 10.6 1.0
C B:PHE213 4.9 10.1 1.0
C B:GLY240 4.9 9.9 1.0
CB B:ARG209 5.0 11.5 1.0
CA B:GLY210 5.0 11.8 1.0
N B:VAL212 5.0 10.2 1.0
CG2 B:THR243 5.0 13.2 1.0

Reference:

C.Decroos, D.W.Christianson. Design, Synthesis, and Evaluation of Polyamine Deacetylase Inhibitors, and High-Resolution Crystal Structures of Their Complexes with Acetylpolyamine Amidohydrolase. Biochemistry V. 54 4692 2015.
ISSN: ISSN 0006-2960
PubMed: 26200446
DOI: 10.1021/ACS.BIOCHEM.5B00536
Page generated: Mon Aug 12 12:49:27 2024

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