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Potassium in PDB 6phr: Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol

Protein crystallography data

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol, PDB code: 6phr 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) 61.77 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.874, 120.680, 65.360, 90.00, 109.09, 90.00
R / Rfree (%) 17.9 / 20.8

Other elements in 6phr:

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol also contains other interesting chemical elements:

Magnesium (Mg) 2 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 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol (pdb code 6phr). 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 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol, PDB code: 6phr:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6phr

Go back to Potassium Binding Sites List in 6phr
Potassium binding site 1 out of 4 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol


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 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K505

b:14.3
occ:0.71
 O A:PHE206 2.6 15.9 1.0
O A:HOH626 2.7 14.8 1.0
O A:VAL212 2.7 12.4 1.0
O A:ARG209 2.8 17.3 1.0
O A:TYR243 3.0 14.0 1.0
O A:HOH666 3.0 14.9 1.0
C A:PHE206 3.6 13.9 1.0
C A:TYR243 3.8 13.5 1.0
CB A:TYR243 3.8 15.4 1.0
CB A:PHE206 3.8 13.5 1.0
OG1 A:THR214 3.9 11.9 1.0
C A:VAL212 4.0 15.2 1.0
C A:ARG209 4.0 16.8 1.0
N A:THR214 4.3 11.6 1.0
CA A:PHE206 4.4 13.6 1.0
CA A:TYR243 4.4 14.9 1.0
N A:ARG209 4.4 16.6 1.0
CA A:TYR207 4.4 15.4 1.0
N A:TYR207 4.4 13.5 1.0
CG2 A:THR214 4.5 13.2 1.0
CA A:LEU213 4.5 12.9 1.0
C A:TYR207 4.6 16.1 1.0
N A:ASN244 4.6 13.2 1.0
O A:TYR207 4.6 15.5 1.0
CA A:ARG209 4.6 17.4 1.0
N A:LEU213 4.7 13.8 1.0
O A:GLY240 4.7 15.9 1.0
CB A:THR214 4.8 10.5 1.0
C A:LEU213 4.8 12.6 1.0
CB A:ARG209 4.9 16.4 1.0
CB A:ASN244 4.9 12.0 1.0
CA A:ASN244 4.9 12.5 1.0
CA A:GLY240 5.0 18.2 1.0

Potassium binding site 2 out of 4 in 6phr

Go back to Potassium Binding Sites List in 6phr
Potassium binding site 2 out of 4 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol


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 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K506

b:7.8
occ:0.56
 O A:ASP195 2.4 10.7 1.0
O A:LEU217 2.4 10.6 1.0
OD1 A:ASP193 2.4 10.5 1.0
O A:HIS197 2.6 10.9 1.0
OG A:SER216 2.7 9.4 1.0
O A:ASP193 2.9 11.2 1.0
CG A:ASP193 3.2 10.7 1.0
C A:ASP195 3.4 9.9 1.0
C A:LEU217 3.5 8.4 1.0
C A:ASP193 3.5 10.1 1.0
N A:ASP195 3.6 11.4 1.0
C A:HIS197 3.6 9.3 1.0
CB A:ASP193 3.7 9.5 1.0
CB A:HIS218 3.8 9.6 1.0
N A:LEU217 3.8 8.4 1.0
CA A:ASP195 3.9 10.7 1.0
CB A:SER216 4.0 10.9 1.0
C A:VAL194 4.0 9.6 1.0
N A:VAL194 4.1 10.3 1.0
OD2 A:ASP193 4.1 13.4 1.0
CB A:ASP195 4.2 9.1 1.0
ND1 A:HIS218 4.2 8.2 1.0
CA A:ASP193 4.2 10.6 1.0
CA A:HIS198 4.3 9.0 1.0
CA A:VAL194 4.3 9.4 1.0
CA A:LEU217 4.3 9.1 1.0
N A:HIS197 4.3 7.7 1.0
N A:HIS198 4.3 8.1 1.0
CA A:HIS218 4.3 8.8 1.0
CA A:SER216 4.4 8.7 1.0
N A:HIS218 4.4 8.2 1.0
N A:GLY199 4.4 9.5 1.0
O A:HOH706 4.4 11.7 1.0
C A:PHE196 4.4 9.0 1.0
C A:SER216 4.5 10.2 1.0
CG A:HIS218 4.5 9.5 1.0
N A:PHE196 4.5 8.6 1.0
CA A:HIS197 4.6 8.4 1.0
O A:PHE196 4.6 8.5 1.0
C A:HIS198 4.7 10.3 1.0
O A:VAL194 4.7 8.8 1.0
CA A:PHE196 4.9 8.0 1.0
OD1 A:ASP195 5.0 9.7 1.0

Potassium binding site 3 out of 4 in 6phr

Go back to Potassium Binding Sites List in 6phr
Potassium binding site 3 out of 4 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol


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 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K505

b:12.0
occ:0.76
 O B:VAL212 2.6 13.3 1.0
O B:HOH707 2.7 13.7 1.0
O B:PHE206 2.7 11.8 1.0
O B:ARG209 2.8 15.0 1.0
O B:TYR243 2.9 10.1 1.0
O B:HOH619 2.9 12.7 1.0
C B:PHE206 3.7 12.3 1.0
C B:TYR243 3.7 11.8 1.0
OG1 B:THR214 3.7 12.7 1.0
CB B:PHE206 3.8 10.1 1.0
C B:VAL212 3.9 13.2 1.0
CB B:TYR243 3.9 12.8 1.0
C B:ARG209 3.9 15.6 1.0
N B:THR214 4.2 9.3 1.0
CA B:PHE206 4.4 11.2 1.0
CA B:LEU213 4.4 12.4 1.0
CA B:TYR243 4.5 14.2 1.0
N B:ARG209 4.5 12.6 1.0
N B:TYR207 4.5 11.8 1.0
CG2 B:THR214 4.5 12.9 1.0
CA B:TYR207 4.6 11.0 1.0
N B:ASN244 4.6 11.6 1.0
N B:LEU213 4.6 13.0 1.0
CB B:THR214 4.6 9.0 1.0
CA B:ARG209 4.7 15.2 1.0
C B:LEU213 4.7 11.9 1.0
C B:TYR207 4.7 12.6 1.0
O B:TYR207 4.7 12.5 1.0
CB B:ARG209 4.9 14.7 1.0
CB B:ASN244 4.9 11.3 1.0
CA B:ASN244 4.9 11.6 1.0
CA B:VAL212 4.9 13.7 1.0
N B:SER210 4.9 15.2 1.0
O B:GLY240 5.0 14.6 1.0

Potassium binding site 4 out of 4 in 6phr

Go back to Potassium Binding Sites List in 6phr
Potassium binding site 4 out of 4 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol


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 5-[(3-Aminopropyl) Amino]Pentane-1-Thiol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K506

b:8.9
occ:0.55
 O B:ASP195 2.3 7.1 1.0
O B:LEU217 2.4 8.9 1.0
OD1 B:ASP193 2.4 10.2 1.0
O B:HIS197 2.7 9.5 1.0
OG B:SER216 2.7 8.8 1.0
O B:ASP193 3.0 9.8 1.0
CG B:ASP193 3.2 10.7 1.0
C B:ASP195 3.4 7.7 1.0
C B:LEU217 3.5 7.6 1.0
C B:ASP193 3.6 9.3 1.0
C B:HIS197 3.6 8.2 1.0
N B:ASP195 3.7 9.7 1.0
CB B:HIS218 3.8 9.3 1.0
CB B:ASP193 3.8 8.1 1.0
N B:LEU217 3.8 7.7 1.0
CA B:ASP195 3.9 7.9 1.0
CB B:SER216 4.0 8.3 1.0
C B:VAL194 4.0 9.6 1.0
OD2 B:ASP193 4.1 12.1 1.0
CB B:ASP195 4.2 8.6 1.0
N B:VAL194 4.2 10.6 1.0
ND1 B:HIS218 4.2 9.9 1.0
CA B:HIS198 4.3 8.9 1.0
N B:HIS197 4.3 8.6 1.0
CA B:HIS218 4.3 6.6 1.0
N B:HIS198 4.3 8.5 1.0
CA B:LEU217 4.3 9.4 1.0
CA B:ASP193 4.3 10.1 1.0
CA B:VAL194 4.3 9.4 1.0
O B:HOH691 4.3 10.1 1.0
N B:HIS218 4.3 7.1 1.0
C B:PHE196 4.3 10.4 1.0
N B:GLY199 4.4 8.3 1.0
CA B:SER216 4.4 9.5 1.0
C B:SER216 4.4 7.6 1.0
CG B:HIS218 4.5 7.9 1.0
N B:PHE196 4.5 8.7 1.0
CA B:HIS197 4.6 8.1 1.0
O B:PHE196 4.6 9.4 1.0
O B:VAL194 4.6 8.7 1.0
C B:HIS198 4.6 9.2 1.0
CA B:PHE196 4.8 9.4 1.0
OD1 B:ASP195 5.0 8.7 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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