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Potassium in PDB 6pi8: Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with Acetate

Protein crystallography data

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with Acetate, PDB code: 6pi8 was solved by J.D.Osko, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.08 / 1.64
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.371, 121.060, 66.556, 90.00, 109.53, 90.00
R / Rfree (%) 16.8 / 19.4

Other elements in 6pi8:

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with Acetate also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Zinc (Zn) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with Acetate (pdb code 6pi8). 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 Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with Acetate, PDB code: 6pi8:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6pi8

Go back to Potassium Binding Sites List in 6pi8
Potassium binding site 1 out of 4 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with Acetate


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 Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K406

b:11.3
occ:0.51
 O A:LEU217 2.4 13.2 1.0
O A:ASP195 2.4 13.2 1.0
OD1 A:ASP193 2.5 15.7 1.0
O A:HIS197 2.6 13.5 1.0
OG A:SER216 2.6 13.7 1.0
O A:ASP193 2.8 14.9 1.0
CG A:ASP193 3.3 14.7 1.0
C A:ASP195 3.4 14.7 1.0
C A:ASP193 3.5 12.9 1.0
C A:LEU217 3.5 11.9 1.0
C A:HIS197 3.6 11.6 1.0
N A:ASP195 3.7 12.6 1.0
CB A:ASP193 3.7 10.9 1.0
CB A:HIS218 3.9 11.3 1.0
N A:LEU217 3.9 12.9 1.0
CB A:SER216 3.9 14.7 1.0
CA A:ASP195 4.0 11.9 1.0
C A:VAL194 4.1 13.4 1.0
N A:VAL194 4.1 14.2 1.0
OD2 A:ASP193 4.2 16.0 1.0
CB A:ASP195 4.2 15.8 1.0
CA A:ASP193 4.2 13.5 1.0
ND1 A:HIS218 4.2 12.0 1.0
N A:HIS197 4.2 12.2 1.0
CA A:HIS198 4.3 11.8 1.0
N A:HIS198 4.3 13.3 1.0
CA A:SER216 4.3 11.7 1.0
CA A:VAL194 4.3 11.8 1.0
CA A:LEU217 4.3 14.3 1.0
CA A:HIS218 4.3 11.2 1.0
N A:GLY199 4.4 13.7 1.0
N A:HIS218 4.4 10.8 1.0
C A:SER216 4.4 11.8 1.0
O A:HOH645 4.4 14.9 1.0
C A:PHE196 4.4 14.4 1.0
CG A:HIS218 4.5 12.2 1.0
CA A:HIS197 4.5 11.5 1.0
N A:PHE196 4.6 11.2 1.0
C A:HIS198 4.6 13.3 1.0
O A:VAL194 4.7 13.8 1.0
O A:PHE196 4.8 11.5 1.0
CE1 A:HIS158 4.9 13.9 1.0
CA A:PHE196 4.9 14.4 1.0

Potassium binding site 2 out of 4 in 6pi8

Go back to Potassium Binding Sites List in 6pi8
Potassium binding site 2 out of 4 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with Acetate


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 Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K407

b:19.4
occ:0.82
 O A:VAL212 2.7 20.9 1.0
O A:PHE206 2.7 17.5 1.0
O A:ARG209 2.8 22.8 1.0
O A:HOH573 2.8 16.4 1.0
O A:TYR243 3.0 15.2 1.0
O A:HOH565 3.0 16.5 1.0
C A:PHE206 3.6 15.1 1.0
C A:TYR243 3.8 14.3 1.0
CB A:PHE206 3.8 15.2 1.0
OG1 A:THR214 3.9 15.7 1.0
CB A:TYR243 3.9 17.0 1.0
C A:VAL212 3.9 21.2 1.0
C A:ARG209 3.9 23.3 1.0
N A:THR214 4.3 15.1 1.0
CA A:PHE206 4.4 17.2 1.0
N A:ARG209 4.4 19.8 1.0
CA A:TYR207 4.4 16.4 1.0
CA A:TYR243 4.5 17.5 1.0
N A:TYR207 4.5 14.4 1.0
O A:TYR207 4.5 17.1 1.0
C A:TYR207 4.6 15.8 1.0
CA A:LEU213 4.6 14.4 1.0
CG2 A:THR214 4.6 16.2 1.0
CA A:ARG209 4.6 19.6 1.0
N A:ASN244 4.6 16.2 1.0
N A:LEU213 4.7 16.6 1.0
CB A:THR214 4.8 17.8 1.0
CB A:ARG209 4.8 15.9 1.0
C A:LEU213 4.8 16.8 1.0
O A:GLY240 4.9 17.0 1.0
CB A:ASN244 4.9 16.7 1.0
CA A:VAL212 5.0 20.1 1.0
CA A:ASN244 5.0 14.4 1.0
N A:SER210 5.0 17.8 1.0

Potassium binding site 3 out of 4 in 6pi8

Go back to Potassium Binding Sites List in 6pi8
Potassium binding site 3 out of 4 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with Acetate


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 Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K405

b:16.7
occ:0.76
 O B:VAL212 2.7 15.2 1.0
O B:HOH630 2.8 15.8 1.0
O B:PHE206 2.8 14.4 1.0
O B:ARG209 2.9 17.0 1.0
O B:TYR243 2.9 14.0 1.0
O B:HOH535 3.0 14.9 1.0
C B:PHE206 3.7 13.3 1.0
C B:TYR243 3.8 14.7 1.0
OG1 B:THR214 3.8 14.7 1.0
C B:VAL212 3.9 12.8 1.0
CB B:TYR243 3.9 14.2 1.0
CB B:PHE206 4.0 15.3 1.0
C B:ARG209 4.0 16.1 1.0
N B:THR214 4.3 12.9 1.0
CA B:TYR243 4.5 15.3 1.0
N B:ARG209 4.5 15.6 1.0
CA B:TYR207 4.5 15.8 1.0
CA B:PHE206 4.5 15.4 1.0
O B:TYR207 4.5 14.7 1.0
CA B:LEU213 4.5 13.6 1.0
N B:TYR207 4.6 13.3 1.0
N B:ASN244 4.6 12.2 1.0
C B:TYR207 4.6 13.7 1.0
CA B:ARG209 4.6 15.0 1.0
N B:LEU213 4.7 14.3 1.0
CG2 B:THR214 4.7 13.1 1.0
C B:LEU213 4.8 14.4 1.0
CB B:ARG209 4.8 13.5 1.0
CB B:THR214 4.8 13.7 1.0
O B:GLY240 4.8 16.7 1.0
CB B:ASN244 4.9 10.3 1.0
CA B:ASN244 4.9 12.4 1.0
CA B:VAL212 5.0 13.8 1.0

Potassium binding site 4 out of 4 in 6pi8

Go back to Potassium Binding Sites List in 6pi8
Potassium binding site 4 out of 4 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with Acetate


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 Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K406

b:11.7
occ:0.56
 O B:ASP195 2.4 13.5 1.0
O B:LEU217 2.5 12.3 1.0
OD1 B:ASP193 2.5 14.9 1.0
O B:HIS197 2.6 10.6 1.0
OG B:SER216 2.7 12.6 1.0
O B:ASP193 2.9 13.3 1.0
CG B:ASP193 3.3 17.0 1.0
C B:ASP195 3.4 12.0 1.0
C B:ASP193 3.5 13.1 1.0
C B:LEU217 3.5 10.1 1.0
C B:HIS197 3.6 13.3 1.0
N B:ASP195 3.6 12.6 1.0
CB B:ASP193 3.7 10.4 1.0
N B:LEU217 3.8 11.7 1.0
CB B:HIS218 3.9 9.5 1.0
CB B:SER216 3.9 10.4 1.0
CA B:ASP195 4.0 11.2 1.0
C B:VAL194 4.0 13.8 1.0
N B:VAL194 4.1 12.2 1.0
OD2 B:ASP193 4.2 15.7 1.0
CB B:ASP195 4.2 12.3 1.0
CA B:ASP193 4.2 11.3 1.0
ND1 B:HIS218 4.2 11.3 1.0
CA B:HIS198 4.3 12.7 1.0
CA B:VAL194 4.3 11.6 1.0
N B:HIS197 4.3 10.8 1.0
N B:HIS198 4.3 11.4 1.0
CA B:SER216 4.3 9.3 1.0
CA B:LEU217 4.3 11.8 1.0
N B:GLY199 4.4 11.7 1.0
CA B:HIS218 4.4 12.0 1.0
O B:HOH646 4.4 15.2 1.0
N B:HIS218 4.4 11.3 1.0
C B:SER216 4.4 10.1 1.0
C B:PHE196 4.4 11.8 1.0
CG B:HIS218 4.5 11.8 1.0
CA B:HIS197 4.6 12.0 1.0
N B:PHE196 4.6 11.9 1.0
C B:HIS198 4.6 13.3 1.0
O B:VAL194 4.7 16.3 1.0
O B:PHE196 4.7 12.8 1.0
CE1 B:HIS158 4.9 13.7 1.0
CA B:PHE196 4.9 13.7 1.0
OD1 B:ASP195 5.0 14.8 1.0

Reference:

J.D.Osko, B.W.Roose, S.A.Shinsky, D.W.Christianson. Structure and Function of the Acetylpolyamine Amidohydrolase From the Deep Earth Halophilemarinobacter Subterrani. Biochemistry V. 58 3755 2019.
ISSN: ISSN 0006-2960
PubMed: 31436969
DOI: 10.1021/ACS.BIOCHEM.9B00582
Page generated: Mon Aug 12 17:07:34 2024

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