Atomistry » Potassium » PDB 6pcd-6qm2 » 6phr
Atomistry »
  Potassium »
    PDB 6pcd-6qm2 »
      6phr »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy