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Potassium in PDB 6pid: Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 8-Amino-N-Hydroxyoctanamide

Protein crystallography data

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 8-Amino-N-Hydroxyoctanamide, PDB code: 6pid 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) 59.53 / 1.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.330, 119.060, 66.220, 90.00, 109.24, 90.00
R / Rfree (%) 24.4 / 28.1

Other elements in 6pid:

The structure of Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 8-Amino-N-Hydroxyoctanamide 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 8-Amino-N-Hydroxyoctanamide (pdb code 6pid). 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 8-Amino-N-Hydroxyoctanamide, PDB code: 6pid:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6pid

Go back to Potassium Binding Sites List in 6pid
Potassium binding site 1 out of 4 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 8-Amino-N-Hydroxyoctanamide


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 8-Amino-N-Hydroxyoctanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K404

b:5.2
occ:0.53
 O A:LEU217 2.4 10.6 1.0
O A:ASP195 2.4 7.5 1.0
OD1 A:ASP193 2.5 11.0 1.0
OG A:SER216 2.7 10.9 1.0
O A:HIS197 2.8 7.4 1.0
O A:ASP193 3.0 10.0 1.0
CG A:ASP193 3.2 7.6 1.0
C A:LEU217 3.4 9.9 1.0
C A:ASP193 3.4 6.0 1.0
C A:ASP195 3.5 7.6 1.0
CB A:ASP193 3.6 8.9 1.0
N A:ASP195 3.6 8.6 1.0
C A:HIS197 3.7 7.2 1.0
N A:LEU217 3.7 11.7 1.0
CB A:HIS218 3.9 8.3 1.0
CA A:ASP195 3.9 5.2 1.0
CB A:SER216 3.9 8.6 1.0
OD2 A:ASP193 4.0 12.2 1.0
C A:VAL194 4.0 8.0 1.0
N A:VAL194 4.0 7.2 1.0
CA A:ASP193 4.1 9.7 1.0
CB A:ASP195 4.1 6.9 1.0
CA A:LEU217 4.2 13.6 1.0
CA A:VAL194 4.2 4.9 1.0
ND1 A:HIS218 4.2 3.9 1.0
CA A:SER216 4.3 9.8 1.0
N A:HIS218 4.3 5.8 1.0
N A:HIS197 4.3 7.8 1.0
C A:SER216 4.3 8.8 1.0
CA A:HIS218 4.4 8.6 1.0
CA A:HIS198 4.4 7.7 1.0
N A:GLY199 4.4 9.8 1.0
O A:HOH561 4.4 7.5 1.0
N A:HIS198 4.4 11.5 1.0
C A:PHE196 4.5 11.1 1.0
CG A:HIS218 4.5 8.9 1.0
N A:PHE196 4.6 4.7 1.0
CA A:HIS197 4.7 9.4 1.0
C A:HIS198 4.7 10.8 1.0
O A:VAL194 4.7 9.8 1.0
O A:PHE196 4.9 10.2 1.0
CA A:PHE196 5.0 11.3 1.0
CE1 A:HIS158 5.0 10.6 1.0
OD1 A:ASP195 5.0 8.6 1.0

Potassium binding site 2 out of 4 in 6pid

Go back to Potassium Binding Sites List in 6pid
Potassium binding site 2 out of 4 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 8-Amino-N-Hydroxyoctanamide


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 8-Amino-N-Hydroxyoctanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K405

b:15.3
occ:1.00
 O A:PHE206 2.7 6.7 1.0
O A:HOH528 2.7 10.6 1.0
O A:VAL212 2.8 16.8 1.0
O A:ARG209 2.9 10.8 1.0
O A:TYR243 2.9 10.9 1.0
O A:HOH531 3.1 11.2 1.0
C A:PHE206 3.6 10.3 1.0
C A:TYR243 3.7 11.6 1.0
CB A:TYR243 3.8 12.4 1.0
OG1 A:THR214 3.8 13.1 1.0
CB A:PHE206 3.9 9.3 1.0
C A:VAL212 4.0 14.4 1.0
C A:ARG209 4.0 15.8 1.0
N A:THR214 4.3 7.6 1.0
CA A:TYR243 4.3 15.2 1.0
CA A:PHE206 4.4 10.9 1.0
N A:ASN244 4.5 8.3 1.0
CA A:TYR207 4.5 12.6 1.0
N A:ARG209 4.5 9.7 1.0
N A:TYR207 4.5 10.5 1.0
O A:TYR207 4.6 13.3 1.0
CG2 A:THR214 4.6 10.7 1.0
C A:TYR207 4.6 13.4 1.0
CA A:LEU213 4.6 10.4 1.0
CA A:ARG209 4.7 11.3 1.0
CB A:THR214 4.7 9.9 1.0
N A:LEU213 4.7 10.7 1.0
O A:GLY240 4.8 17.6 1.0
CB A:ASN244 4.8 8.7 1.0
CA A:ASN244 4.9 7.9 1.0
C A:LEU213 4.9 9.8 1.0
CB A:ARG209 4.9 6.8 1.0

Potassium binding site 3 out of 4 in 6pid

Go back to Potassium Binding Sites List in 6pid
Potassium binding site 3 out of 4 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 8-Amino-N-Hydroxyoctanamide


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 8-Amino-N-Hydroxyoctanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K403

b:5.6
occ:0.49
 O B:LEU217 2.4 9.6 1.0
O B:ASP195 2.5 8.3 1.0
OD1 B:ASP193 2.5 11.4 1.0
O B:HIS197 2.7 4.8 1.0
OG B:SER216 2.7 8.2 1.0
O B:ASP193 2.9 9.8 1.0
CG B:ASP193 3.3 9.9 1.0
C B:ASP193 3.4 11.0 1.0
C B:LEU217 3.5 6.4 1.0
C B:ASP195 3.5 7.3 1.0
N B:ASP195 3.7 11.6 1.0
C B:HIS197 3.7 4.8 1.0
CB B:ASP193 3.7 9.4 1.0
N B:LEU217 3.7 9.5 1.0
CB B:HIS218 3.9 6.7 1.0
CB B:SER216 4.0 5.5 1.0
C B:VAL194 4.0 11.0 1.0
N B:VAL194 4.0 12.5 1.0
CA B:ASP195 4.0 9.6 1.0
CA B:VAL194 4.2 12.6 1.0
CA B:ASP193 4.2 6.3 1.0
ND1 B:HIS218 4.2 5.6 1.0
OD2 B:ASP193 4.2 12.1 1.0
CB B:ASP195 4.2 8.7 1.0
CA B:LEU217 4.2 12.3 1.0
CA B:SER216 4.3 8.7 1.0
CA B:HIS198 4.3 4.1 1.0
N B:HIS197 4.3 3.0 1.0
N B:HIS218 4.4 5.5 1.0
N B:HIS198 4.4 5.6 1.0
CA B:HIS218 4.4 10.4 1.0
O B:HOH531 4.4 8.6 1.0
C B:SER216 4.4 8.0 1.0
N B:GLY199 4.4 8.0 1.0
C B:PHE196 4.5 9.2 1.0
CG B:HIS218 4.5 3.6 1.0
N B:PHE196 4.6 9.5 1.0
O B:VAL194 4.6 8.5 1.0
CA B:HIS197 4.7 4.6 1.0
C B:HIS198 4.7 9.9 1.0
O B:PHE196 4.8 7.0 1.0
CB B:LEU217 5.0 9.5 1.0

Potassium binding site 4 out of 4 in 6pid

Go back to Potassium Binding Sites List in 6pid
Potassium binding site 4 out of 4 in the Crystal Structure of Marinobacter Subterrani Acetylpolyamine Amidohydrolase (Msapah) Complexed with 8-Amino-N-Hydroxyoctanamide


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 8-Amino-N-Hydroxyoctanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K404

b:12.0
occ:1.00
 O B:HOH567 2.6 11.9 1.0
O B:VAL212 2.7 9.2 1.0
O B:PHE206 2.7 12.6 1.0
O B:HOH510 2.9 9.6 1.0
O B:ARG209 2.9 10.8 1.0
O B:TYR243 2.9 12.2 1.0
C B:PHE206 3.6 9.6 1.0
OG1 B:THR214 3.8 11.0 1.0
C B:TYR243 3.8 6.9 1.0
CB B:PHE206 3.9 9.2 1.0
C B:VAL212 3.9 7.6 1.0
CB B:TYR243 4.0 9.0 1.0
C B:ARG209 4.1 13.2 1.0
N B:THR214 4.3 9.8 1.0
CA B:PHE206 4.4 11.3 1.0
CA B:LEU213 4.4 8.7 1.0
CA B:TYR207 4.5 8.8 1.0
N B:ARG209 4.5 11.5 1.0
N B:TYR207 4.5 11.7 1.0
CA B:TYR243 4.5 10.9 1.0
O B:TYR207 4.6 10.7 1.0
C B:TYR207 4.6 14.3 1.0
N B:LEU213 4.6 6.9 1.0
N B:ASN244 4.6 13.1 1.0
CA B:ARG209 4.7 10.3 1.0
CG2 B:THR214 4.7 9.5 1.0
C B:LEU213 4.8 9.6 1.0
CB B:THR214 4.8 11.5 1.0
CB B:ARG209 4.8 7.3 1.0
O B:GLY240 4.9 11.1 1.0
CB B:ASN244 4.9 7.8 1.0
CA B:VAL212 4.9 11.1 1.0
CA B:ASN244 5.0 11.5 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 17:10:14 2024

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